Comparison of loop-mediated isothermal amplification (LAMP) and nested-PCR assay targeting the RE and B1 gene for detection of Toxoplasma gondii in blood samples of children with leukaemia.

PubMed

Fallahi, Shirzad; Seyyed Tabaei, Seyyed Javad; Pournia, Yadollah; Zebardast, Nozhat; Kazemi, Bahram

2014-07-01

Toxoplasmosis diagnosis constitutes an important measure for disease prevention and control. In this paper, a newly described DNA amplification technique, loop-mediated isothermal amplification (LAMP), and nested-PCR targeting the repeated element (RE) and B1 gene, were compared to each other for the detection of Toxoplasma gondii DNA in blood samples of children with leukaemia. One hundred ten blood samples from these patients were analyzed by LAMP and nested-PCR. Out of 50 seropositive samples (IgM+, IgG+), positive results were obtained with 92% and 86% on RE, B1-LAMP and 82% and 68% on RE, B1-nested PCR analyses, respectively. Of the 50 seronegative samples, three, two and one samples were detected positive by RE-LAMP, B1-LAMP and RE-nested PCR assays, respectively, while none were detected positive by B1-nested PCR. None of the 10 IgM-, IgG+ samples was detected positive after testing LAMP and nested-PCR assays in duplicate. This is the first report of a study in which the LAMP method was applied with high sensitivity and efficacy for the diagnosis of T. gonii in blood samples of children with leukaemia. Copyright © 2014 Elsevier Inc. All rights reserved.

Establishment of a nested-ASP-PCR method to determine the clarithromycin resistance of Helicobacter pylori.

PubMed

Luo, Xiao-Feng; Jiao, Jian-Hua; Zhang, Wen-Yue; Pu, Han-Ming; Qu, Bao-Jin; Yang, Bing-Ya; Hou, Min; Ji, Min-Jun

2016-07-07

To investigate clarithromycin resistance positions 2142, 2143 and 2144 of the 23SrRNA gene in Helicobacter pylori (H. pylori) by nested-allele specific primer-polymerase chain reaction (nested-ASP-PCR). The gastric tissue and saliva samples from 99 patients with positive results of the rapid urease test (RUT) were collected. The nested-ASP-PCR method was carried out with the external primers and inner allele-specific primers corresponding to the reference strain and clinical strains. Thirty gastric tissue and saliva samples were tested to determine the sensitivity of nested-ASP-PCR and ASP-PCR methods. Then, clarithromycin resistance was detected for 99 clinical samples by using different methods, including nested-ASP-PCR, bacterial culture and disk diffusion. The nested-ASP-PCR method was successfully established to test the resistance mutation points 2142, 2143 and 2144 of the 23SrRNA gene of H. pylori. Among 30 samples of gastric tissue and saliva, the H. pylori detection rate of nested-ASP-PCR was 90% and 83.33%, while the detection rate of ASP-PCR was just 63% and 56.67%. Especially in the saliva samples, nested-ASP-PCR showed much higher sensitivity in H. pylori detection and resistance mutation rates than ASP-PCR. In the 99 RUT-positive gastric tissue and saliva samples, the H. pylori-positive detection rate by nested-ASP-PCR was 87 (87.88%) and 67 (67.68%), in which there were 30 wild-type and 57 mutated strains in gastric tissue and 22 wild-type and 45 mutated strains in saliva. Genotype analysis showed that three-points mixed mutations were quite common, but different resistant strains were present in gastric mucosa and saliva. Compared to the high sensitivity shown by nested-ASP-PCR, the positive detection of bacterial culture with gastric tissue samples was 50 cases, in which only 26 drug-resistant strains were found through analyzing minimum inhibitory zone of clarithromycin. The nested-ASP-PCR assay showed higher detection sensitivity than ASP-PCR and drug sensitivity testing, which could be performed to evaluate clarithromycin resistance of H. pylori.

Establishment of a nested-ASP-PCR method to determine the clarithromycin resistance of Helicobacter pylori

PubMed Central

Luo, Xiao-Feng; Jiao, Jian-Hua; Zhang, Wen-Yue; Pu, Han-Ming; Qu, Bao-Jin; Yang, Bing-Ya; Hou, Min; Ji, Min-Jun

2016-01-01

AIM: To investigate clarithromycin resistance positions 2142, 2143 and 2144 of the 23SrRNA gene in Helicobacter pylori (H. pylori) by nested-allele specific primer-polymerase chain reaction (nested-ASP-PCR). METHODS: The gastric tissue and saliva samples from 99 patients with positive results of the rapid urease test (RUT) were collected. The nested-ASP-PCR method was carried out with the external primers and inner allele-specific primers corresponding to the reference strain and clinical strains. Thirty gastric tissue and saliva samples were tested to determine the sensitivity of nested-ASP-PCR and ASP-PCR methods. Then, clarithromycin resistance was detected for 99 clinical samples by using different methods, including nested-ASP-PCR, bacterial culture and disk diffusion. RESULTS: The nested-ASP-PCR method was successfully established to test the resistance mutation points 2142, 2143 and 2144 of the 23SrRNA gene of H. pylori. Among 30 samples of gastric tissue and saliva, the H. pylori detection rate of nested-ASP-PCR was 90% and 83.33%, while the detection rate of ASP-PCR was just 63% and 56.67%. Especially in the saliva samples, nested-ASP-PCR showed much higher sensitivity in H. pylori detection and resistance mutation rates than ASP-PCR. In the 99 RUT-positive gastric tissue and saliva samples, the H. pylori-positive detection rate by nested-ASP-PCR was 87 (87.88%) and 67 (67.68%), in which there were 30 wild-type and 57 mutated strains in gastric tissue and 22 wild-type and 45 mutated strains in saliva. Genotype analysis showed that three-points mixed mutations were quite common, but different resistant strains were present in gastric mucosa and saliva. Compared to the high sensitivity shown by nested-ASP-PCR, the positive detection of bacterial culture with gastric tissue samples was 50 cases, in which only 26 drug-resistant strains were found through analyzing minimum inhibitory zone of clarithromycin. CONCLUSION: The nested-ASP-PCR assay showed higher detection sensitivity than ASP-PCR and drug sensitivity testing, which could be performed to evaluate clarithromycin resistance of H. pylori. PMID:27433095

Nest materials as a source of genetic data for avian ecological studies

USGS Publications Warehouse

Pearce, J.M.; Fields, R.L.; Scribner, K.T.

1997-01-01

We examined the utility of feathers and egg shell membranes, deposited in the nests of Spectacled Eiders (Somateria fischeri), as a source of DNA for genetic studies at both the population and individual level. The potential for feather DNA contamination as a result of female behavioral interactions (e.g. nest parasitism), reuse of nest sites from previous years, or other unknown occurrences was acknowledged and specifically tested. DNA was successfully extracted from both feathers and egg shell membranes and waterfowl microsatellite loci were used to construct individual genotypes. We found no difference in the genotypes obtained from nest feathers or blood of the incubating female. Detection of nest feather contamination was possible with as little as one feather when samples from multiple females were intentionally mixed. Triplicate DNA extractions from 33 nests provided a means of detecting contamination in 3 nests. Egg membranes proved a viable source of offspring DNA and can contribute valuable data to investigations of parentage when assayed jointly with maternal feather DNA. Nest materials provide an efficient, non-invasive method of genetic sampling that can be readily incorporated into field research. However, the natural history traits and mating strategies of a species must be considered during sample collection to identify the possible sources of nest materials (e.g., paternal, maternal, parasite, etc.). Specific experiments should also be designed to test sampling assumptions.

Assessing relative abundance and reproductive success of shrubsteppe raptors

USGS Publications Warehouse

Lehman, Robert N.; Carpenter, L.B.; Steenhof, Karen; Kochert, Michael N.

1998-01-01

From 1991-1994, we quantified relative abundance and reproductive success of the Ferruginous Hawk (Buteo regalis), Northern Harrier (Circus cyaneus), Burrowing Owl (Speotytoc unicularia), and Short-eared Owl (Asio flammeus) on the shrubsteppe plateaus (benchlands) in and near the Snake River Birds of Prey National Conservation Area in southwestern Idaho. To assess relative abundance, we searched randomly selected plots using four sampling methods: point counts, line transects, and quadrats of two sizes. On a persampling-effort basis, transects were slightly more effective than point counts and quadrats for locating raptor nests (3.4 pairs detected/100 h of effort vs. 2.2-3.1 pairs). Random sampling using quadrats failed to detect a Short-eared Owl population increase from 1993 to 1994. To evaluate nesting success, we tried to determine reproductive outcome for all nesting attempts located during random, historical, and incidental nest searches. We compared nesting success estimates based on all nesting attempts, on attempts found during incubation, and the Mayfield model. Most pairs used to evaluate success were pairs found incidentally. Visits to historical nesting areas yielded the highest number of pairs per sampling effort (14.6/100 h), but reoccupancy rates for most species decreased through time. Estimates based on all attempts had the highest sample sizes but probably overestimated success for all species except the Ferruginous Hawk. Estimates of success based on nesting attempts found during incubation had the lowest sample sizes. All three methods yielded biased nesting snccess estimates for the Northern Harrier and Short-eared Owl. The estimate based on pairs found during incubation probably provided the least biased estimate for the Burrowing Owl. Assessments of nesting success were hindered by difficulties in confirming egg laying and nesting success for all species except the Ferruginous hawk.

A semi-nested PCR assay for molecular detection of Paracoccidioides brasiliensis in tissue samples.

PubMed

Koishi, Andrea Cristine; Vituri, Débora Fonseca; Dionízio Filho, Pedro Sebastião Raimundo; Sasaki, Alexandre Augusto; Felipe, Maria Sueli Soares; Venancio, Emerson José

2010-01-01

Paracoccidioidomycosis is a systemic infection caused by Paracoccidioides brasiliensis. In this study, a semi-nested PCR for paracoccidioidomycosis diagnosis was developed. The primers ITS1 and ITS4 were used in the first reaction, while the primers MJ03 and ITS1 primer were used in the second reaction. The semi-nested PCR was used to investigate biopsies of five patients with oral lesions that resembled paracoccidioidomycosis. The semi-nested PCR was positive for four samples and negative for a sample from a patient later diagnosed with leishmaniasis. The new semi-nested PCR describe is useful for paracoccidioidomycosis diagnosis.

Clinical and epidemiological use of nested PCR targeting the repetitive element IS1111 associated with the transposase gene from Coxiella burnetii.

PubMed

Mares-Guia, Maria Angélica M M; Guterres, Alexandro; Rozental, Tatiana; Ferreira, Michelle Dos Santos; Lemos, Elba R S

Q fever is a worldwide zoonosis caused by Coxiella burnetii-a small obligate intracellular Gram-negative bacterium found in a variety of animals. It is transmitted to humans by inhalation of contaminated aerosols from urine, feces, milk, amniotic fluid, placenta, abortion products, wool, and rarely by ingestion of raw milk from infected animals. Nested PCR can improve the sensitivity and specificity of testing while offering a suitable amplicon size for sequencing. Serial dilutions were performed tenfold to test the limit of detection, and the result was 10× detection of C. burnetti DNA with internal nested PCR primers relative to trans-PCR. Different biological samples were tested and identified only in nested PCR. This demonstrates the efficiency and effectiveness of the primers. Of the 19 samples, which amplify the partial sequence of C. burnetii, 12 were positive by conventional PCR and nested PCR. Seven samples-five spleen tissue samples from rodents and two tick samples-were only positive in nested PCR. With these new internal primers for trans-PCR, we demonstrate that our nested PCR assay for C. burnetii can achieve better results than conventional PCR. Published by Elsevier Editora Ltda.

Comparison of Nested Polymerase Chain Reaction and Real-Time Polymerase Chain Reaction with Parasitological Methods for Detection of Strongyloides stercoralis in Human Fecal Samples

PubMed Central

Sharifdini, Meysam; Mirhendi, Hossein; Ashrafi, Keyhan; Hosseini, Mostafa; Mohebali, Mehdi; Khodadadi, Hossein; Kia, Eshrat Beigom

2015-01-01

This study was performed to evaluate nested polymerase chain reaction (PCR) and real-time PCR methods for detection of Strongyloides stercoralis in fecal samples compared with parasitological methods. A total of 466 stool samples were examined by conventional parasitological methods (formalin ether concentration [FEC] and agar plate culture [APC]). DNA was extracted using an in-house method, and mitochondrial cytochrome c oxidase subunit 1 and 18S ribosomal genes were amplified by nested PCR and real-time PCR, respectively. Among 466 samples, 12.7% and 18.2% were found infected with S. stercoralis by FEC and APC, respectively. DNA of S. stercoralis was detected in 18.9% and 25.1% of samples by real-time PCR and nested PCR, respectively. Considering parasitological methods as the diagnostic gold standard, the sensitivity and specificity of nested PCR were 100% and 91.6%, respectively, and that of real-time PCR were 84.7% and 95.8%, respectively. However, considering sequence analyzes of the selected nested PCR products, the specificity of nested PCR is increased. In general, molecular methods were superior to parasitological methods. They were more sensitive and more reliable in detection of S. stercoralis in comparison with parasitological methods. Between the two molecular methods, the sensitivity of nested PCR was higher than real-time PCR. PMID:26350449

Ground-nesting by the chimpanzees of the Nimba Mountains, Guinea: environmentally or socially determined?

PubMed

Koops, Kathelijne; Humle, Tatyana; Sterck, Elisabeth H M; Matsuzawa, Tetsuro

2007-04-01

The chimpanzees (Pan troglodytes verus) of the Nimba Mountains, Guinea, West Africa, commonly make both elaborate ("night") and simple ("day") nests on the ground. In this study we investigated which factors might influence ground-nesting in this population, and tested two ecological hypotheses: 1) climatic conditions, such as high wind speeds at high altitudes, may deter chimpanzees from nesting in trees; and 2) a lack of appropriate arboreal nesting opportunities may drive the chimpanzees to nest on the ground. In addition to testing these two hypotheses, we explored whether ground-nesting is a sex-linked behavior. Data were collected monthly between August 2003 and May 2004 along transects and ad libitum. To identify the sex of ground-nesting individuals, we used DNA extracted from hair samples. The results showed that the occurrence and distribution of ground nests were not affected by climatic conditions or a lack of appropriate nest trees. Support was found for the notion that ground-nesting is a sex-linked behavior, as males were responsible for building all of the elaborate ground nests and most of the simple ground nests sampled. Elaborate ground nests occurred mostly in nest groups associated with tree nests, whereas simple ground nests usually occurred without tree nests in their vicinity. These results suggest that ground-nesting may be socially, rather than ecologically, determined.

A Gradient-Based Multistart Algorithm for Multimodal Aerodynamic Shape Optimization Problems Based on Free-Form Deformation

NASA Astrophysics Data System (ADS)

Streuber, Gregg Mitchell

Environmental and economic factors motivate the pursuit of more fuel-efficient aircraft designs. Aerodynamic shape optimization is a powerful tool in this effort, but is hampered by the presence of multimodality in many design spaces. Gradient-based multistart optimization uses a sampling algorithm and multiple parallel optimizations to reliably apply fast gradient-based optimization to moderately multimodal problems. Ensuring that the sampled geometries remain physically realizable requires manually developing specialized linear constraints for each class of problem. Utilizing free-form deformation geometry control allows these linear constraints to be written in a geometry-independent fashion, greatly easing the process of applying the algorithm to new problems. This algorithm was used to assess the presence of multimodality when optimizing a wing in subsonic and transonic flows, under inviscid and viscous conditions, and a blended wing-body under transonic, viscous conditions. Multimodality was present in every wing case, while the blended wing-body was found to be generally unimodal.

Detection of Mycobacterium tuberculosis in extrapulmonary biopsy samples using PCR targeting IS6110, rpoB, and nested-rpoB PCR Cloning

PubMed Central

Meghdadi, Hossein; Khosravi, Azar D.; Ghadiri, Ata A.; Sina, Amir H.; Alami, Ameneh

2015-01-01

Present study was aimed to examine the diagnostic utility of polymerase chain reaction (PCR) and nested PCR techniques for the detection of Mycobacterium tuberculosis (MTB) DNA in samples from patients with extra pulmonary tuberculosis (EPTB). In total 80 formalin-fixed, paraffin-embedded (FFPE) samples comprising 70 samples with definite diagnosis of EPTB and 10 samples from known non- EPTB on the basis of histopathology examination, were included in the study. PCR amplification targeting IS6110, rpoB gene and nested PCR targeting the rpoB gene were performed on the extracted DNAs from 80 FFPE samples. The strong positive samples were directly sequenced. For negative samples and those with weak band in nested-rpoB PCR, TA cloning was performed by cloning the products into the plasmid vector with subsequent sequencing. The 95% confidence intervals (CI) for the estimates of sensitivity and specificity were calculated for each method. Fourteen (20%), 34 (48.6%), and 60 (85.7%) of the 70 positive samples confirmed by histopathology, were positive by rpoB-PCR, IS6110-PCR, and nested-rpoB PCR, respectively. By performing TA cloning on samples that yielded weak (n = 8) or negative results (n = 10) in the PCR methods, we were able to improve their quality for later sequencing. All samples with weak band and 7 out of 10 negative samples, showed strong positive results after cloning. So nested-rpoB PCR cloning revealed positivity in 67 out of 70 confirmed samples (95.7%). The sensitivity of these combination methods was calculated as 95.7% in comparison with histopathology examination. The CI for sensitivity of the PCR methods were calculated as 11.39–31.27% for rpoB-PCR, 36.44–60.83% for IS6110- PCR, 75.29–92.93% for nested-rpoB PCR, and 87.98–99.11% for nested-rpoB PCR cloning. The 10 true EPTB negative samples by histopathology, were negative by all tested methods including cloning and were used to calculate the specificity of the applied methods. The CI for 100% specificity of each PCR method were calculated as 69.15–100%. Our results indicated that nested-rpoB PCR combined with TA cloning and sequencing is a preferred method for the detection of MTB DNA in EPTB samples with high sensitivity and specificity which confirm the histopathology results. PMID:26191059

Detection of Mycobacterium tuberculosis in extrapulmonary biopsy samples using PCR targeting IS6110, rpoB, and nested-rpoB PCR Cloning.

PubMed

Meghdadi, Hossein; Khosravi, Azar D; Ghadiri, Ata A; Sina, Amir H; Alami, Ameneh

2015-01-01

Present study was aimed to examine the diagnostic utility of polymerase chain reaction (PCR) and nested PCR techniques for the detection of Mycobacterium tuberculosis (MTB) DNA in samples from patients with extra pulmonary tuberculosis (EPTB). In total 80 formalin-fixed, paraffin-embedded (FFPE) samples comprising 70 samples with definite diagnosis of EPTB and 10 samples from known non- EPTB on the basis of histopathology examination, were included in the study. PCR amplification targeting IS6110, rpoB gene and nested PCR targeting the rpoB gene were performed on the extracted DNAs from 80 FFPE samples. The strong positive samples were directly sequenced. For negative samples and those with weak band in nested-rpoB PCR, TA cloning was performed by cloning the products into the plasmid vector with subsequent sequencing. The 95% confidence intervals (CI) for the estimates of sensitivity and specificity were calculated for each method. Fourteen (20%), 34 (48.6%), and 60 (85.7%) of the 70 positive samples confirmed by histopathology, were positive by rpoB-PCR, IS6110-PCR, and nested-rpoB PCR, respectively. By performing TA cloning on samples that yielded weak (n = 8) or negative results (n = 10) in the PCR methods, we were able to improve their quality for later sequencing. All samples with weak band and 7 out of 10 negative samples, showed strong positive results after cloning. So nested-rpoB PCR cloning revealed positivity in 67 out of 70 confirmed samples (95.7%). The sensitivity of these combination methods was calculated as 95.7% in comparison with histopathology examination. The CI for sensitivity of the PCR methods were calculated as 11.39-31.27% for rpoB-PCR, 36.44-60.83% for IS6110- PCR, 75.29-92.93% for nested-rpoB PCR, and 87.98-99.11% for nested-rpoB PCR cloning. The 10 true EPTB negative samples by histopathology, were negative by all tested methods including cloning and were used to calculate the specificity of the applied methods. The CI for 100% specificity of each PCR method were calculated as 69.15-100%. Our results indicated that nested-rpoB PCR combined with TA cloning and sequencing is a preferred method for the detection of MTB DNA in EPTB samples with high sensitivity and specificity which confirm the histopathology results.

Showing or Telling a Story: A Comparative Study of Public Education Texts in Multimodality and Monomodality

ERIC Educational Resources Information Center

Wang, Kelu

2013-01-01

Multimodal texts that combine words and images produce meaning in a different way from monomodal texts that rely on words. They differ not only in representing the subject matter, but also constructing relationships between text producers and text receivers. This article uses two multimodal texts and one monomodal written text as samples, which…

Separating generalized anxiety disorder from major depression using clinical, hormonal, and structural MRI data: A multimodal machine learning study.

PubMed

Hilbert, Kevin; Lueken, Ulrike; Muehlhan, Markus; Beesdo-Baum, Katja

2017-03-01

Generalized anxiety disorder (GAD) is difficult to recognize and hard to separate from major depression (MD) in clinical settings. Biomarkers might support diagnostic decisions. This study used machine learning on multimodal biobehavioral data from a sample of GAD, MD and healthy subjects to differentiate subjects with a disorder from healthy subjects (case-classification) and to differentiate GAD from MD (disorder-classification). Subjects with GAD ( n  = 19), MD without GAD ( n  = 14), and healthy comparison subjects ( n  = 24) were included. The sample was matched regarding age, sex, handedness and education and free of psychopharmacological medication. Binary support vector machines were used within a nested leave-one-out cross-validation framework. Clinical questionnaires, cortisol release, gray matter (GM), and white matter (WM) volumes were used as input data separately and in combination. Questionnaire data were well-suited for case-classification but not disorder-classification (accuracies: 96.40%, p  < .001; 56.58%, p  > .22). The opposite pattern was found for imaging data (case-classification GM/WM: 58.71%, p  = .09/43.18%, p  > .66; disorder-classification GM/WM: 68.05%, p  = .034/58.27%, p  > .15) and for cortisol data (38.02%, p  = .84; 74.60%, p  = .009). All data combined achieved 90.10% accuracy ( p  < .001) for case-classification and 67.46% accuracy ( p  = .0268) for disorder-classification. In line with previous evidence, classification of GAD was difficult using clinical questionnaire data alone. Particularly cortisol and GM volume data were able to provide incremental value for the classification of GAD. Findings suggest that neurobiological biomarkers are a useful target for further research to delineate their potential contribution to diagnostic processes.

Stabilities of ant nests and their adjacent soils

NASA Astrophysics Data System (ADS)

Echezona, B. C.; Igwe, C. A.

2012-10-01

Nests habour ants and termites and protect them from harsh environmental conditions. The structural stabilities of nests were studied to ascertain their relative vulnerability to environmental stresses. Arboreal-ant nests were pried from different trees, while epigeous-termite nests were excavated from soil surface within the sample area. Soils without any visible sign of ant or termite activity were also sampled 6 m away from the nests as control. Laboratory analysis result showed that irrespective of the tree hosts, the aggregate stabilities of the ant nests were lower than those of the ground termite, with nests formed on Cola nitida significantly showing lower aggregate stability (19.7%) than other antnest structures. Clay dispersion ratio, moisture content, water stable aggregate class <0.25mm and sand mass were each negatively correlated with aggregate stability, while water stable aggregate class1.00-0.50 mm gave a positive correlation. Nest structures were dominated more by water stable aggregate class >2.00 mm but path analysis demonstrated that water stable aggregate class <0.25 mm contributed most to the higher aggregate stability of the termite nest than the other nest. Nest aggregates had greater structural stability compared to the control soil. The higher structural stability of termite nests over other nest and soil was considered a better adaptive mechanism against body desiccation.

Usefulness of in-house PCR methods for hepatitis B virus DNA detection.

PubMed

Portilho, Moyra Machado; Baptista, Marcia Leite; da Silva, Messias; de Sousa, Paulo Sérgio Fonseca; Lewis-Ximenez, Lia Laura; Lampe, Elisabeth; Villar, Livia Melo

2015-10-01

The aim of the present study was to evaluate the performance of three in-house PCR techniques for HBV DNA detection and compare it with commercial quantitative methods to evaluate the usefulness of in-house methods for HBV diagnosis. Three panels of HBsAg reactive sera samples were evaluated: (i) 50 samples were examined using three methods for in-house qualitative PCR and the Cobas Amplicor HBV Monitor Assay; (ii) 87 samples were assayed using in-house semi-nested PCR and the Cobas TaqMan HBV test; (iii) 11 serial samples obtained from 2 HBV-infected individuals were assayed using the Cobas Amplicor HBV test and semi-nested PCR. In panel I, HBV DNA was detected in 44 samples using the Cobas Amplicor HBV test, 42 samples using semi-nested PCR (90% concordance with Cobas Amplicor), 22 samples using PCR for the core gene (63.6% concordance) and 29 samples using single-round PCR for the pre-S/S gene (75% concordance). In panel II, HBV DNA was quantified in 78 of the 87 HBsAg reactive samples using Cobas TaqMan but 52 samples using semi-nested PCR (67.8% concordance). HBV DNA was detected in serial samples until the 17th and 26th week after first donation using in-house semi-nested PCR and the Cobas Amplicor HBV test, respectively. In-house semi-nested PCR presented adequate concordance with commercial methods as an alternative method for HBV molecular diagnosis in low-resource settings. Copyright © 2015 Elsevier B.V. All rights reserved.

Discovering Event Structure in Continuous Narrative Perception and Memory.

PubMed

Baldassano, Christopher; Chen, Janice; Zadbood, Asieh; Pillow, Jonathan W; Hasson, Uri; Norman, Kenneth A

2017-08-02

During realistic, continuous perception, humans automatically segment experiences into discrete events. Using a novel model of cortical event dynamics, we investigate how cortical structures generate event representations during narrative perception and how these events are stored to and retrieved from memory. Our data-driven approach allows us to detect event boundaries as shifts between stable patterns of brain activity without relying on stimulus annotations and reveals a nested hierarchy from short events in sensory regions to long events in high-order areas (including angular gyrus and posterior medial cortex), which represent abstract, multimodal situation models. High-order event boundaries are coupled to increases in hippocampal activity, which predict pattern reinstatement during later free recall. These areas also show evidence of anticipatory reinstatement as subjects listen to a familiar narrative. Based on these results, we propose that brain activity is naturally structured into nested events, which form the basis of long-term memory representations. Copyright © 2017 Elsevier Inc. All rights reserved.

Detection of Mycoplasma hyopneumoniae by Air Sampling with a Nested PCR Assay

PubMed Central

Stärk, Katharina D. C.; Nicolet, Jacques; Frey, Joachim

1998-01-01

This article describes the first successful detection of airborne Mycoplasma hyopneumoniae under experimental and field conditions with a new nested PCR assay. Air was sampled with polyethersulfone membranes (pore size, 0.2 μm) mounted in filter holders. Filters were processed by dissolution and direct extraction of DNA for PCR analysis. For the PCR, two nested pairs of oligonucleotide primers were designed by using an M. hyopneumoniae-specific DNA sequence of a repeated gene segment. A nested PCR assay was developed and used to analyze samples collected in eight pig houses where respiratory problems had been common. Air was also sampled from a mycoplasma-free herd. The nested PCR was highly specific and 104 times as sensitive as a one-step PCR. Under field conditions, the sampling system was able to detect airborne M. hyopneumoniae on 80% of farms where acute respiratory disease was present. No airborne M. hyopneumoniae was detected on infected farms without acute cases. The chance of successful detection was increased if air was sampled at several locations within a room and at a lower air humidity. PMID:9464391

Thermal regimes of Mexican spotted owl nest stands

Treesearch

Joseph L. Ganey

2004-01-01

To evaluate the hypothesis that spotted owls (Strix occidentalis) select habitats with cool microclimates to avoid high daytime temperatures, I sampled thermal regimes in nest areas used by Mexican spotted owls (S. o. lucida) in northern Arizona. I sampled air temperature at 30-min intervals in 30 pairs of nest and random sites...

The Influences of Soil Characteristics on Nest-Site Selection in Painted Turtles (Chrysemys picta)

NASA Astrophysics Data System (ADS)

Page, R.

2017-12-01

A variety of animals dig nests and lay their eggs in soil, leaving them to incubate and hatch without assistance from the parents. Nesting habitat is important for these organisms many of which exhibit temperature dependent sex determination (TSD) whereby the incubation temperature determines the sex of each hatchling. However, suitable nesting habitat may be limited due to anthropogenic activities and global temperature increases. Soil thermal properties are critical to these organisms and are positively correlated with water retention and soil carbon; carbon-rich soils result in higher incubation temperatures. We investigated nest-site selection in painted turtles (Chrysemys picta) inhabiting an anthropogenic pond in south central Pennsylvania. We surveyed for turtle nests and documented location, depth, width, temperature, canopy coverage, clutch size, and hatch success for a total of 31 turtle nests. To address the influence of soil carbon and particle size on nest selection, we analyzed samples collected from: 1) actual nests that were depredated, 2) false nests, incomplete nests aborted during digging prior to nest completion, and 3) randomized locations. Soil samples were separated into coarse, medium, and fine grain size fractions through a stack of sieves. Samples were combusted in a total carbon analyzer to measure weight percent organic carbon. We found that anthropogenic activity at this site has created homogenous, sandy, compacted soils at the uppermost layer that may limit females' access to appropriate nesting habitat. Turtle nesting activity was limited to a linear region north of the pond and was constrained by an impassable rail line. Relative to other studies, turtle nests were notably shallow (5.8±0.9 cm) and placed close to the pond. Compared to false nests and random locations, turtle-selected sites averaged greater coarse grains (35% compared to 20.24 and 20.57%) and less fine grains (47% compared to 59 and 59, respectively). Despite remarkably high soil carbon along the rail line (47.08%) turtles nested here with slightly higher hatch success. We suggest that the turtles are limited to sandy, compact soils with low heat capacities and may compensate for this by also nesting adjacent to the rail line where high soil carbon could increase incubation temperatures.

Multimodal hard x-ray imaging with resolution approaching 10 nm for studies in material science

NASA Astrophysics Data System (ADS)

Yan, Hanfei; Bouet, Nathalie; Zhou, Juan; Huang, Xiaojing; Nazaretski, Evgeny; Xu, Weihe; Cocco, Alex P.; Chiu, Wilson K. S.; Brinkman, Kyle S.; Chu, Yong S.

2018-03-01

We report multimodal scanning hard x-ray imaging with spatial resolution approaching 10 nm and its application to contemporary studies in the field of material science. The high spatial resolution is achieved by focusing hard x-rays with two crossed multilayer Laue lenses and raster-scanning a sample with respect to the nanofocusing optics. Various techniques are used to characterize and verify the achieved focus size and imaging resolution. The multimodal imaging is realized by utilizing simultaneously absorption-, phase-, and fluorescence-contrast mechanisms. The combination of high spatial resolution and multimodal imaging enables a comprehensive study of a sample on a very fine length scale. In this work, the unique multimodal imaging capability was used to investigate a mixed ionic-electronic conducting ceramic-based membrane material employed in solid oxide fuel cells and membrane separations (compound of Ce0.8Gd0.2O2‑x and CoFe2O4) which revealed the existence of an emergent material phase and quantified the chemical complexity at the nanoscale.

Development of a Highly Sensitive Nested-PCR Procedure Using a Single Closed Tube for Detection of Erwinia amylovora in Asymptomatic Plant Material

PubMed Central

Llop, Pablo; Bonaterra, Anna; Peñalver, Javier; López, María M.

2000-01-01

A novel method, which involves a nested PCR in a single closed tube, was developed for the sensitive detection of Erwinia amylovora in plant material. The external and internal primer pairs used had different annealing temperatures and directed the amplification of a specific DNA fragment from plasmid pEA29. The procedure involved two consecutive PCRs, the first of which was performed at a higher annealing temperature that allowed amplification only by the external primer pair. Using pure cultures of E. amylovora, the sensitivity of the nested PCR in one tube was similar to that of a standard nested PCR in two tubes. The specificity and sensitivity were greater than those of standard PCR procedures that used a single primer pair. The presence of inhibitors in plant material, very common in E. amylovora hosts, is overcome with this system in combination with a simple DNA extraction protocol because it eliminates many of the inhibitory compounds. In addition, it needs a very small sample volume (1 μl of DNA extracted). With 83 samples of naturally infected material, this method achieved better results than any other PCR technique: standard PCR detected 55% of positive samples, two-tube nested PCR detected 71% of positive samples, and nested PCR in a single closed tube detected 78% of positive samples. When analyzing asymptomatic plant material, the number of positive samples detected by the developed nested PCR was also the highest, compared with the PCR protocols indicated previously (17, 20, and 25% of 251 samples analyzed, respectively). This method is proposed for the detection of endophytic and epiphytic populations of E. amylovora in epidemiological studies and for routine use in quarantine surveys, due to its high sensitivity, specificity, speed, and simplicity. PMID:10788384

The dynamics of multimodal integration: The averaging diffusion model.

PubMed

Turner, Brandon M; Gao, Juan; Koenig, Scott; Palfy, Dylan; L McClelland, James

2017-12-01

We combine extant theories of evidence accumulation and multi-modal integration to develop an integrated framework for modeling multimodal integration as a process that unfolds in real time. Many studies have formulated sensory processing as a dynamic process where noisy samples of evidence are accumulated until a decision is made. However, these studies are often limited to a single sensory modality. Studies of multimodal stimulus integration have focused on how best to combine different sources of information to elicit a judgment. These studies are often limited to a single time point, typically after the integration process has occurred. We address these limitations by combining the two approaches. Experimentally, we present data that allow us to study the time course of evidence accumulation within each of the visual and auditory domains as well as in a bimodal condition. Theoretically, we develop a new Averaging Diffusion Model in which the decision variable is the mean rather than the sum of evidence samples and use it as a base for comparing three alternative models of multimodal integration, allowing us to assess the optimality of this integration. The outcome reveals rich individual differences in multimodal integration: while some subjects' data are consistent with adaptive optimal integration, reweighting sources of evidence as their relative reliability changes during evidence integration, others exhibit patterns inconsistent with optimality.

Genetic Relatedness of Low Solitary Nests of Apis dorsata from Marang, Terengganu, Malaysia

PubMed Central

Ali, Abdul Manaf; Tan, Soon Guan; Adam, Nur Azura; Lau, Wei Hong

2012-01-01

Knowledge on the population of genetic structure and ecological behaviour of Apis dorsata from Peninsular Malaysia is needed for effective management and conservation of this species since unsustainable whole solitary low nest cutting for product harvesting is the current common practice here. The analysis of 15 single locus DNA microsatellite markers on samples from 20 solitary nests of A. dorsata showed that while these markers were polymorphic, high intracolonial relatedness existed. Furthermore, in general, slightly negative values of intercolony relatedness (R) among the nests of A. dorsata were found. However, positive values of mean intercolony relatedness were observed between 54 pairs of nests out of 190 possible combinations. The R values among nest pairs 3–4 and 3–5 was higher than 0.50 showing that their queens were half siblings, whereas nest pair 19–20 showed relatedness of 0.95 indicating that the same queen was sampled. The results that we obtained could not conclusively support the hypothesis of this study that the honey hunters in Marang district of Malaysia repeatedly harvest the same nest located at a different site and at a different time during the same honey harvesting season. However, our finding of an appreciable level of intercolonial relatedness between several pairs of nests in this pioneer study indicated that a comprehensive study with a larger sample size of solitary nests found throughout the region would be necessary to provide concrete proof for this novel idea. PMID:22911733

Multi-Modal Homing in Sea Turtles: Modeling Dual Use of Geomagnetic and Chemical Cues in Island-Finding.

PubMed

Endres, Courtney S; Putman, Nathan F; Ernst, David A; Kurth, Jessica A; Lohmann, Catherine M F; Lohmann, Kenneth J

2016-01-01

Sea turtles are capable of navigating across large expanses of ocean to arrive at remote islands for nesting, but how they do so has remained enigmatic. An interesting example involves green turtles (Chelonia mydas) that nest on Ascension Island, a tiny land mass located approximately 2000 km from the turtles' foraging grounds along the coast of Brazil. Sensory cues that turtles are known to detect, and which might hypothetically be used to help locate Ascension Island, include the geomagnetic field, airborne odorants, and waterborne odorants. One possibility is that turtles use magnetic cues to arrive in the vicinity of the island, then use chemical cues to pinpoint its location. As a first step toward investigating this hypothesis, we used oceanic, atmospheric, and geomagnetic models to assess whether magnetic and chemical cues might plausibly be used by turtles to locate Ascension Island. Results suggest that waterborne and airborne odorants alone are insufficient to guide turtles from Brazil to Ascension, but might permit localization of the island once turtles arrive in its vicinity. By contrast, magnetic cues might lead turtles into the vicinity of the island, but would not typically permit its localization because the field shifts gradually over time. Simulations reveal, however, that the sequential use of magnetic and chemical cues can potentially provide a robust navigational strategy for locating Ascension Island. Specifically, one strategy that appears viable is following a magnetic isoline into the vicinity of Ascension Island until an odor plume emanating from the island is encountered, after which turtles might either: (1) initiate a search strategy; or (2) follow the plume to its island source. These findings are consistent with the hypothesis that sea turtles, and perhaps other marine animals, use a multi-modal navigational strategy for locating remote islands.

Multi-Modal Homing in Sea Turtles: Modeling Dual Use of Geomagnetic and Chemical Cues in Island-Finding

PubMed Central

Endres, Courtney S.; Putman, Nathan F.; Ernst, David A.; Kurth, Jessica A.; Lohmann, Catherine M. F.; Lohmann, Kenneth J.

2016-01-01

Sea turtles are capable of navigating across large expanses of ocean to arrive at remote islands for nesting, but how they do so has remained enigmatic. An interesting example involves green turtles (Chelonia mydas) that nest on Ascension Island, a tiny land mass located approximately 2000 km from the turtles’ foraging grounds along the coast of Brazil. Sensory cues that turtles are known to detect, and which might hypothetically be used to help locate Ascension Island, include the geomagnetic field, airborne odorants, and waterborne odorants. One possibility is that turtles use magnetic cues to arrive in the vicinity of the island, then use chemical cues to pinpoint its location. As a first step toward investigating this hypothesis, we used oceanic, atmospheric, and geomagnetic models to assess whether magnetic and chemical cues might plausibly be used by turtles to locate Ascension Island. Results suggest that waterborne and airborne odorants alone are insufficient to guide turtles from Brazil to Ascension, but might permit localization of the island once turtles arrive in its vicinity. By contrast, magnetic cues might lead turtles into the vicinity of the island, but would not typically permit its localization because the field shifts gradually over time. Simulations reveal, however, that the sequential use of magnetic and chemical cues can potentially provide a robust navigational strategy for locating Ascension Island. Specifically, one strategy that appears viable is following a magnetic isoline into the vicinity of Ascension Island until an odor plume emanating from the island is encountered, after which turtles might either: (1) initiate a search strategy; or (2) follow the plume to its island source. These findings are consistent with the hypothesis that sea turtles, and perhaps other marine animals, use a multi-modal navigational strategy for locating remote islands. PMID:26941625

Assessment of a Pan-Dermatophyte Nested-PCR Compared with Conventional Methods for Direct Detection and Identification of Dermatophytosis Agents in Animals.

PubMed

Piri, Fahimeh; Zarei Mahmoudabadi, Ali; Ronagh, Ali; Ahmadi, Bahram; Makimura, Koichi; Rezaei-Matehkolaei, Ali

2018-06-26

Conventional direct microscopy with potassium hydroxide (KOH) and culture were found to lack the ability to establish a fast and specific diagnosis of dermatophytosis. A pan-dermatophyte nested-PCR assay was developed using a novel primer pair targeting the translation elongation factor 1-α (Tef-1α) sequences for direct detection and identification of most veterinary relevant dermatophytes in animal samples suspected to dermatophytosis. A total of 140 animal skin and hair samples were subjected to direct microscopy, culture, and ITS-RFLP/ITS-sequencing of culture isolates for the detection and identification of dermatophytosis agents. Nested-PCR sequencing was performed on all the extracted DNAs using a commercial kit after dissolving the specimens by mechanical beating. Nested-PCR was positive in 90% of samples, followed by direct microscopy (85.7%) and culture (75%). The degree of agreement between nested-PCR and direct microscopy (94.4%) was higher than with culture (83.3%). In 105 culture positive cases, the measures of agreement for the identification of dermatophytosis agents were as follows: 100% between nested-PCR sequencing and ITS-RFLP/ITS-sequencing and 63.8% between nested-PCR sequencing and culture. The developed nested-PCR was faster as well as more sensitive and specific than conventional methods for detection and identification of dermatophytes in clinical samples, which was particularly suitable for epidemiological studies. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Methane and carbon dioxide flux in the profile of wood ant (Formica aquilonia) nests and the surrounding forest floor during a laboratory incubation.

PubMed

Jílková, Veronika; Picek, Tomáš; Šestauberová, Martina; Krištůfek, Václav; Cajthaml, Tomáš; Frouz, Jan

2016-10-01

We compared methane (CH4) and carbon dioxide (CO2) fluxes in samples collected from the aboveground parts of wood ant nests and in the organic and mineral layer of the surrounding forest floor. Gas fluxes were measured during a laboratory incubation, and microbial properties (abundance of fungi, bacteria and methanotrophic bacteria) and nutrient contents (total and available carbon and nitrogen) were also determined. Both CO2 and CH4 were produced from ant nest samples, indicating that the aboveground parts of wood ant nests act as sources of both gases; in comparison, the forest floor produced about four times less CO2 and consumed rather than produced CH4 Fluxes of CH4 and CO2 were positively correlated with contents of available carbon and nitrogen. The methanotrophic community was represented by type II methanotrophic bacteria, but their abundance did not explain CH4 flux. Fungal abundance was greater in ant nest samples than in forest floor samples, but bacterial abundance was similar in both kinds of samples, suggesting that the organic materials in the nests may have been too recalcitrant for bacteria to decompose. The results indicate that the aboveground parts of wood ant nests are hot spots of CO2 and CH4 production in the forest floor. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Comparison of nested PCR and qPCR for the detection and quantitation of BoHV6 DNA.

PubMed

Kubiś, Piotr; Materniak, Magdalena; Kuźmak, Jacek

2013-12-01

Nested PCR and qPCR (quantitative PCR) tests based on glycoprotein B (gB) gene were designed for detecting Bovine herpesvirus 6 (BoHV6) in bovine whole blood samples and wild ruminant blood clots (deer and roe-deer). This virus, commonly known as BLHV (bovine lymphotropic herpesvirus) belongs to the Herpesviridae family, subfamily Gammaherpesvirinae and Macavirus genus. DNA isolated from 92 dairy cow blood samples and 69 wild ruminant clots were examined for the presence of BoHV6 using nested PCR and qPCR tests. Viral DNA was detected by using nested PCR in 59 out of 92 bovine blood samples (64.1%), and by qPCR in 68 out of 92 bovine blood samples (73.9%), but none out of 69 DNA samples isolated from wild ruminant blood clots, was positive in both assays. The specificity of nested PCR and qPCR was confirmed by using BoHV1, BoHV4, BoHV6, BFV, BIV, and BLV DNA. The sensitivity of nested PCR and qPCR was determined using a serially 10-fold diluted vector pCR2.1HgB (2 × 10(0)-2 × 10(6)copies/reaction). In this testing, qPCR was more sensitive than the nested PCR, detecting two copies of BoHV6 whilst the limit of detection for nested PCR was 20 copies. In all qPCR assays, the coefficients of determination (R(2)) ranged between 0.990 and 0.999, and the calculated amplification efficiencies (Eff%) within the range of 89.7-106.9. The intra- and inter-assay CV (coefficient of variation) values did not exceed 4%. Copyright © 2013 Elsevier B.V. All rights reserved.

Increased discriminability of authenticity from multimodal laughter is driven by auditory information.

PubMed

Lavan, Nadine; McGettigan, Carolyn

2017-10-01

We present an investigation of the perception of authenticity in audiovisual laughter, in which we contrast spontaneous and volitional samples and examine the contributions of unimodal affective information to multimodal percepts. In a pilot study, we demonstrate that listeners perceive spontaneous laughs as more authentic than volitional ones, both in unimodal (audio-only, visual-only) and multimodal contexts (audiovisual). In the main experiment, we show that the discriminability of volitional and spontaneous laughter is enhanced for multimodal laughter. Analyses of relationships between affective ratings and the perception of authenticity show that, while both unimodal percepts significantly predict evaluations of audiovisual laughter, it is auditory affective cues that have the greater influence on multimodal percepts. We discuss differences and potential mismatches in emotion signalling through voices and faces, in the context of spontaneous and volitional behaviour, and highlight issues that should be addressed in future studies of dynamic multimodal emotion processing.

Collecting a sample of loggerhead sea turtle hatchlings before a natural emergence does not reduce nest productivity

USGS Publications Warehouse

Salmon, Michael; Carthy, Raymond R.; Lohmann, Catherine M. F.; Lohmann, Kenneth J.; Wyneken, Jeanette

2012-01-01

 In numerous studies involving hatchling sea turtles, researchers have collected small numbers of hatchlings from nests a few hours before the turtles would otherwise have emerged naturally. This procedure makes it possible to do experiments in which the behavioral or physiological responses of numerous hatchlings must be tested in a limited period of time, and also allows hatchlings to be released back into the sea in time to migrate offshore before dawn. In principle, however, the procedure might inadvertently reduce nest productivity (the number of hatchlings that successfully leave the nest), if digging into a nest prior to emergence somehow reduces the ability of the remaining turtles to emerge. We compared nest productivity in 67 experimental loggerhead nests, from which we removed 10 hatchlings before a natural emergence, to 95 control nests left undisturbed before a natural emergence. The 2 groups showed no statistical differences in productivity. We conclude that taking a few hatchlings from a loggerhead nest shortly before a natural emergence has no negative impact on hatchling production if sampling is done with care at locations where there are few nest predators, and at sites where an emergence can be predicted because nest deposition dates are known.

Linking species richness curves from non-contiguous sampling to contiguous-nested SAR: An empirical study

NASA Astrophysics Data System (ADS)

Lazarina, Maria; Kallimanis, Athanasios S.; Pantis, John D.; Sgardelis, Stefanos P.

2014-11-01

The species-area relationship (SAR) is one of the few generalizations in ecology. However, many different relationships are denoted as SARs. Here, we empirically evaluated the differences between SARs derived from nested-contiguous and non-contiguous sampling designs, using plants, birds and butterflies datasets from Great Britain, Greece, Massachusetts, New York and San Diego. The shape of SAR depends on the sampling scheme, but there is little empirical documentation on the magnitude of the deviation between different types of SARs and the factors affecting it. We implemented a strictly nested sampling design to construct nested-contiguous SAR (SACR), and systematic nested but non-contiguous, and random designs to construct non-contiguous species richness curves (SASRs for systematic and SACs for random designs) per dataset. The SACR lay below any SASR and most of the SACs. The deviation between them was related to the exponent f of the power law relationship between sampled area and extent. The lower the exponent f, the higher was the deviation between the curves. We linked SACR to SASR and SAC through the concept of "effective" area (Ae), i.e. the nested-contiguous area containing equal number of species with the accumulated sampled area (AS) of a non-contiguous sampling. The relationship between effective and sampled area was modeled as log(Ae) = klog(AS). A Generalized Linear Model was used to estimate the values of k from sampling design and dataset properties. The parameter k increased with the average distance between samples and with beta diversity, while k decreased with f. For both systematic and random sampling, the model performed well in predicting effective area in both the training set and in the test set which was totally independent from the training one. Through effective area, we can link different types of species richness curves based on sampling design properties, sampling effort, spatial scale and beta diversity patterns.

Multi-mode horn antenna simulation

NASA Technical Reports Server (NTRS)

Dod, L. R.; Wolf, J. D.

1980-01-01

Radiation patterns were computed for a circular multimode horn antenna using waveguide electric field radiation expressions. The circular multimode horn was considered as a possible reflector feed antenna for the Large Antenna Multifrequency Microwave Radiometer (LAMMR). This horn antenna uses a summation of the TE sub 11 deg and TM sub 11 deg modes to generate far field primary radiation patterns with equal E and H plane beamwidths and low sidelobes. A computer program for the radiation field expressions using the summation of waveguide radiation modes is described. The sensitivity of the multimode horn antenna radiation patterns to phase variations between the two modes is given. Sample radiation pattern calculations for a reflector feed horn for LAMMR are shown. The multimode horn antenna provides a low noise feed suitable for radiometric applications.

Validation and clinical application of a nested PCR for paracoccidioidomycosis diagnosis in clinical samples from Colombian patients.

PubMed

Gaviria, Marcela; Rivera, Vanessa; Muñoz-Cadavid, Cesar; Cano, Luz Elena; Naranjo, Tonny Williams

2015-01-01

Paracoccidioidomycosis is a systemic and endemic mycosis, restricted to tropical and subtropical areas of Latin America. The infection is caused by the thermal dimorphic fungus Paracoccidioides brasiliensis and Paracoccidioides lutzii. The diagnosis of paracoccidioidomycosis is usually performed by microscopic examination, culture and immunodiagnostic tests to respiratory specimens, body fluids and/or biopsies; however these methods require laboratory personnel with experience and several days to produce a result. In the present study, we have validated and evaluated a nested PCR assay targeting the gene encoding the Paracoccidioides gp43 membrane protein in 191 clinical samples: 115 samples from patients with proven infections other than paracoccidioidomycosis, 51 samples as negative controls, and 25 samples from patients diagnosed with paracoccidioidomycosis. Additionally, the specificity of the nested PCR assay was also evaluated using purified DNA isolated from cultures of different microorganisms (n=35) previously identified by culture and/or sequencing. The results showed that in our hands, this nested PCR assay for gp43 protein showed specificity and sensitivity rates of 100%. The optimized nested PCR conditions in our laboratory allowed detection down to 1fg of P. brasiliensis DNA. Copyright © 2015 Elsevier Editora Ltda. All rights reserved.

Detection of Toxoplasma gondii oocysts in soils in northwestern China using a new semi-nested PCR assay.

PubMed

Wang, Meng; Meng, Peng; Ye, Qiang; Pu, Yuan-Hua; Yang, Xiao-Yu; Luo, Jian-Xun; Zhang, Nian-Zhang; Zhang, De-Lin

2014-09-28

Toxoplasma gondii is a zoonotic pathogen that can infect a range of animals and humans. Ingestion of T. gondii oocysts in soil is a significant transmission route for humans and animals acquiring toxoplasmosis. In the present study, we developed a new semi-nested PCR method to determine T. gondii oocysts distribution in soils in northwestern China. The one tube semi-nested PCR assay was developed to detect the oocysts of T. gondii in soil, targeting the repetitive 529 bp fragment of T. gondii genomic DNA. Then a total of 268 soil samples, including 148 samples from Gansu Province and 120 samples from Qinghai Province, northwestern China, were examined by the semi-nested PCR method. One third of the positive samples were sequenced. The sensitivity of the semi-nested PCR assay was 10(2)  T. gondii oocysts in 5 g soil sample. Investigation of soil samples from northwestern China showed that 34 out of 268 soil samples (12.69%) were T. gondii positive. Sequences of the partial 529 bp fragments varied from 0-1.2% among the sequenced samples. The prevalence of T. gondii oocysts in soil from cities (24/163) was slightly higher than that in soils from pasturing areas (10/105) (P = 0.21). Among the different regions in cities, the prevalence of T. gondii oocysts in soils from parks was 14.15%, whereas that in soils from schools was 19.05%. The present study firstly reported the prevalence of T. gondii oocysts in soils in northwest China using a novel semi-nested PCR assay, which provided baseline data for the effective prevention and control of toxoplasmosis in this region.

Molecular diagnosis of strongyloidiasis in a population of an endemic area through nested-PCR.

PubMed

Sharifdini, Meysam; Keyhani, Amir; Eshraghian, Mohammad Reza; Beigom Kia, Eshrat

2018-01-01

This study is aimed to diagnose and analyze strongyloidiasis in a population of an endemic area of Iran using nested-PCR, coupled with parasitological methods. Screening of strongyloidiasis infected people using reliable diagnostic techniques are essential to decrease the mortality and morbidity associated with this infection. Molecular methods have been proved to be highly sensitive and specific for detection of Strongyloides stercoralis in stool samples. A total of 155 fresh single stool samples were randomly collected from residents of north and northwest of Khouzestan Province, Iran. All samples were examined by parasitological methods including formalin-ether concentration and nutrient agar plate culture, and molecular method of nested-PCR. Infections with S. stercoralis were analyzed according to demographic criteria. Based on the results of nested-PCR method 15 cases (9.7%) were strongyloidiasis positive. Nested-PCR was more sensitive than parasitological techniques on single stool sampling. Elderly was the most important population index for higher infectivity with S. stercoralis . In endemic areas of S. stercoralis , old age should be considered as one of the most important risk factors of infection, especially among the immunosuppressed individuals.

Mode synthesizing atomic force microscopy and mode-synthesizing sensing

DOEpatents

Passian, Ali; Thundat, Thomas George; Tetard, Laurene

2013-05-17

A method of analyzing a sample that includes applying a first set of energies at a first set of frequencies to a sample and applying, simultaneously with the applying the first set of energies, a second set of energies at a second set of frequencies, wherein the first set of energies and the second set of energies form a multi-mode coupling. The method further includes detecting an effect of the multi-mode coupling.

Mode-synthesizing atomic force microscopy and mode-synthesizing sensing

DOEpatents

Passain, Ali; Thundat, Thomas George; Tetard, Laurene

2014-07-22

A method of analyzing a sample that includes applying a first set of energies at a first set of frequencies to a sample and applying, simultaneously with the applying the first set of energies, a second set of energies at a second set of frequencies, wherein the first set of energies and the second set of energies form a multi-mode coupling. The method further includes detecting an effect of the multi-mode coupling.

A Multi-Modality CMOS Sensor Array for Cell-Based Assay and Drug Screening.

PubMed

Chi, Taiyun; Park, Jong Seok; Butts, Jessica C; Hookway, Tracy A; Su, Amy; Zhu, Chengjie; Styczynski, Mark P; McDevitt, Todd C; Wang, Hua

2015-12-01

In this paper, we present a fully integrated multi-modality CMOS cellular sensor array with four sensing modalities to characterize different cell physiological responses, including extracellular voltage recording, cellular impedance mapping, optical detection with shadow imaging and bioluminescence sensing, and thermal monitoring. The sensor array consists of nine parallel pixel groups and nine corresponding signal conditioning blocks. Each pixel group comprises one temperature sensor and 16 tri-modality sensor pixels, while each tri-modality sensor pixel can be independently configured for extracellular voltage recording, cellular impedance measurement (voltage excitation/current sensing), and optical detection. This sensor array supports multi-modality cellular sensing at the pixel level, which enables holistic cell characterization and joint-modality physiological monitoring on the same cellular sample with a pixel resolution of 80 μm × 100 μm. Comprehensive biological experiments with different living cell samples demonstrate the functionality and benefit of the proposed multi-modality sensing in cell-based assay and drug screening.

Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets

PubMed Central

Yu, Guoqin; Fadrosh, Doug; Goedert, James J.; Ravel, Jacques; Goldstein, Alisa M.

2015-01-01

Background Sequencing of the PCR-amplified 16S rRNA gene has become a common approach to microbial community investigations in the fields of human health and environmental sciences. This approach, however, is difficult when the amount of DNA is too low to be amplified by standard PCR. Nested PCR can be employed as it can amplify samples with DNA concentration several-fold lower than standard PCR. However, potential biases with nested PCRs that could affect measurement of community structure have received little attention. Results In this study, we used 17 DNAs extracted from vaginal swabs and 12 DNAs extracted from stool samples to study the influence of nested PCR amplification of the 16S rRNA gene on the estimation of microbial community structure using Illumina MiSeq sequencing. Nested and standard PCR methods were compared on alpha- and beta-diversity metrics and relative abundances of bacterial genera. The effects of number of cycles in the first round of PCR (10 vs. 20) and microbial diversity (relatively low in vagina vs. high in stool) were also investigated. Vaginal swab samples showed no significant difference in alpha diversity or community structure between nested PCR and standard PCR (one round of 40 cycles). Stool samples showed significant differences in alpha diversity (except Shannon’s index) and relative abundance of 13 genera between nested PCR with 20 cycles in the first round and standard PCR (P<0.01), but not between nested PCR with 10 cycles in the first round and standard PCR. Operational taxonomic units (OTUs) that had low relative abundance (sum of relative abundance <0.167) accounted for most of the distortion (>27% of total OTUs in stool). Conclusions Nested PCR introduced bias in estimated diversity and community structure. The bias was more significant for communities with relatively higher diversity and when more cycles were applied in the first round of PCR. We conclude that nested PCR could be used when standard PCR does not work. However, rare taxa detected by nested PCR should be validated by other technologies. PMID:26196512

Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets.

PubMed

Yu, Guoqin; Fadrosh, Doug; Goedert, James J; Ravel, Jacques; Goldstein, Alisa M

2015-01-01

Sequencing of the PCR-amplified 16S rRNA gene has become a common approach to microbial community investigations in the fields of human health and environmental sciences. This approach, however, is difficult when the amount of DNA is too low to be amplified by standard PCR. Nested PCR can be employed as it can amplify samples with DNA concentration several-fold lower than standard PCR. However, potential biases with nested PCRs that could affect measurement of community structure have received little attention. In this study, we used 17 DNAs extracted from vaginal swabs and 12 DNAs extracted from stool samples to study the influence of nested PCR amplification of the 16S rRNA gene on the estimation of microbial community structure using Illumina MiSeq sequencing. Nested and standard PCR methods were compared on alpha- and beta-diversity metrics and relative abundances of bacterial genera. The effects of number of cycles in the first round of PCR (10 vs. 20) and microbial diversity (relatively low in vagina vs. high in stool) were also investigated. Vaginal swab samples showed no significant difference in alpha diversity or community structure between nested PCR and standard PCR (one round of 40 cycles). Stool samples showed significant differences in alpha diversity (except Shannon's index) and relative abundance of 13 genera between nested PCR with 20 cycles in the first round and standard PCR (P<0.01), but not between nested PCR with 10 cycles in the first round and standard PCR. Operational taxonomic units (OTUs) that had low relative abundance (sum of relative abundance <0.167) accounted for most of the distortion (>27% of total OTUs in stool). Nested PCR introduced bias in estimated diversity and community structure. The bias was more significant for communities with relatively higher diversity and when more cycles were applied in the first round of PCR. We conclude that nested PCR could be used when standard PCR does not work. However, rare taxa detected by nested PCR should be validated by other technologies.

Evaluation of efficiency of nested multiplex allele-specific PCR assay for detection of multidrug resistant tuberculosis directly from sputum samples.

PubMed

Mistri, S K; Sultana, M; Kamal, S M M; Alam, M M; Irin, F; Nessa, J; Ahsan, C R; Yasmin, M

2016-05-01

For an effective control of tuberculosis, rapid detection of multidrug resistant tuberculosis (MDR-TB) is necessary. Therefore, we developed a modified nested multiplex allele-specific polymerase chain reaction (MAS-PCR) method that enables rapid MDR-TB detection directly from sputum samples. The efficacy of this method was evaluated using 79 sputum samples collected from suspected tuberculosis patients. The performance of nested MAS-PCR method was compared with other MDR-TB detection methods like drug susceptibility testing (DST) and DNA sequencing. As rifampicin (RIF) resistance conforms to MDR-TB in greater than 90% cases, only the presence of RIF-associated mutations in rpoB gene was determined by DNA sequencing and nested MAS-PCR to detect MDR-TB. The concordance between nested MAS-PCR and DNA sequencing results was found to be 96·3%. When compared with DST, the sensitivity and specificity of nested MAS-PCR for RIF-resistance detection were determined to be 92·9 and 100% respectively. For developing- and high-TB burden countries, molecular-based tests have been recommended by the World Health Organization for rapid detection of MDR-TB. The results of this study indicate that, nested MAS-PCR assay might be a practical and relatively cost effective molecular method for rapid detection of MDR-TB from suspected sputum samples in developing countries with resource poor settings. © 2016 The Society for Applied Microbiology.

Evaluation of hsp65 Nested PCR-Restriction Analysis (PRA) for Diagnosing Tuberculosis in a High Burden Country

PubMed Central

Macente, Sara; Fujimura Leite, Clarice Queico; Santos, Adolfo Carlos Barreto; Siqueira, Vera Lúcia Dias; Machado, Luzia Neri Cosmo; Marcondes, Nadir Rodrigues; Hirata, Mario Hiroyuki; Hirata, Rosário Dominguez Crespo

2013-01-01

Current study evaluated the hsp65 Nested PCR Restriction Fragment Length Polymorphism Analysis (hsp65 Nested PCR-PRA) to detect and identify Mycobacterium tuberculosis complex directly in clinical samples for a rapid and specific diagnosis of tuberculosis (TB). hsp65 Nested PCR-PRA was applied directly to 218 clinical samples obtained from 127 patients suspected of TB or another mycobacterial infection from July 2009 to July 2010. The hsp65 Nested PCR-PRA showed 100% sensitivity and 95.0 and 93.1% specificity in comparison with culture and microscopy (acid fast bacillus smear), respectively. hsp65 Nested PCR-PRA was shown to be a fast and reliable assay for diagnosing TB, which may contribute towards a fast diagnosis that could help the selection of appropriate chemotherapeutic and early epidemiological management of the cases which are of paramount importance in a high TB burden country. PMID:24260739

[Sensitivity and specificity of nested PCR pyrosequencing in hepatitis B virus drug resistance gene testing].

PubMed

Sun, Shumei; Zhou, Hao; Zhou, Bin; Hu, Ziyou; Hou, Jinlin; Sun, Jian

2012-05-01

To evaluate the sensitivity and specificity of nested PCR combined with pyrosequencing in the detection of HBV drug-resistance gene. RtM204I (ATT) mutant and rtM204 (ATG) nonmutant plasmids mixed at different ratios were detected for mutations using nested-PCR combined with pyrosequencing, and the results were compared with those by conventional PCR pyrosequencing to analyze the linearity and consistency of the two methods. Clinical specimens with different viral loads were examined for drug-resistant mutations using nested PCR pyrosequencing and nested PCR combined with dideoxy sequencing (Sanger) for comparison of the detection sensitivity and specificity. The fitting curves demonstrated good linearity of both conventional PCR pyrosequencing and nested PCR pyrosequencing (R(2)>0.99, P<0.05). Nested PCR showed a better consistency with the predicted value than conventional PCR, and was superior to conventional PCR for detection of samples containing 90% mutant plasmid. In the detection of clinical specimens, Sanger sequencing had a significantly lower sensitivity than nested PCR pyrosequencing (92% vs 100%, P<0.01). The detection sensitivity of Sanger sequencing varied with the viral loads, especially in samples with low viral copies (HBV DNA ≤3log10 copies/ml), where the sensitivity was 78%, significantly lower than that of pyrosequencing (100%, P<0.01). Neither of the two methods yielded positive results for the negative control samples, suggesting their good specificity. Compared with nested PCR and Sanger sequencing method, nested PCR pyrosequencing has a higher sensitivity especially in clinical specimens with low viral copies, which can be important for early detection of HBV mutant strains and hence more effective clinical management.

Soil attributes drive nest-site selection by the campo miner Geositta poeciloptera.

PubMed

Meireles, Ricardo Camargos de; Teixeira, João Paulo Gusmão; Solar, Ricardo; Vasconcelos, Bruno Nery F; Fernandes, Raphael B A; Lopes, Leonardo Esteves

2018-01-01

Substrate type is a key-factor in nest-site selection and nest architecture of burrowing birds. However, little is known about which factors drive nest-site selection for these species, especially in the tropics. We studied the influence of soil attributes on nest-site selection by the campo miner Geositta poeciloptera, an open grassland bird that builds its nests within soil cavities. For all nests found, we measured the depth of the nest cavity and the resistance of the soil to penetration, and identified the soil horizon in which the nest was located. In soil banks with nests, we collected soil samples for granulometric analysis around each nest cavity, while in soil banks without nests we collected these samples at random points. From 43 nests found, 86% were located in the deeper soil horizons (C-horizon), and only 14% in the shallower horizons (B-horizon). Granulometric analysis showed that the C-horizons possessed a high similar granulometric composition, with high silt and low clay contents. These characteristics are associated with a low degree of structural development of the soil, which makes it easier to excavate. Contrarily, soil resistance to penetration does not seem to be an important criterion for nest site selection, although nests in more resistant the soils tend to have shallower nest cavities. Among the soil banks analyzed, 40% of those without cavities possessed a larger proportion of B-horizon relative to the C-horizon, and their texture was more clayey. On the other hand, almost all soil banks containing nest cavities had a larger C-horizon and a silty texture, indicating that soil attributes drive nest-site selection by G. poeciloptera. Thus, we conclude that the patchy distribution of G. poeciloptera can attributed to the infrequent natural exposure of the C-horizon in the tropical region, where well developed, deep and permeable soils are more common.

Soil attributes drive nest-site selection by the campo miner Geositta poeciloptera

PubMed Central

Teixeira, João Paulo Gusmão; Solar, Ricardo; Vasconcelos, Bruno Nery F.; Fernandes, Raphael B. A.; Lopes, Leonardo Esteves

2018-01-01

Substrate type is a key-factor in nest-site selection and nest architecture of burrowing birds. However, little is known about which factors drive nest-site selection for these species, especially in the tropics. We studied the influence of soil attributes on nest-site selection by the campo miner Geositta poeciloptera, an open grassland bird that builds its nests within soil cavities. For all nests found, we measured the depth of the nest cavity and the resistance of the soil to penetration, and identified the soil horizon in which the nest was located. In soil banks with nests, we collected soil samples for granulometric analysis around each nest cavity, while in soil banks without nests we collected these samples at random points. From 43 nests found, 86% were located in the deeper soil horizons (C-horizon), and only 14% in the shallower horizons (B-horizon). Granulometric analysis showed that the C-horizons possessed a high similar granulometric composition, with high silt and low clay contents. These characteristics are associated with a low degree of structural development of the soil, which makes it easier to excavate. Contrarily, soil resistance to penetration does not seem to be an important criterion for nest site selection, although nests in more resistant the soils tend to have shallower nest cavities. Among the soil banks analyzed, 40% of those without cavities possessed a larger proportion of B-horizon relative to the C-horizon, and their texture was more clayey. On the other hand, almost all soil banks containing nest cavities had a larger C-horizon and a silty texture, indicating that soil attributes drive nest-site selection by G. poeciloptera. Thus, we conclude that the patchy distribution of G. poeciloptera can attributed to the infrequent natural exposure of the C-horizon in the tropical region, where well developed, deep and permeable soils are more common. PMID:29381768

Comparison of the diagnostic performance of microscopic examination with nested polymerase chain reaction for optimum malaria diagnosis in Upper Myanmar.

PubMed

Kang, Jung-Mi; Cho, Pyo-Yun; Moe, Mya; Lee, Jinyoung; Jun, Hojong; Lee, Hyeong-Woo; Ahn, Seong Kyu; Kim, Tae Im; Pak, Jhang Ho; Myint, Moe Kyaw; Lin, Khin; Kim, Tong-Soo; Na, Byoung-Kuk

2017-03-16

Accurate diagnosis of Plasmodium infection is crucial for prompt malaria treatment and surveillance. Microscopic examination has been widely applied as the gold standard for malaria diagnosis in most part of malaria endemic areas, but its diagnostic value has been questioned, particularly in submicroscopic malaria. In this study, the diagnostic performance of microscopic examination and nested polymerase chain reaction (PCR) was evaluated to establish optimal malaria diagnosis method in Myanmar. A total of 1125 blood samples collected from residents in the villages and towns located in Naung Cho, Pyin Oo Lwin, Tha Beik Kyin townships and Mandalay of Upper Myanmar were screened by microscopic examination and species-specific nested PCR method. Among the 1125 blood samples, 261 samples were confirmed to be infected with malaria by microscopic examination. Evaluation of the 1125 samples by species-specific nested PCR analysis revealed that the agreement between microscopic examination and nested PCR was 87.3% (261/299). Nested PCR successfully detected 38 Plasmodium falciparum or Plasmodium vivax infections, which were missed in microscopic examination. Microscopic examinations also either misdiagnosed the infected Plasmodium species, or did not detect mixed infections with different Plasmodium species in 31 cases. The nested PCR method is more reliable than conventional microscopic examination for the diagnosis of malaria infections, and this is particularly true in cases of mixed infections and submicroscopic infections. Given the observed higher sensitivity and specificity of nested PCR, the molecular method holds enormous promise in malaria diagnosis and species differentiation, and can be applied as an effective monitoring tool for malaria surveillance, control and elimination in Myanmar.

Characteristics of the Least Bell's Vireo Nest Sites Along the Santa Ynez River, Santa Barbara County

Treesearch

Thomas E. Olson; M. Violet Gray

1989-01-01

Due primarily to alteration of riparian vegetation and nest parasitism by brown-headed cowbirds (Molothrus ater), the least Bell's vireo (Vireo bellii pusillus) has under-gone a tremendous decline in range and numbers since the 1920's. In 1987, we sampled vegetation at 32 nest sites to characterize nesting habitat of...

Optimized nested polymerase chain reaction for antemortem detection of Mycobacteria in Amazon parrots (Amazona aestiva) and orange-winged Amazons (Amazona amazonica).

PubMed

Baquião, Arianne Costa; Luna, Janaina Oliveira; Medina, Aziz Orro; Sanfilippo, Luiz Francisco; de Faria, Maria Jacinta; dos Santos, Manuel Armando Azevedo

2014-03-01

The objectives of this study were to optimize nested polymerase chain reaction (PCR) for Mycobacterium avium complex and Mycobacterium tuberculosis complex and apply them on samples from parrots. Results were negative for the presence of these Mycobacterium in the samples, and nested PCR was specific, faster, and more sensitive than other tests, thereby justifying its use in antemortem diagnosis.

DEVELOPING ATMOSPHERIC RETRIEVAL METHODS FOR DIRECT IMAGING SPECTROSCOPY OF GAS GIANTS IN REFLECTED LIGHT. I. METHANE ABUNDANCES AND BASIC CLOUD PROPERTIES

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

Lupu, Roxana E.; Marley, Mark S.; Zahnle, Kevin

Upcoming space-based coronagraphic instruments in the next decade will perform reflected light spectroscopy and photometry of cool directly imaged extrasolar giant planets. We are developing a new atmospheric retrieval methodology to help assess the science return and inform the instrument design for such future missions, and ultimately interpret the resulting observations. Our retrieval technique employs a geometric albedo model coupled with both a Markov chain Monte Carlo Ensemble Sampler ( emcee ) and a multimodal nested sampling algorithm ( MultiNest ) to map the posterior distribution. This combination makes the global evidence calculation more robust for any given model andmore » highlights possible discrepancies in the likelihood maps. As a proof of concept, our current atmospheric model contains one or two cloud layers, methane as a major absorber, and a H{sub 2}–He background gas. This 6-to-9 parameter model is appropriate for Jupiter-like planets and can be easily expanded in the future. In addition to deriving the marginal likelihood distribution and confidence intervals for the model parameters, we perform model selection to determine the significance of methane and cloud detection as a function of expected signal-to-noise ratio in the presence of spectral noise correlations. After internal validation, the method is applied to realistic spectra of Jupiter, Saturn, and HD 99492c, a model observing target. We find that the presence or absence of clouds and methane can be determined with high confidence, while parameter uncertainties are model dependent and correlated. Such general methods will also be applicable to the interpretation of direct imaging spectra of cloudy terrestrial planets.« less

Developing Atmospheric Retrieval Methods for Direct Imaging Spectroscopy of Gas Giants in Reflected Light I: Methane Abundances and Basic Cloud Properties

NASA Technical Reports Server (NTRS)

Lupu, R. E.; Marley, M. S.; Lewis, N.; Line, M.; Traub, W.; Zahnle, K.

2016-01-01

Reflected light spectroscopy and photometry of cool, directly imaged extrasolar giant planets are expected to be performed in the next decade by space-based telescopes equipped with optical wavelength coronagraphs and integral field spectrographs, such as the Wide-Field Infrared Survey Telescope (WFIRST). We are developing a new atmospheric retrieval methodology to help assess the science return and inform the instrument design for such future missions, and ultimately interpret the resulting observations. Our retrieval technique employs an albedo model coupled with both a Markov chain Monte Carlo Ensemble Sampler (emcee) and a multimodal nested sampling algorithm (MultiNest) to map the posterior distribution. This combination makes the global evidence calculation more robust for any given model, and highlights possible discrepancies in the likelihood maps. Here we apply this methodology to simulated spectra of cool giant planets. As a proof-of-concept, our current atmospheric model contains 1 or 2 cloud layers, methane as a major absorber, and a H2-He background gas. This 6-to-9 parameter model is appropriate for Jupiter-like planets and can be easily expanded in the future. In addition to deriving the marginal likelihood distribution and confidence intervals for the model parameters, we perform model selection to determine the significance of methane and cloud detection as a function of expected signal-to-noise, in the presence of spectral noise correlations. After internal validation, the method is applied to realistic reflected-light spectra of Jupiter, Saturn, and HD 99492 c, a likely observing target. We find that the presence or absence of clouds and methane can be determined with high accuracy, while parameters uncertainties are model-dependent.

Construction of nested maximin designs based on successive local enumeration and modified novel global harmony search algorithm

NASA Astrophysics Data System (ADS)

Yi, Jin; Li, Xinyu; Xiao, Mi; Xu, Junnan; Zhang, Lin

2017-01-01

Engineering design often involves different types of simulation, which results in expensive computational costs. Variable fidelity approximation-based design optimization approaches can realize effective simulation and efficiency optimization of the design space using approximation models with different levels of fidelity and have been widely used in different fields. As the foundations of variable fidelity approximation models, the selection of sample points of variable-fidelity approximation, called nested designs, is essential. In this article a novel nested maximin Latin hypercube design is constructed based on successive local enumeration and a modified novel global harmony search algorithm. In the proposed nested designs, successive local enumeration is employed to select sample points for a low-fidelity model, whereas the modified novel global harmony search algorithm is employed to select sample points for a high-fidelity model. A comparative study with multiple criteria and an engineering application are employed to verify the efficiency of the proposed nested designs approach.

Estimating nest detection probabilities for white-winged dove nest transects in Tamaulipas, Mexico

USGS Publications Warehouse

Nichols, J.D.; Tomlinson, R.E.; Waggerman, G.

1986-01-01

Nest transects in nesting colonies provide one source of information on White-winged Dove (Zenaida asiatica asiatica) population status and reproduction. Nests are counted along transects using standardized field methods each year in Texas and northeastern Mexico by personnel associated with Mexico's Office of Flora and Fauna, the Texas Parks and Wildlife Department, and the U.S. Fish and Wildlife Service. Nest counts on transects are combined with information on the size of nesting colonies to estimate total numbers of nests in sampled colonies. Historically, these estimates have been based on the actual nest counts on transects and thus have required the assumption that all nests lying within transect boundaries are detected (seen) with a probability of one. Our objectives were to test the hypothesis that nest detection probability is one and, if rejected, to estimate this probability.

Nest survival modelling using a multi-species approach in forests managed for timber and biofuel feedstock

USGS Publications Warehouse

Loman, Zachary G.; Monroe, Adrian; Riffell, Samuel K.; Miller, Darren A.; Vilella, Francisco; Wheat, Bradley R.; Rush, Scott A.; Martin, James A.

2018-01-01

Switchgrass (Panicum virgatum) intercropping is a novel forest management practice for biomass production intended to generate cellulosic feedstocks within intensively managed loblolly pine‐dominated landscapes. These pine plantations are important for early‐successional bird species, as short rotation times continually maintain early‐successional habitat. We tested the efficacy of using community models compared to individual surrogate species models in understanding influences on nest survival. We analysed nest data to test for differences in habitat use for 14 bird species in plots managed for switchgrass intercropping and controls within loblolly pine (Pinus taeda) plantations in Mississippi, USA.We adapted hierarchical models using hyper‐parameters to incorporate information from both common and rare species to understand community‐level nest survival. This approach incorporates rare species that are often discarded due to low sample sizes, but can inform community‐level demographic parameter estimates. We illustrate use of this approach in generating both species‐level and community‐wide estimates of daily survival rates for songbird nests. We were able to include rare species with low sample size (minimum n = 5) to inform a hyper‐prior, allowing us to estimate effects of covariates on daily survival at the community level, then compare this with a single‐species approach using surrogate species. Using single‐species models, we were unable to generate estimates below a sample size of 21 nests per species.Community model species‐level survival and parameter estimates were similar to those generated by five single‐species models, with improved precision in community model parameters.Covariates of nest placement indicated that switchgrass at the nest site (<4 m) reduced daily nest survival, although intercropping at the forest stand level increased daily nest survival.Synthesis and applications. Community models represent a viable method for estimating community nest survival rates and effects of covariates while incorporating limited data for rarely detected species. Intercropping switchgrass in loblolly pine plantations slightly increased daily nest survival at the research plot scale (0.1 km2), although at a local scale (50 m2) switchgrass negatively influenced nest survival. A likely explanation is intercropping shifted community composition, favouring species with greater disturbance tolerance.

Detection of canine distemper virus (CDV) through one step RT-PCR combined with nested PCR.

PubMed

Kim, Y H; Cho, K W; Youn, H Y; Yoo, H S; Han, H R

2001-04-01

A one step reverse transcription PCR (RT-PCR) combined nested PCR was set up to increase efficiency in the diagnosis of canine distemper virus (CDV) infection after developement of nested PCR. Two PCR primer sets were designed based on the sequence of nucleocapsid gene of CDV Onderstepoort strain. One-step RT-PCR with the outer primer pair was revealed to detect 10(2) PFU/ml. The sensitivity was increased hundredfold using the one-step RT-PCR combined with the nested PCR. Specificity of the PCR was also confirmed using other related canine virus and peripheral blood mononuclear cells (PBMC) and body secretes of healthy dogs. Of the 51 blood samples from dogs clinically suspected of CD, 45 samples were revealed as positive by one-step RT-PCR combined with nested PCR. However, only 15 samples were identified as positive with a single one step RT-PCR. Therefore approximately 60% increase in the efficiency of the diagnosis was observed by the combined method. These results suggested that one step RT-PCR combined with nested PCR could be a sensitive, specific, and practical method for diagnosis of CDV infection.

Changes in plasma levels of adrenaline, noradrenaline, glucose, lactate and CO2 in the green turtle, Chelonia mydas, during peak period of nesting.

PubMed

Alkindi, A Y A; Al-Habsi, A A; Mahmoud, I Y

2008-02-01

Plasma concentrations of stress hormones [adrenaline (ADR), noradrenaline (NR)], lactate, glucose and CO2 were monitored during peak nesting period (May-October) at different phases of nesting in the green turtle, Chelonia mydas. These include, emergence from sea, excavating body and nest chambers, oviposition, covering and camouflaging the nest and then returning to sea. Turtles that completed all phases of nesting including oviposition before returning to sea were considered "successful" turtles, while those that completed all phases but failed to lay their eggs were "unsuccessful". Blood samples were taken from the cervical sinus within 5min of capture to avoid stress due to handling. The turtles were usually sampled for blood between 20:00 and 1:00h of nesting time to ensure uniformity in the sampling. Plasma ADR and NR values were highly significant (P<0.001) in successful turtles over emergence, excavating and unsuccessful turtles. Plasma glucose levels remained stable throughout the nesting phases while lactate levels were significantly higher in successful turtles over the other phases (P<0.05) which signifies anaerobic metabolism during nesting. Plasma CO2 values were negatively correlated with ADR and NR (r=-0.258, P=0.03; r=-0.304, P=0.010), respectively. Hematocrit was significantly higher in successful phase (P<0.05) compared to other phases, and this may signify a higher degree of stress in successful turtles. Body temperature were significantly lower (P<0.005) in the excavating phase compared to the other three phases. Overall, body temperatures were lower than sand temperatures around the nest, which may indicate a behavioral thermoregulation used by the turtles during nesting. This information will be of value to the ongoing conservation program at Ras Al-Hadd Reserve in the Sultanate of Oman.

Genealogical Properties of Subsamples in Highly Fecund Populations

NASA Astrophysics Data System (ADS)

Eldon, Bjarki; Freund, Fabian

2018-03-01

We consider some genealogical properties of nested samples. The complete sample is assumed to have been drawn from a natural population characterised by high fecundity and sweepstakes reproduction (abbreviated HFSR). The random gene genealogies of the samples are—due to our assumption of HFSR—modelled by coalescent processes which admit multiple mergers of ancestral lineages looking back in time. Among the genealogical properties we consider are the probability that the most recent common ancestor is shared between the complete sample and the subsample nested within the complete sample; we also compare the lengths of `internal' branches of nested genealogies between different coalescent processes. The results indicate how `informative' a subsample is about the properties of the larger complete sample, how much information is gained by increasing the sample size, and how the `informativeness' of the subsample varies between different coalescent processes.

Sensitivity of nested-PCR for plasmodium detection in pooled whole blood samples and its usefulness to blood donor screening in endemic areas.

PubMed

de Freitas, Daniel Roberto Coradi; Gomes, Luciano Teixeira; Fontes, Cor Jesus F; Tauil, Pedro Luiz; Pang, Lorrin W; Duarte, Elisabeth Carmen

2014-04-01

Transfusion-transmitted malaria is a severe disease with high fatality rate. Most Brazilian blood banks in the Amazon region perform malaria screening using microscopic examination (thick smears). Since low parasite concentrations are expected in asymptomatic blood donors a high sensitivity test should be used for donor screening. This study determined the sensitivity of a nested-PCR for plasmodium detection in pooled samples. We performed a one-stage criterion validation study with 21 positive samples pooled with samples from ten negative volunteer until three different concentrations were reached (0.33; 0.25; 0.20 parasites/μL - p/μL). Nested PCR was performed as described by Snounou et al. (1993). Sensitivities (and confidence intervals) were determined by stratum of final parasite concentration on the pooled samples. All samples with parasitemia values of 0.33 and 0.25 p/μL had 100% sensitivity (95%CI=86.3-100). One negative result was obtained from a sample with 0.20 p/μL sensitivity=95.2% (95%CI=76.2-99.9). Compared to parasitemia detectable under ideal conditions of thick smear, this nested-PCR in pooled sample was able to detect 40 times more parasites per microliter. Nested-PCR in pooled samples should be considered as a high sensitive alternative to thick smear for donor screening in blood banks at endemic regions. Local authorities need to assess cost:benefit advantages of this method compared to alternatives. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comprehensive Comparison between Empty Nest and Non-Empty Nest Elderly: A Cross-Sectional Study among Rural Populations in Northeast China

PubMed Central

Chang, Ye; Guo, Xiaofan; Guo, Liang; Li, Zhao; Yang, Hongmei; Yu, Shasha; Sun, Guozhe; Sun, Yingxian

2016-01-01

This study aimed to comprehensively compare the general characteristics, lifestyles, serum parameters, ultrasonic cardiogram (UCG) parameters, depression, quality of life, and various comorbidities between empty nest and non-empty nest elderly among rural populations in northeast China. This analysis was based on our previous study which was conducted from January 2012 to August 2013, using a multistage, stratified, random cluster sampling scheme. The final analyzed sample consisted of 3208 participants aged no less than 60 years, which was further classified into three groups: non-empty nest group, empty nest group (living as a couple), and empty nest group (living alone). More than half of the participants were empty nest elderly (60.5%). There were no significant statistical differences for serum parameters, UCG parameters, lifestyles, dietary pattern, and scores of Patient Health Questionnaire-9 (PHQ-9) and World Health Organization Quality of Life questionnaire, abbreviated version (WHOQOL-BREF) among the three groups. Empty nest elderly showed no more risk for comorbidities such as general obesity, abdominal obesity, hyperuricemia, hyperhomocysteinemia, diabetes, dyslipidemia, left atrial enlargement (LAE), and stroke. Our study indicated that empty nest elderly showed no more risk for depression, low quality of life and comorbidities such as general obesity, abdominal obesity, hyperuricemia, hyperhomocysteinemia, diabetes, dyslipidemia, LAE, and stroke among rural populations in northeast China. PMID:27618905

Comprehensive Comparison between Empty Nest and Non-Empty Nest Elderly: A Cross-Sectional Study among Rural Populations in Northeast China.

PubMed

Chang, Ye; Guo, Xiaofan; Guo, Liang; Li, Zhao; Yang, Hongmei; Yu, Shasha; Sun, Guozhe; Sun, Yingxian

2016-08-27

This study aimed to comprehensively compare the general characteristics, lifestyles, serum parameters, ultrasonic cardiogram (UCG) parameters, depression, quality of life, and various comorbidities between empty nest and non-empty nest elderly among rural populations in northeast China. This analysis was based on our previous study which was conducted from January 2012 to August 2013, using a multistage, stratified, random cluster sampling scheme. The final analyzed sample consisted of 3208 participants aged no less than 60 years, which was further classified into three groups: non-empty nest group, empty nest group (living as a couple), and empty nest group (living alone). More than half of the participants were empty nest elderly (60.5%). There were no significant statistical differences for serum parameters, UCG parameters, lifestyles, dietary pattern, and scores of Patient Health Questionnaire-9 (PHQ-9) and World Health Organization Quality of Life questionnaire, abbreviated version (WHOQOL-BREF) among the three groups. Empty nest elderly showed no more risk for comorbidities such as general obesity, abdominal obesity, hyperuricemia, hyperhomocysteinemia, diabetes, dyslipidemia, left atrial enlargement (LAE), and stroke. Our study indicated that empty nest elderly showed no more risk for depression, low quality of life and comorbidities such as general obesity, abdominal obesity, hyperuricemia, hyperhomocysteinemia, diabetes, dyslipidemia, LAE, and stroke among rural populations in northeast China.

Evaluation of a nested-PCR for mycobacterium tuberculosis detection in blood and urine samples.

PubMed

da Cruz, Heidi Lacerda Alves; de Albuquerque Montenegro, Rosana; de Araújo Lima, Juliana Falcão; da Rocha Poroca, Diogo; da Costa Lima, Juliana Figueirêdo; Maria Lapa Montenegro, Lílian; Crovella, Sergio; Charifker Schindler, Haiana

2011-01-01

The polymerase chain reaction (PCR) and its variations, such as the nested-PCR, have been described as promising techniques for rapid diagnosis of tuberculosis (TB). With the aim of evaluating the usefulness of a nested-PCR method on samples of blood and urine of patients suspected of tuberculosis we analyzed 192 clinical samples, using as a molecular target the insertion element IS6110 specific of M. tuberculosis genome. Nested-PCR method showed higher sensitivity in patients with extrapulmonary tuberculosis (47.8% and 52% in blood and urine) when compared to patients with the pulmonary form of the disease (sensitivity of 29% and 26.9% in blood and urine), regardless of the type of biological sample used. The nested-PCR is a rapid technique that, even if not showing a good sensitivity, should be considered as a helpful tool especially in the extrapulmonary cases or in cases where confirmatory diagnosis is quite difficult to be achieved by routine methods. The performance of PCR-based techniques should be considered and tested in future works on other types of biological specimens besides sputum, like blood and urine, readily obtainable in most cases. The improving of M. tuberculosis nested-PCR detection in TB affected patients will give the possibility of an earlier detection of bacilli thus interrupting the transmission chain of the disease.

Development and evaluation of a nested-PCR assay for Senecavirus A diagnosis.

PubMed

Feronato, Cesar; Leme, Raquel A; Diniz, Jaqueline A; Agnol, Alais Maria Dall; Alfieri, Alice F; Alfieri, Amauri A

2018-02-01

Senecavirus A (SVA) has been associated with vesicular disease in weaned and adult pigs and with high mortality of newborn piglets. This study aimed to establish a nested-PCR assay for the routine diagnosis of SVA infection. Tissue samples (n = 177) were collected from 37 piglets of 18 pig farms located in four different Brazilian states. For the nested-PCR, a primer set was defined to amplify an internal VP1 fragment of 316 bp of SVA genome. Of the 37 piglets, 15 (40.5%) and 23 (62.2%) were positive for the SVA in the RT-PCR and nested-PCR assays, respectively. The SVA RNA was detected in 61/177 (34.5%) samples with the RT-PCR, while the nested-PCR assay showed 84/177 (47.5%) samples with the virus (p < 0.05). According to the herds, 11 (61.1%) and 16 (88.9%) of the 18 pig herds were positive for the SVA in the RT-PCR and nested-PCR assays, respectively. Nucleotide sequencing analysis revealed similarities of 98.7-100% among SVA Brazilian strains and of 86.6-98% with SVA strains from other countries. The nested-PCR assay in this study was suitable to recover the SVA RNA in biological specimens, piglets, and/or herds that were considered as negative in the RT-PCR assay, and is proposed for the routine investigation of the SVA infection in piglets, especially when other techniques are not available or when a great number of samples has to be examined.

Dye-enhanced multimodal confocal imaging as a novel approach to intraoperative diagnosis of brain tumors.

PubMed

Snuderl, Matija; Wirth, Dennis; Sheth, Sameer A; Bourne, Sarah K; Kwon, Churl-Su; Ancukiewicz, Marek; Curry, William T; Frosch, Matthew P; Yaroslavsky, Anna N

2013-01-01

Intraoperative diagnosis plays an important role in accurate sampling of brain tumors, limiting the number of biopsies required and improving the distinction between brain and tumor. The goal of this study was to evaluate dye-enhanced multimodal confocal imaging for discriminating gliomas from nonglial brain tumors and from normal brain tissue for diagnostic use. We investigated a total of 37 samples including glioma (13), meningioma (7), metastatic tumors (9) and normal brain removed for nontumoral indications (8). Tissue was stained in 0.05 mg/mL aqueous solution of methylene blue (MB) for 2-5 minutes and multimodal confocal images were acquired using a custom-built microscope. After imaging, tissue was formalin fixed and paraffin embedded for standard neuropathologic evaluation. Thirteen pathologists provided diagnoses based on the multimodal confocal images. The investigated tumor types exhibited distinctive and complimentary characteristics in both the reflectance and fluorescence responses. Images showed distinct morphological features similar to standard histology. Pathologists were able to distinguish gliomas from normal brain tissue and nonglial brain tumors, and to render diagnoses from the images in a manner comparable to haematoxylin and eosin (H&E) slides. These results confirm the feasibility of multimodal confocal imaging for intravital intraoperative diagnosis. © 2012 The Authors; Brain Pathology © 2012 International Society of Neuropathology.

Nest marking behavior and chemical composition of olfactory cues involved in nest recognition in Megachile rotundata.

PubMed

Guédot, Christelle; Buckner, James S; Hagen, Marcia M; Bosch, Jordi; Kemp, William P; Pitts-Singer, Theresa L

2013-08-01

In-nest observations of the solitary bee, Megachile rotundata (F.), revealed that nesting females apply olfactory cues to nests for nest recognition. On their way in and out of the nest, females drag the abdomen along the entire length of the nest, and sometimes deposit fluid droplets from the tip of the abdomen. The removal of bee-marked sections of the nest resulted in hesitation and searching behavior by females, indicating the loss of olfactory cues used for nest recognition. Chemical analysis of female cuticles and the deposits inside marked nesting tubes revealed the presence of hydrocarbons, wax esters, fatty aldehydes, and fatty alcohol acetate esters. Chemical compositions were similar across tube samples, but proportionally different from cuticular extracts. These findings reveal the importance of lipids as chemical signals for nest recognition and suggest that the nest-marking cues are derived from a source in addition to, or other than, the female cuticle.

Cost-efficient designs for three-arm trials with treatment delivered by health professionals: Sample sizes for a combination of nested and crossed designs

PubMed Central

Moerbeek, Mirjam

2018-01-01

Background This article studies the design of trials that compare three treatment conditions that are delivered by two types of health professionals. The one type of health professional delivers one treatment, and the other type delivers two treatments, hence, this design is a combination of a nested and crossed design. As each health professional treats multiple patients, the data have a nested structure. This nested structure has thus far been ignored in the design of such trials, which may result in an underestimate of the required sample size. In the design stage, the sample sizes should be determined such that a desired power is achieved for each of the three pairwise comparisons, while keeping costs or sample size at a minimum. Methods The statistical model that relates outcome to treatment condition and explicitly takes the nested data structure into account is presented. Mathematical expressions that relate sample size to power are derived for each of the three pairwise comparisons on the basis of this model. The cost-efficient design achieves sufficient power for each pairwise comparison at lowest costs. Alternatively, one may minimize the total number of patients. The sample sizes are found numerically and an Internet application is available for this purpose. The design is also compared to a nested design in which each health professional delivers just one treatment. Results Mathematical expressions show that this design is more efficient than the nested design. For each pairwise comparison, power increases with the number of health professionals and the number of patients per health professional. The methodology of finding a cost-efficient design is illustrated using a trial that compares treatments for social phobia. The optimal sample sizes reflect the costs for training and supervising psychologists and psychiatrists, and the patient-level costs in the three treatment conditions. Conclusion This article provides the methodology for designing trials that compare three treatment conditions while taking the nesting of patients within health professionals into account. As such, it helps to avoid underpowered trials. To use the methodology, a priori estimates of the total outcome variances and intraclass correlation coefficients must be obtained from experts’ opinions or findings in the literature. PMID:29316807

Incidence of pulmonary aspergillosis and correlation of conventional diagnostic methods with nested PCR and real-time PCR assay using BAL fluid in intensive care unit patients.

PubMed

Zarrinfar, Hossein; Makimura, Koichi; Satoh, Kazuo; Khodadadi, Hossein; Mirhendi, Hossein

2013-05-01

Although the incidence of invasive aspergillosis in the intensive care unit (ICU) is scarce, it has emerged as major problems in critically ill patients. In this study, the incidence of pulmonary aspergillosis (PA) in ICU patients has evaluated and direct microscopy and culture has compared with nested polymerase chain reaction (PCR) and real-time PCR for detection of Aspergillus fumigatus and A. flavus in bronchoalveolar lavage (BAL) samples of the patients. Thirty BAL samples obtained from ICU patients during a 16-month period were subjected to direct examinations on 20% potassium hydroxide (KOH) and culture on two culture media. Nested PCR targeting internal transcribed spacer ribosomal DNA and TaqMan real-time PCR assay targeting β-tubulin gene were used for the detection of A. fumigatus and A. flavus. Of 30 patients, 60% were men and 40% were women. The diagnosis of invasive PA was probable in 1 (3%), possible in 11 (37%), and not IPA in 18 (60%). Nine samples were positive in nested PCR including seven samples by A. flavus and two by A. fumigatus specific primers. The lowest amount of DNA that TaqMan real-time PCR could detect was ≥40 copy numbers. Only one of the samples had a positive result of A. flavus real-time PCR with Ct value of 37.5. Although a significant number of specimens were positive in nested PCR, results of this study showed that establishment of a correlation between the conventional methods with nested PCR and real-time PCR needs more data confirmed by a prospective study with a larger sample group. © 2013 Wiley Periodicals, Inc.

A Minimally Invasive Method for Sampling Nest and Roost Cavities for Fungi: a Novel Approach to Identify the Fungi Associated with Cavity-Nesting Birds

Treesearch

Michelle A. Jusino; Daniel Lindner; John K. Cianchetti; Adam T. Grisé; Nicholas J. Brazee; Jeffrey R. Walters

2014-01-01

Relationships among cavity-nesting birds, trees, and wood decay fungi pose interesting management challenges and research questions in many systems. Ornithologists need to understand the relationships between cavity-nesting birds and fungi in order to understand the habitat requirements of these birds. Typically, researchers rely on fruiting body surveys to identify...

[Effect of landscape change on the structure of the sting-less bee community (Hymenoptera: Apidae) in Meta, Colombia].

PubMed

Nates-Parra, Guiomar; Palacios, Eliana; Parra-H, Alejandro

2008-09-01

Stingless bees represent one of the most diversified components of the natural Apoidea fauna of pollinators in the tropics. They use diverse kinds of substrates and inhabit varied habitats. Some species are typical for some natural either artificial place. The landscape alteration were this group of bees nests, has and important impact on the natural composition of its community structure, fact which is reflected in the nest density. We analyzed the structure composition of the stingless bees' community in three environments in the Colombian Ilanos piedmont, an important region that represents the transition between Andean ecosystems and a savannah that is seriously threatened by cattle practices. We made systematic samples in secondary forest, agro-ecosystems and urban areas, recording the presence of 204 nests from 11 genera (24 species). The nest density per landscape was heterogeneous and never higher than 16 nests/Ha. We observed two nesting patterns and an effect of sampling criterion on the measured biodiversity.

Design and demonstration of multimodal optical scanning microscopy for confocal and two-photon imaging

NASA Astrophysics Data System (ADS)

Chun, Wanhee; Do, Dukho; Gweon, Dae-Gab

2013-01-01

We developed a multimodal microscopy based on an optical scanning system in order to obtain diverse optical information of the same area of a sample. Multimodal imaging researches have mostly depended on a commercial microscope platform, easy to use but restrictive to extend imaging modalities. In this work, the beam scanning optics, especially including a relay lens, was customized to transfer broadband (400-1000 nm) lights to a sample without any optical error or loss. The customized scanning optics guarantees the best performances of imaging techniques utilizing the lights within the design wavelength. Confocal reflection, confocal fluorescence, and two-photon excitation fluorescence images were obtained, through respective implemented imaging channels, to demonstrate imaging feasibility for near-UV, visible, near-IR continuous light, and pulsed light in the scanning optics. The imaging performances for spatial resolution and image contrast were verified experimentally; the results were satisfactory in comparison with theoretical results. The advantages of customization, containing low cost, outstanding combining ability and diverse applications, will contribute to vitalize multimodal imaging researches.

Factors influencing nesting success of king eiders on northern Alaska's Coastal Plain

USGS Publications Warehouse

Bentzen, R.L.; Powell, A.N.; Suydam, R.S.

2008-01-01

King eider (Somateria spectabilis) populations have declined markedly in recent decades for unknown reasons. Nest survival is one component of recruitment, and a female's chance of reproductive success increases with her ability to choose an appropriate nesting strategy. We estimated variation in daily nest survival of king eiders at 2 sites, Teshekpuk and Kuparuk, Alaska, USA, 2002-2005. We evaluated both a priori and exploratory competing models of nest survival that considered importance of nest concealment, seclusion, and incubation constancy as strategies to avoid 2 primary egg predators, avian (Larus spp., Stercorarius spp., and Corvus corax) and fox (Alopex lagopus). We used generalized nonlinear techniques to examine factors affecting nest survival rates and information-theoretic approaches to select among competing models. Estimated nest survival, accounting for a nest visitation effect, varied considerably across sites and years (0.21-0.57); however, given our small sample size, much of this variation maybe attributable to sampling variation (??process = 0.007, 95% CI: 0.003-0.070). Nest survival was higher at Kuparuk than Teshekpuk in all years; however, due to the correlative nature of our data, we cannot determine the underlying causes with any certainty. We found mixed support for the concealed breeding strategy, females derived no benefit from nesting in areas with more willow (Salix spp.; measure of concealment) except that the observer effect diminished as willow cover increased. We suggest these patterns are due to conflicting predation pressures. Nest survival was not higher on islands (measure of seclusion) or with increased incubation constancy but was higher post-fox removal, indicating that predator control on breeding grounds could be a viable management option. Nest survival was negatively affected by our nest visitations, most likely by exposing the nest to avian scavengers. We recommend precautions be taken to limit the effects of nest visits in future studies and to consider them as a possible negative bias in estimated nest survival. Future models of the impacts of development within the breeding grounds of king eider should consider the influence of humans in the vicinity of nests.

The effects of ant nests on soil fertility and plant performance: a meta-analysis.

PubMed

Farji-Brener, Alejandro G; Werenkraut, Victoria

2017-07-01

Ants are recognized as one of the major sources of soil disturbance world-wide. However, this view is largely based on isolated studies and qualitative reviews. Here, for the first time, we quantitatively determined whether ant nests affect soil fertility and plant performance, and identified the possible sources of variation of these effects. Using Bayesian mixed-models meta-analysis, we tested the hypotheses that ant effects on soil fertility and plant performance depend on the substrate sampled, ant feeding type, latitude, habitat and the plant response variable measured. Ant nests showed higher nutrient and cation content than adjacent non-nest soil samples, but similar pH. Nutrient content was higher in ant refuse materials than in nest soils. The fertilizer effect of ant nests was also higher in dry habitats than in grasslands or savannas. Cation content was higher in nests of plant-feeding ants than in nests of omnivorous species, and lower in nests from agro-ecosystems than in nests from any other habitat. Plants showed higher green/root biomass and fitness on ant nests soils than in adjacent, non-nest sites; but plant density and diversity were unaffected by the presence of ant nests. Root growth was particularly higher in refuse materials than in ant nest soils, in leaf-cutting ant nests and in deserts habitats. Our results confirm the major role of ant nests in influencing soil fertility and vegetation patterns and provide information about the factors that mediate these effects. First, ant nests improve soil fertility mainly through the accumulation of refuse materials. Thus, different refuse dump locations (external or in underground nest chambers) could benefit different vegetation life-forms. Second, ant nests could increase plant diversity at larger spatial scales only if the identity of favoured plants changes along environmental gradients (i.e. enhancing β-diversity). Third, ant species that feed on plants play a relevant role fertilizing soils, which may balance their known influence as primary consumers. Fourth, the effects of ant nests as fertility islands are larger in arid lands, possibly because fertility is intrinsically lower in these habitats. Overall, this study provide novel and quantitative evidence confirming that ant nests are key soil modifiers, emphasizing their role as ecological engineers. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Probability of detection of nests and implications for survey design

USGS Publications Warehouse

Smith, P.A.; Bart, J.; Lanctot, Richard B.; McCaffery, B.J.; Brown, S.

2009-01-01

Surveys based on double sampling include a correction for the probability of detection by assuming complete enumeration of birds in an intensively surveyed subsample of plots. To evaluate this assumption, we calculated the probability of detecting active shorebird nests by using information from observers who searched the same plots independently. Our results demonstrate that this probability varies substantially by species and stage of the nesting cycle but less by site or density of nests. Among the species we studied, the estimated single-visit probability of nest detection during the incubation period varied from 0.21 for the White-rumped Sandpiper (Calidris fuscicollis), the most difficult species to detect, to 0.64 for the Western Sandpiper (Calidris mauri), the most easily detected species, with a mean across species of 0.46. We used these detection probabilities to predict the fraction of persistent nests found over repeated nest searches. For a species with the mean value for detectability, the detection rate exceeded 0.85 after four visits. This level of nest detection was exceeded in only three visits for the Western Sandpiper, but six to nine visits were required for the White-rumped Sandpiper, depending on the type of survey employed. Our results suggest that the double-sampling method's requirement of nearly complete counts of birds in the intensively surveyed plots is likely to be met for birds with nests that survive over several visits of nest searching. Individuals with nests that fail quickly or individuals that do not breed can be detected with high probability only if territorial behavior is used to identify likely nesting pairs. ?? The Cooper Ornithological Society, 2009.

Molecular diagnosis of lyssaviruses and sequence comparison of Australian bat lyssavirus samples.

PubMed

Foord, A J; Heine, H G; Pritchard, L I; Lunt, R A; Newberry, K M; Rootes, C L; Boyle, D B

2006-07-01

To evaluate and implement molecular diagnostic tests for the detection of lyssaviruses in Australia. A published hemi-nested reverse transcriptase polymerase chain reaction (RT-PCR) for the detection of all lyssavirus genotypes was modified to a fully nested RT-PCR format and compared with the original assay. TaqMan assays for the detection of Australian bat lyssavirus (ABLV) were compared with both the nested and hemi-nested RT-PCR assays. The sequences of RT-PCR products were determined to assess sequence variations of the target region (nucleocapsid gene) in samples of ABLV originating from different regions. The nested RT-PCR assay was highly analytically specific, and at least as analytically sensitive as the hemi-nested assay. The TaqMan assays were highly analytically specific and more analytically sensitive than either RT-PCR assay, with a detection level of approximately 10 genome equivalents per microl. Sequence of the first 544 nucleotides of the nucleocapsid protein coding sequence was obtained from all samples of ABLV received at Australian Animal Health Laboratory during the study period. The nested RT-PCR provided a means for molecular diagnosis of all tested genotypes of lyssavirus including classical rabies virus and Australian bat lyssavirus. The published TaqMan assay proved to be superior to the RT-PCR assays for the detection of ABLV in terms of analytical sensitivity. The TaqMan assay would also be faster and cross contamination is less likely. Nucleotide sequence analyses of samples of ABLV from a wide geographical range in Australia demonstrated the conserved nature of this region of the genome and therefore the suitability of this region for molecular diagnosis.

Rapid direct identification of Cryptococcus neoformans from pigeon droppings by nested PCR using CNLAC1 gene.

PubMed

Chae, H S; Park, G N; Kim, S H; Jo, H J; Kim, J T; Jeoung, H Y; An, D J; Kim, N H; Shin, B W; Kang, Y I; Chang, K S

2012-08-01

Isolation and identification of Cryptococcus neoformans and pathogenic yeast-like fungi from pigeon droppings has been taken for a long time and requires various nutrients for its growth. In this study, we attempted to establish a rapid direct identification method of Cr. neoformans from pigeon dropping samples by nested-PCR using internal transcribed spacer (ITS) CAP64 and CNLAC1 genes, polysaccharide capsule gene and laccase-associated gene to produce melanin pigment, respectively, which are common genes of yeasts. The ITS and CAP64 genes were amplified in all pathogenic yeasts, but CNLAC1 was amplified only in Cr. neoformans. The ITS gene was useful for yeast genotyping depending on nucleotide sequence. Homology of CAP64 genes among the yeasts were very high. The specificity of PCR using CNLAC1 was demonstrated in Cr. neoformans environmental strains but not in other yeast-like fungi. The CNLAC1 gene was detected in 5 serotypes of Cr. neoformans. The nested-PCR amplified up to 10(-11) μg of the genomic DNA and showed high sensitivity. All pigeon droppings among 31 Cr. neoformans-positive samples were positive and all pigeon droppings among 348 Cr. neoformans-negative samples were negative by the direct nested-PCR. In addition, after primary enrichment of pigeon droppings in Sabouraud dextrose broth, all Cr. neoformans-negative samples were negative by the nested-PCR, which showed high specificity. The nested-PCR showed high sensitivity without culture of pigeon droppings. Nested-PCR using CNLAC1 provides a rapid and reliable molecular diagnostic method to overcome weak points such as long culture time of many conventional methods.

Detection of Mycobacterium bovis in Bovine and Bubaline Tissues Using Nested-PCR for TbD1

PubMed Central

Araújo, Cristina P.; Osório, Ana Luiza A. R.; Jorge, Kláudia S. G.; Ramos, Carlos Alberto N.; Filho, Antonio Francisco S.; Vidal, Carlos Eugênio S.; Roxo, Eliana; Nishibe, Christiane; Almeida, Nalvo F.; Júnior, Antônio A. F.; Silva, Marcio R.; Neto, José Diomedes B.; Cerqueira, Valíria D.; Zumárraga, Martín J.; Araújo, Flábio R.

2014-01-01

In the present study, a nested-PCR system, targeting the TbD1 region, involving the performance of conventional PCR followed by real-time PCR, was developed to detect Mycobacterium bovis in bovine/bubaline tissue homogenates. The sensitivity and specificity of the reactions were assessed with DNA samples extracted from tuberculous and non-tuberculous mycobacteria, as well as other actinomycetales species and DNA samples extracted directly from bovine and bubaline tissue homogenates. In terms of analytical sensitivity, the DNA of M. bovis AN5 was detected up to 1.56 ng with conventional PCR, 97.6 pg with real-time PCR, and 1.53 pg with nested-PCR in the reaction mixture. The nested-PCR exhibited 100% analytical specificity for M. bovis when tested with the DNA of reference strains of environmental mycobacteria and closely-related Actinomycetales. A clinical sensitivity value of 76.0% was detected with tissue samples from animals that exhibited positive results in the comparative intradermal tuberculin test (CITT), as well as from those with lesions compatible with tuberculosis (LCT) that rendered positive cultures. A clinical specificity value of 100% was detected with tissue samples from animals with CITT- results, with no visible lesions (NVL) and negative cultures. No significant differences were found between the nested-PCR and culture in terms of detecting CITT+ animals with LCT or with NVL. No significant differences were recorded in the detection of CITT- animals with NVL. However, nested-PCR detected a significantly higher number of positive animals than the culture in the group of animals exhibiting LCT with no previous records of CITT. The use of the nested-PCR assay to detect M. bovis in tissue homogenates provided a rapid diagnosis of bovine and bubaline tuberculosis. PMID:24618787

Detection of Mycobacterium bovis in bovine and bubaline tissues using nested-PCR for TbD1.

PubMed

Araújo, Cristina P; Osório, Ana Luiza A R; Jorge, Kláudia S G; Ramos, Carlos Alberto N; Filho, Antonio Francisco S; Vidal, Carlos Eugênio S; Roxo, Eliana; Nishibe, Christiane; Almeida, Nalvo F; Júnior, Antônio A F; Silva, Marcio R; Neto, José Diomedes B; Cerqueira, Valíria D; Zumárraga, Martín J; Araújo, Flábio R

2014-01-01

In the present study, a nested-PCR system, targeting the TbD1 region, involving the performance of conventional PCR followed by real-time PCR, was developed to detect Mycobacterium bovis in bovine/bubaline tissue homogenates. The sensitivity and specificity of the reactions were assessed with DNA samples extracted from tuberculous and non-tuberculous mycobacteria, as well as other actinomycetales species and DNA samples extracted directly from bovine and bubaline tissue homogenates. In terms of analytical sensitivity, the DNA of M. bovis AN5 was detected up to 1.56 ng with conventional PCR, 97.6 pg with real-time PCR, and 1.53 pg with nested-PCR in the reaction mixture. The nested-PCR exhibited 100% analytical specificity for M. bovis when tested with the DNA of reference strains of environmental mycobacteria and closely-related Actinomycetales. A clinical sensitivity value of 76.0% was detected with tissue samples from animals that exhibited positive results in the comparative intradermal tuberculin test (CITT), as well as from those with lesions compatible with tuberculosis (LCT) that rendered positive cultures. A clinical specificity value of 100% was detected with tissue samples from animals with CITT- results, with no visible lesions (NVL) and negative cultures. No significant differences were found between the nested-PCR and culture in terms of detecting CITT+ animals with LCT or with NVL. No significant differences were recorded in the detection of CITT- animals with NVL. However, nested-PCR detected a significantly higher number of positive animals than the culture in the group of animals exhibiting LCT with no previous records of CITT. The use of the nested-PCR assay to detect M. bovis in tissue homogenates provided a rapid diagnosis of bovine and bubaline tuberculosis.

Organochlorine contaminant exposure and reproductive success of Black-Crowned Night Herons (Nycticorax nycticorax) nesting in Baltimore Harbor, Maryland

USGS Publications Warehouse

Rattner, B.A.; McGowan, P.C.; Hatfield, J.S.; Hong, C.-S.; Chu, S.G.

2001-01-01

The declining size of the Baltimore Harbor black-crowned night heron (Nycticorax nycticorax) colony has been hypothesized to be linked to PCB exposure. In 1998, a 'sample egg' was collected from 65 black-crowned night heron nests (each containing > three eggs) for contaminant analysis, and the remaining eggs in these 65 nests, plus four two-egg nests, were monitored for hatching and fledging success. Eggs were also collected from 12 nests at Holland Island, a reference site in southern Chesapeake Bay. Samples were analyzed for 26 organochlorine pesticides and metabolites, and 145 PCB congeners. Pesticide and metabolite concentrations, including p,p'-DDE, were well below thresholds associated with adverse reproductive effects at both sites. Average concentration of total PCBs, 12 Ah receptor-active PCB congeners, and toxic equivalents in eggs from Baltimore Harbor were greater (up to 35- fold) than that observed in Holland Island samples. Overall nest success at the Baltimore Harbor heronry was estimated by the Mayfield method to be 0.74, and the mean number of young fledged/hen was 2.05, which is within published productivity estimates for maintaining a stable black-crowned night heron population. Using logistic regression, no significant relationships were found between organochlorine contaminant concentrations in sample eggs and hatching, fledging, or overall reproductive success. Processes other than poor reproduction (e.g., low post- fledging survival, emigration, habitat degradation) may be responsible for the declining size of the Baltimore Harbor colony.

Toxic industrial deposit remediation by ant activity

NASA Astrophysics Data System (ADS)

Jilkova, Veronika; Frouz, Jan

2016-04-01

Toxic industrial deposits are often contaminated by heavy metals and the substrates have low pH values. In such systems, soil development is thus slowed down by high toxicity and acidic conditions which are unfavourable to soil fauna. Ants (Hymenoptera, Formicidae) are considered tolerant to heavy metal pollution and are known to increase organic matter content and microbial activity in their nests. Here, we focused on soil remediation caused by three ant species (Formica sanguinea, Lasius niger, and Tetramorium sp.) in an ore-washery sedimentation basin near Chvaletice (Czech Republic). Soil samples were taken from the centre of ant nests and from the nest surroundings (>3 m from nests). Samples were then analyzed for microbial activity and biomass and contents of organic matter and nutrients. As a result, ant species that most influenced soil properties was F. sanguinea as there were higher microbial activity and total nitrogen and ammonia contents in ant nests than in the surrounding soil. We expected such a result because F. sanguinea builds conspicuous large nests and is a carnivorous species that brings substantial amounts of nitrogen in insect prey to their nests. Effects of the other two ant species might be lower because of smaller nests and different feeding habits as they rely mainly on honeydew from aphids or on plant seeds that do not contain much nutrients.

An adaptive importance sampling algorithm for Bayesian inversion with multimodal distributions

DOE PAGES

Li, Weixuan; Lin, Guang

2015-03-21

Parametric uncertainties are encountered in the simulations of many physical systems, and may be reduced by an inverse modeling procedure that calibrates the simulation results to observations on the real system being simulated. Following Bayes’ rule, a general approach for inverse modeling problems is to sample from the posterior distribution of the uncertain model parameters given the observations. However, the large number of repetitive forward simulations required in the sampling process could pose a prohibitive computational burden. This difficulty is particularly challenging when the posterior is multimodal. We present in this paper an adaptive importance sampling algorithm to tackle thesemore » challenges. Two essential ingredients of the algorithm are: 1) a Gaussian mixture (GM) model adaptively constructed as the proposal distribution to approximate the possibly multimodal target posterior, and 2) a mixture of polynomial chaos (PC) expansions, built according to the GM proposal, as a surrogate model to alleviate the computational burden caused by computational-demanding forward model evaluations. In three illustrative examples, the proposed adaptive importance sampling algorithm demonstrates its capabilities of automatically finding a GM proposal with an appropriate number of modes for the specific problem under study, and obtaining a sample accurately and efficiently representing the posterior with limited number of forward simulations.« less

An adaptive importance sampling algorithm for Bayesian inversion with multimodal distributions

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

Li, Weixuan; Lin, Guang, E-mail: guanglin@purdue.edu

2015-08-01

Parametric uncertainties are encountered in the simulations of many physical systems, and may be reduced by an inverse modeling procedure that calibrates the simulation results to observations on the real system being simulated. Following Bayes' rule, a general approach for inverse modeling problems is to sample from the posterior distribution of the uncertain model parameters given the observations. However, the large number of repetitive forward simulations required in the sampling process could pose a prohibitive computational burden. This difficulty is particularly challenging when the posterior is multimodal. We present in this paper an adaptive importance sampling algorithm to tackle thesemore » challenges. Two essential ingredients of the algorithm are: 1) a Gaussian mixture (GM) model adaptively constructed as the proposal distribution to approximate the possibly multimodal target posterior, and 2) a mixture of polynomial chaos (PC) expansions, built according to the GM proposal, as a surrogate model to alleviate the computational burden caused by computational-demanding forward model evaluations. In three illustrative examples, the proposed adaptive importance sampling algorithm demonstrates its capabilities of automatically finding a GM proposal with an appropriate number of modes for the specific problem under study, and obtaining a sample accurately and efficiently representing the posterior with limited number of forward simulations.« less

[Application of Nested PCR in the Diagnosis of Imported Plasmodium Ovale Infection].

PubMed

Huang, Bing-cheng; Xu, Chao; Li, Jin; Xiao, Ting; Yin, Kun; Liu, Gong-zhen; Wang, Wei-yan; Zhao, Gui-hua; Wei, Yan-bin; Wang, Yong-bin; Zhao, Chang-lei; Wei, Qing-kuan

2015-02-01

To identity Plasmodium ovale infection by 18S rRNA gene nested PCR. Whole blood and filter paper blood samples of malaria patients in Shandong Province were collected during 2012-2013. The parasites were observed under a microscope with Giemsa staining. The genome DNA of blood samples were extracted as PCR templates. Genus- and species-specific primers were designed according to the Plasmodium 18S rRNA gene sequences. Plasmodium ovale-positive specimens were identified by nested PCR as well as verified by sequencing. There were 7 imported cases of P. ovale infection in the province during 2012-2013. Nested PCR results showed that the P. ovale specific band (800 bp) was amplified in all the 7 specimens. Blast results indicated that the PCR products were consistent with the Plasmodium ovale reference sequence in GenBank. Seven imported cases of ovale malaria in Shandong Province in 2012-2013 are confirmed by nested PCR.

Conducting Three-Level Longitudinal Analyses

ERIC Educational Resources Information Center

Peugh, James L.; Heck, Ronald H.

2017-01-01

Researchers in the field of early adolescence interested in quantifying the environmental influences on a response variable of interest over time would use cluster sampling (i.e., obtaining repeated measures from students nested within classrooms and/or schools) to obtain the needed sample size. The resulting longitudinal data would be nested at…

Nest Mosquito Trap quantifies contact rates between nesting birds and mosquitoes.

PubMed

Caillouët, Kevin A; Riggan, Anna E; Rider, Mark; Bulluck, Lesley P

2012-06-01

Accurate estimates of host-vector contact rates are required for precise determination of arbovirus transmission intensity. We designed and tested a novel mosquito collection device, the Nest Mosquito Trap (NMT), to collect mosquitoes as they attempt to feed on unrestrained nesting birds in artificial nest boxes. In the laboratory, the NMT collected nearly one-third of the mosquitoes introduced to the nest boxes. We then used these laboratory data to estimate our capture efficiency of field-collected bird-seeking mosquitoes collected over 66 trap nights. We estimated that 7.5 mosquitoes per trap night attempted to feed on nesting birds in artificial nest boxes. Presence of the NMT did not have a negative effect on avian nest success when compared to occupied nest boxes that were not sampled with the trap. Future studies using the NMT may elucidate the role of nestlings in arbovirus transmission and further refine estimates of nesting bird and vector contact rates. © 2012 The Society for Vector Ecology.

Nest Mosquito Trap quantifies contact rates between nesting birds and mosquitoes

PubMed Central

Caillouët, Kevin A.; Riggan, Anna E.; Rider, Mark; Bulluck, Lesley P.

2012-01-01

Accurate estimates of host-vector contact rates are required for precise determination of arbovirus transmission intensity. We designed and tested a novel mosquito collection device, the Nest Mosquito Trap (NMT), to collect mosquitoes as they attempt to feed on unrestrained nesting birds in artificial nest boxes. In the laboratory, the NMT collected nearly one-third of the mosquitoes introduced to the nest boxes. We then used these laboratory data to estimate our capture efficiency of field-collected bird-seeking mosquitoes collected over 66 trap nights. We estimated that 7.5 mosquitoes per trap night attempted to feed on nesting birds in artificial nest boxes. Presence of the NMT did not have a negative effect on avian nest success when compared to occupied nest boxes that were not sampled with the trap. Future studies using the NMT may elucidate the role of nestlings in arbovirus transmission and further refine estimates of nesting bird and vector contact rates. PMID:22548555

Use of radio-telemetry to reduce bias in nest searching

USGS Publications Warehouse

Powell, L.A.; Lang, J.D.; Krementz, D.G.; Conroy, M.J.

2005-01-01

We used traditional searching, as well as radio-telemetry, to find 125 Wood Thrush (Hylocichla mustelina) nests during 1994?1996 at the Piedmont National Wildlife Refuge in Georgia, USA. We compared daily nest survival rates for 66 nests of radio-marked birds with 59 nests of birds found through systematic searching. By using radio-telemetry, we found Wood Thrush nests in higher elevation pine habitats, in addition to the more usual hardwood forests with moist soils. We found nests of radio-marked birds farther from streams than nests found by systematic searching. Thirty-two percent of radio-marked birds' nests were found at the tops of slopes, compared to 15% of the nests found by traditional searching. In addition, radio-marked birds generally moved up-slope for re-nesting attempts. Although the distribution of nests found with telemetry and searching varied, daily nest survival did not vary between the two groups. Radio-telemetry provided new information about Wood Thrush nesting habitats. We believe radio-telemetry can be a valuable addition to traditional searching techniques; it has the potential to provide a sample of nests free from a priori habitat biases.

Leaf Cutter Ant (Atta cephalotes) Soil Modification and In Situ CO2 Gas Dynamics in a Neotropical Wet Forest

NASA Astrophysics Data System (ADS)

Fernandez Bou, A. S.; Carrasquillo Quintana, O.; Dierick, D.; Harmon, T. C.; Johnson, S.; Schwendenmann, L.; Zelikova, T. J.

2016-12-01

The goal of this work is to advance our understanding of soil carbon cycling in highly productive neotropical wet forests. More specifically, we are investigating the influence of leaf cutter ants (LCA) on soil CO2 gas dynamics in primary and secondary forest soils at La Selva Biological Station, Costa Rica. LCA are the dominant herbivore in tropical Americas, responsible for as much as 50% of the total herbivory. Their presence is increasing and their range is expanding because of forest fragmentation and other human impacts. We installed gas sampling wells in LCA (Atta cephalotes) nest and control sites (non-nests in the same soil and forest settings). The experimental design encompassed land cover (primary and secondary forest) and soil type (residual and alluvial). We collected gas samples monthly over an 18-month period. Several of the LCA nests were abandoned during this period. Nevertheless, we continued to sample these sites for LCA legacy effects. In several of the sites, we also installed sensors to continuously monitor soil moisture content, temperature, and CO2 levels. Within the 18-month period we conducted a 2-month field campaign to collect soil and nest vent CO2 efflux data from 3 of the nest-control pairs. Integrating the various data sets, we observed that for most of the sites nest and control soils behaved similarly during the tropical dry season. However, during the wet season gas well CO2 concentrations increased in the control sites while levels in the nests remained at dry season levels. This outcome suggests that ants modify soil gas transport properties (e.g., tortuosity). In situ time series and efflux sampling campaign data corroborated these findings. Abandoned nest CO2 levels were similar to those of the active nests, supporting the notion of a legacy effect from LCA manipulations. For this work, the period of abandonment was relatively short (several months to 1 year maximum), which appears to be insufficient for estimating the duration effect. Overall, these results demonstrate that LCA exert a significant effect on carbon cycling in rain forest soils.

Highly controlled nest homeostasis of honey bees helps deactivate phenolics in nectar

NASA Astrophysics Data System (ADS)

Liu, Fanglin; He, Jianzhong; Fu, Wenjun

2005-06-01

Honey bees have a highly developed nest homeostasis, for example, maintaining low CO2 levels and stable nest temperatures at 35°C.We investigate the role of nest homeostasis in deactivating phenolic compounds present in the nectar of Aloe littoralis. We show that the phenolic content in nectar was reduced (from 0.65% to 0.49%) after nectar was incubated in a nest of Apis cerana, and that it was reduced still more (from 0.65% to 0.37%) if nectar was mixed with hypopharyngeal gland proteins (HGP) of worker bees before being placed inside a nest. HGP had little effect on samples outside a nest, indicating that nest conditions are necessary for HGP to deactivate phenolics in nectar. Consequently, the highly controlled nest homeostasis of honey bees facilitates direct deactivation of phenolics in nectar, and plays a role in the action of HGP as well.

Description of Nesting Habitat for Least Bell's Vireo in San Diego County

Treesearch

Bonnie J. Hendricks; John P. Rieger

1989-01-01

Least Bell's Vireo (Vireo bellii pusillus) nesting sites on three rivers in coastal southern California were characterized to provide data for a habitat restoration plan for this endangered species. In addition, riparian areas outside vireo territories were sampled to compare with nesting habitat. The parameters measured were percent cover,...

Double-Crested Cormorant ( Phalacrocorax auritus) Nesting Effects on Understory Composition and Diversity on Island Ecosystems in Lake Erie

NASA Astrophysics Data System (ADS)

McGrath, Darby M.; Murphy, Stephen D.

2012-08-01

The context for this study is the management concerns over the severity and extent of the impact of cormorants on island flora in the recent past on Lake Erie islands. Accordingly, this study sought to quantify the nesting colonies' influence on coarse woody litter and how nest densities and litter depth may influence the herbaceous layer, the seed bank composition and viability across the extent of three Lake Erie islands. The data for this study were collected from 2004 to 2008 on East Sister Island and Middle Island using two main strategies. First, herbaceous layer surveys, cormorant nest counts, soil seed bank cores, and litter depth measurements were executed using a plotless-point quarter method to test island-wide impacts from nesting activities (data were also collected on a third island, West Sister Island as a reference for the other two islands). Secondly, a sub-sample of the entire plot set was examined in particularly high nesting density areas for two islands (Middle Island and East Sister Island). Kruskal-Wallis tests indicated that there are subtle changes in the herbaceous diversity (total, native and exotic) and seed bank composition across the islands. The sub sample set of the plots demonstrated that Phalacrocorax auritus nest density does influence litter depth, herbaceous species abundance and diversity. Cormorant nesting pressures are restricted to areas of high nesting pressures and competition. However, there remains a risk to the interior herbaceous layer of the island if the effects of nesting pressures at the edges advance inward from this perimeter.

Maternal transfer and sublethal immune system effects of brevetoxin exposure in nesting loggerhead sea turtles (Caretta caretta) from western Florida.

PubMed

Perrault, Justin R; Bauman, Katherine D; Greenan, Taylor M; Blum, Patricia C; Henry, Michael S; Walsh, Catherine J

2016-11-01

Blooms of Karenia brevis (also called red tides) occur almost annually in the Gulf of Mexico. The health effects of the neurotoxins (i.e., brevetoxins) produced by this toxic dinoflagellate on marine turtles are poorly understood. Florida's Gulf Coast represents an important foraging and nesting area for a number of marine turtle species. Most studies investigating brevetoxin exposure in marine turtles thus far focus on dead and/or stranded individuals and rarely examine the effects in apparently "healthy" free-ranging individuals. From May-July 2014, one year after the last red tide bloom, we collected blood from nesting loggerhead sea turtles (Caretta caretta) on Casey Key, Florida USA. These organisms show both strong nesting and foraging site fidelity. The plasma was analyzed for brevetoxin concentrations in addition to a number of health and immune-related parameters in an effort to establish sublethal effects of this toxin. Lastly, from July-September 2014, we collected unhatched eggs and liver and yolk sacs from dead-in-nest hatchlings from nests laid by the sampled females and tested these samples for brevetoxin concentrations to determine maternal transfer and effects on reproductive success. Using a competitive enzyme-linked immunosorbent assay (ELISA), all plasma samples from nesting females tested positive for brevetoxin (reported as ng brevetoxin-3[PbTx-3] equivalents [eq]/mL) exposure (2.1-26.7ng PbTx-3eq/mL). Additionally, 100% of livers (1.4-13.3ng PbTx-3eq/mL) and yolk sacs (1.7-6.6ng PbTx-3eq/mL) from dead-in-nest hatchlings and 70% of eggs (<1.0-24.4ng PbTx-3eq/mL) tested positive for brevetoxin exposure with the ELISA. We found that plasma brevetoxin concentrations determined by an ELISA in nesting females positively correlated with gamma-globulins, indicating a potential for immunomodulation as a result of brevetoxin exposure. While the sample sizes were small, we also found that plasma brevetoxin concentrations determined by an ELISA in nesting females significantly correlated with liver brevetoxin concentrations of dead-in-nest hatchlings and that brevetoxins could be related to a decreased reproductive success in this species. This study suggests that brevetoxins can still elicit negative effects on marine life long after a bloom has dissipated. These results improve our understanding of maternal transfer and sublethal effects of brevetoxin exposure in marine turtles. Copyright © 2016 Elsevier B.V. All rights reserved.

Bayesian model comparison and parameter inference in systems biology using nested sampling.

PubMed

Pullen, Nick; Morris, Richard J

2014-01-01

Inferring parameters for models of biological processes is a current challenge in systems biology, as is the related problem of comparing competing models that explain the data. In this work we apply Skilling's nested sampling to address both of these problems. Nested sampling is a Bayesian method for exploring parameter space that transforms a multi-dimensional integral to a 1D integration over likelihood space. This approach focuses on the computation of the marginal likelihood or evidence. The ratio of evidences of different models leads to the Bayes factor, which can be used for model comparison. We demonstrate how nested sampling can be used to reverse-engineer a system's behaviour whilst accounting for the uncertainty in the results. The effect of missing initial conditions of the variables as well as unknown parameters is investigated. We show how the evidence and the model ranking can change as a function of the available data. Furthermore, the addition of data from extra variables of the system can deliver more information for model comparison than increasing the data from one variable, thus providing a basis for experimental design.

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

Barstow, Del R; Patlolla, Dilip Reddy; Mann, Christopher J

Abstract The data captured by existing standoff biometric systems typically has lower biometric recognition performance than their close range counterparts due to imaging challenges, pose challenges, and other factors. To assist in overcoming these limitations systems typically perform in a multi-modal capacity such as Honeywell s Combined Face and Iris (CFAIRS) [21] system. While this improves the systems performance, standoff systems have yet to be proven as accurate as their close range equivalents. We will present a standoff system capable of operating up to 7 meters in range. Unlike many systems such as the CFAIRS our system captures high qualitymore » 12 MP video allowing for a multi-sample as well as multi-modal comparison. We found that for standoff systems multi-sample improved performance more than multi-modal. For a small test group of 50 subjects we were able to achieve 100% rank one recognition performance with our system.« less

Development of a nested polymerase chain reaction for amplification of a sequence of the p57 gene of Renibacterium salmoninarum that provides a highly sensitive method for detection of the bacterium in salmonid kidney

USGS Publications Warehouse

Chase, D.M.; Pascho, R.J.

1998-01-01

Nucleic acid-based assays have shown promise for diagnosing Renibacterium salmoninarum in tissues and body fluids of salmonids. DeVelopment of a nested polymerase chain reaction (PCR) method to detect a 320 bp DNA segment of the gene encoding the p57 protein of R. salmoninarum is described. Whereas a conventional PCR for a 383 bp segment of the p57 gene reliably detected 1000 R. salmoninarum cells per reaction in kidney tissue, the nested PCR detected as few as 10 R. salmoninarum per reaction in kidney tissue. Two DNA extraction methods for the nested PCR were compared and the correlation between replicate samples was generally higher in samples extracted by the QIAamp system compared with those extracted by the phenol/chloroform method. The specificity of the nested PCR was confirmed by testing DNA extracts of common bacterial fish pathogens and a panel of bacterial species reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA) and the fluorescent antibody test (FAT) for R. salmoninarum. Kidney samples from 74 naturally infected chinook Salmon were examined by the nested PCR, the ELISA, and the FAT, and the detected prevalences of R. salmoninarum were 61, 47, and 43%, respectively.

Detection and molecular characterization of Cryptosporidium spp. in captive canaries (Serinus canaria) using different diagnostic methods.

PubMed

Camargo, Vinícius da Silva; Santana, Bruna Nicoleti; Ferrari, Elis Domingos; Nakamura, Alex Akira; Nagata, Walter Bertequini; Nardi, Ana Rita Moraes; Meireles, Marcelo Vasconcelos

2018-01-01

This study used several diagnostic methods to examine the occurrence of and molecularly characterize Cryptosporidium spp. in captive canaries (Serinus canaria) in southern and southeastern Brazil. A total of 498 fecal samples were purified by centrifugal-flotation using Sheather's solution. Cryptosporidium spp. diagnosis was performed using three diagnostic methods: malachite green negative staining, nested PCR targeting the 18S rRNA gene, followed by sequencing the amplified fragments, and duplex real-time PCR targeting the 18S rRNA specific to detect Cryptosporidium galli and Cryptosporidium avian genotype III. The overall positivity for Cryptosporidium spp. (total samples positive in at least one protocol) from the microscopic analysis, nested PCR and duplex real-time PCR protocol results was 13.3% (66/498). The positivity rates were 2.0% (10/498) and 4.6% (23/498) for Cryptosporidium spp. by microscopy and nested PCR, respectively. Sequencing of 20 samples amplified by nested PCR identified C. galli (3.0%; 15/498), Cryptosporidium avian genotype I (0.8%; 4/498) and Cryptosporidium avium (0.2%; 1/498). Duplex real-time PCR revealed a positivity of 7.8% (39/498) for C. galli and 2.4% (12/498) for avian genotype III. Malachite green negative staining differed significantly from nested PCR in detecting Cryptosporidium spp. Duplex real-time PCR was more sensitive than nested PCR/sequencing for detecting gastric Cryptosporidium in canaries.

Nested PCR Assay for Detection of Leishmania donovani in Slit Aspirates from Post-Kala-Azar Dermal Leishmaniasis Lesions

PubMed Central

Sreenivas, Gannavaram; Ansari, N. A.; Kataria, Joginder; Salotra, Poonam

2004-01-01

A nested PCR assay to detect parasite DNA in slit aspirates from skin lesions of patients with post-kala-azar dermal lesihmaniasis (PKDL) is described. PCR results were positive in 27 of 29 (93%) samples by nested PCR assay, while only 20 of 29 (69%) were positive in a primary PCR assay. The nested PCR assay allowed reliable diagnosis of PKDL in a noninvasive manner. PMID:15071047

Determination of an effective sampling regime to detect salmonella enteritidis in the environment of poultry units.

PubMed

Davies, R H; Wray, C

1996-05-01

A study of the dissemination of Salmonella enteritidis in the poultry breeder industry in the UK showed that the choice of sites for sampling the environment of occupied houses and empty houses which had been disinfected after depopulation had a significant influence on the outcome. Increased isolation rates could be achieved by sampling nest box floors and dust in open slave feed hoppers in occupied poultry houses. Nest box floors were the most sensitive sites for detection of residual environmental contamination in poultry houses where enrofloxacin treatment had been used. Floor sweepings, nest box floors, slave feed hoppers, hydrated wall fabric junctions and high beams and pipes were the most sensitive sample sites in cleansed and disinfected poultry houses. The use of universal disinfectant neutralisers gave good results in laboratory trials but appeared to reduce the isolation rate from field samples.

Baseline plasma corticosterone, haematological and biochemical results in nesting and rehabilitating loggerhead sea turtles (Caretta caretta).

PubMed

Flower, Jennifer E; Norton, Terry M; Andrews, Kimberly M; Nelson, Steven E; Parker, Clare E; Romero, L Michael; Mitchell, Mark A

2015-01-01

The evaluation of hormonal responses to stress in reptiles relies on acquisition of baseline corticosterone concentrations; however, the stress associated with the restraint needed to collect the blood samples can affect the results. The purpose of this study was to determine a time limit for the collection of blood samples to evaluate baseline corticosterone, haematological and biochemical results in nesting (n = 11) and rehabilitating (n = 16) loggerhead sea turtles (Caretta caretta). Blood samples were collected from the dorsal cervical sinus of each turtle immediately after touching the animal (t 0; 0-3 min) and 3 (t 3; 3-6 min), 6 (t 6; 6-9 min; nesting turtles only), 10 (t 10; 10-13 min) and 30 min (t 30; rehabilitating turtles only) after the initial hands-on time. Consistent between the rehabilitating and nesting turtles, there was a subtle yet significant increase in white blood cell counts over time. Despite the fact that white blood cell counts increased during the sampling period, there was no direct correlation between white blood cell count and corticosterone in the sampled turtles. In the nesting turtles, significant elevations in corticosterone were noted between t 0 and t 3 (P = 0.014) and between t 0 and t 6 (P = 0.022). Values at t 10 were not significantly different from those at t 0 (P = 0.102); however, there was a trend for the corticosterone values to continue to increase. These results suggest that sampling of nesting loggerhead sea turtles within 3 min of handling will provide baseline corticosterone concentrations in their natural environment. Significant elevations in corticosterone were also noted in the rehabilitating loggerhead sea turtles between t 0 and t 10 (P = 0.02) and between t 0 and t 30 of sampling (P = 0.0001). These results suggest that sampling of loggerhead sea turtles within 6 min of handling should provide baseline corticosterone concentrations in a rehabilitation setting. The delay in the corticosterone response noted in the rehabilitating turtles may be associated with the daily contact (visual or direct) they have with their human caretakers.

The effect of canopy closure on chimpanzee nest abundance in Lagoas de Cufada National Park, Guinea-Bissau.

PubMed

Sousa, Joana; Casanova, Catarina; Barata, André V; Sousa, Cláudia

2014-04-01

The present study aimed to gather baseline information about chimpanzee nesting and density in Lagoas de Cufada Natural Park (LCNP), in Guinea-Bissau. Old and narrow trails were followed to estimate chimpanzee density through marked-nest counts and to test the effect of canopy closure (woodland savannah, forest with a sparse canopy, and forest with a dense canopy) on nest distribution. Chimpanzee abundance was estimated at 0.79 nest builders/km(2), the lowest among the areas of Guinea-Bissau with currently studied chimpanzee populations. Our data suggest that sub-humid forest with a dense canopy accounts for significantly higher chimpanzee nest abundance (1.50 nests/km of trail) than sub-humid forest with a sparse canopy (0.49 nests/km of trail) or woodland savannah (0.30 nests/km of trail). Dense-canopy forests play an important role in chimpanzee nesting in the patchy and highly humanized landscape of LCNP. The tree species most frequently used for nesting are Dialium guineense (46%) and Elaeis guineensis (28%). E. guineensis contain nests built higher in the canopy, while D. guineense contain nests built at lower heights. Nests observed during baseline sampling and replications suggest seasonal variations in the tree species used for nest building.

An optimized one-tube, semi-nested PCR assay for Paracoccidioides brasiliensis detection.

PubMed

Pitz, Amanda de Faveri; Koishi, Andrea Cristine; Tavares, Eliandro Reis; Andrade, Fábio Goulart de; Loth, Eduardo Alexandre; Gandra, Rinaldo Ferreira; Venancio, Emerson José

2013-01-01

Herein, we report a one-tube, semi-nested-polymerase chain reaction (OTsn-PCR) assay for the detection of Paracoccidioides brasiliensis. We developed the OTsn-PCR assay for the detection of P. brasiliensis in clinical specimens and compared it with other PCR methods. The OTsn-PCR assay was positive for all clinical samples, and the detection limit was better or equivalent to the other nested or semi-nested PCR methods for P. brasiliensis detection. The OTsn-PCR assay described in this paper has a detection limit similar to other reactions for the molecular detection of P. brasiliensis, but this approach is faster and less prone to contamination than other conventional nested or semi-nested PCR assays.

The Joker: A Custom Monte Carlo Sampler for Binary-star and Exoplanet Radial Velocity Data

NASA Astrophysics Data System (ADS)

Price-Whelan, Adrian M.; Hogg, David W.; Foreman-Mackey, Daniel; Rix, Hans-Walter

2017-03-01

Given sparse or low-quality radial velocity measurements of a star, there are often many qualitatively different stellar or exoplanet companion orbit models that are consistent with the data. The consequent multimodality of the likelihood function leads to extremely challenging search, optimization, and Markov chain Monte Carlo (MCMC) posterior sampling over the orbital parameters. Here we create a custom Monte Carlo sampler for sparse or noisy radial velocity measurements of two-body systems that can produce posterior samples for orbital parameters even when the likelihood function is poorly behaved. The six standard orbital parameters for a binary system can be split into four nonlinear parameters (period, eccentricity, argument of pericenter, phase) and two linear parameters (velocity amplitude, barycenter velocity). We capitalize on this by building a sampling method in which we densely sample the prior probability density function (pdf) in the nonlinear parameters and perform rejection sampling using a likelihood function marginalized over the linear parameters. With sparse or uninformative data, the sampling obtained by this rejection sampling is generally multimodal and dense. With informative data, the sampling becomes effectively unimodal but too sparse: in these cases we follow the rejection sampling with standard MCMC. The method produces correct samplings in orbital parameters for data that include as few as three epochs. The Joker can therefore be used to produce proper samplings of multimodal pdfs, which are still informative and can be used in hierarchical (population) modeling. We give some examples that show how the posterior pdf depends sensitively on the number and time coverage of the observations and their uncertainties.

High-tech or field techs: Radio-telemetry is a cost-effective method for reducing bias in songbird nest searching

USGS Publications Warehouse

Peterson, Sean M.; Streby, Henry M.; Lehman, Justin A.; Kramer, Gunnar R.; Fish, Alexander C.; Andersen, David E.

2015-01-01

We compared the efficacy of standard nest-searching methods with finding nests via radio-tagged birds to assess how search technique influenced our determination of nest-site characteristics and nest success for Golden-winged Warblers (Vermivora chrysoptera). We also evaluated the cost-effectiveness of using radio-tagged birds to find nests. Using standard nest-searching techniques for 3 populations, we found 111 nests in locations with habitat characteristics similar to those described in previous studies: edges between forest and relatively open areas of early successional vegetation or shrubby wetlands, with 43% within 5 m of forest edge. The 83 nests found using telemetry were about half as likely (23%) to be within 5 m of forest edge. We spent little time searching >25 m into forest because published reports state that Golden-winged Warblers do not nest there. However, 14 nests found using telemetry (18%) were >25 m into forest. We modeled nest success using nest-searching method, nest age, and distance to forest edge as explanatory variables. Nest-searching method explained nest success better than nest age alone; we estimated that nests found using telemetry were 10% more likely to fledge young than nests found using standard nest-searching methods. Although radio-telemetry was more expensive than standard nest searching, the cost-effectiveness of both methods differed depending on searcher experience, amount of equipment owned, and bird population density. Our results demonstrate that telemetry can be an effective method for reducing bias in Golden-winged Warbler nest samples, can be cost competitive with standard nest-searching methods in some situations, and is likely to be a useful approach for finding nests of other forest-nesting songbirds.

Automation software for a materials testing laboratory

NASA Technical Reports Server (NTRS)

Mcgaw, Michael A.; Bonacuse, Peter J.

1990-01-01

The software environment in use at the NASA-Lewis Research Center's High Temperature Fatigue and Structures Laboratory is reviewed. This software environment is aimed at supporting the tasks involved in performing materials behavior research. The features and capabilities of the approach to specifying a materials test include static and dynamic control mode switching, enabling multimode test control; dynamic alteration of the control waveform based upon events occurring in the response variables; precise control over the nature of both command waveform generation and data acquisition; and the nesting of waveform/data acquisition strategies so that material history dependencies may be explored. To eliminate repetitive tasks in the coventional research process, a communications network software system is established which provides file interchange and remote console capabilities.

An Iterative Local Updating Ensemble Smoother for Estimation and Uncertainty Assessment of Hydrologic Model Parameters With Multimodal Distributions

NASA Astrophysics Data System (ADS)

Zhang, Jiangjiang; Lin, Guang; Li, Weixuan; Wu, Laosheng; Zeng, Lingzao

2018-03-01

Ensemble smoother (ES) has been widely used in inverse modeling of hydrologic systems. However, for problems where the distribution of model parameters is multimodal, using ES directly would be problematic. One popular solution is to use a clustering algorithm to identify each mode and update the clusters with ES separately. However, this strategy may not be very efficient when the dimension of parameter space is high or the number of modes is large. Alternatively, we propose in this paper a very simple and efficient algorithm, i.e., the iterative local updating ensemble smoother (ILUES), to explore multimodal distributions of model parameters in nonlinear hydrologic systems. The ILUES algorithm works by updating local ensembles of each sample with ES to explore possible multimodal distributions. To achieve satisfactory data matches in nonlinear problems, we adopt an iterative form of ES to assimilate the measurements multiple times. Numerical cases involving nonlinearity and multimodality are tested to illustrate the performance of the proposed method. It is shown that overall the ILUES algorithm can well quantify the parametric uncertainties of complex hydrologic models, no matter whether the multimodal distribution exists.

Survey of pathogens in threatened wild red-tailed Amazon parrot (Amazona brasiliensis) nestlings in Rasa Island, Brazil.

PubMed

Vaz, Frederico Fontanelli; Serafini, Patrícia Pereira; Locatelli-Dittrich, Rosangela; Meurer, Rafael; Durigon, Edison Luiz; de Araújo, Jansen; Thomazelli, Luciano Matsumiya; Ometto, Tatiana; Sipinski, Elenise Angelotti Bastos; Sezerban, Rafael Meirelles; Abbud, Maria Cecília; Raso, Tânia Freitas

The red-tailed Amazon parrot (Amazona brasiliensis) is a threatened species of psittacine bird that inhabit coastal regions of Brazil. In view of the threat of this species, the aim of this study was to perform a health evaluation in wild nestlings in Rasa Island, determining the prevalence of enterobacteria and infectious agents according to type of nest. Blood samples were collected from 64 birds and evaluated for antibodies of Chlamydia psittaci by commercial dot-blot ELISA. Cloacal and oropharyngeal swabs samples were collected from 23 birds from artificial wooden nests, 15 birds from PVC nests and 2 birds from natural nests for microbiological analysis. Swab samples were collected from 58 parrots for C. psittaci detection by PCR and from 50 nestlings for Avian Influenza, Newcastle Disease and West Nile viruses' detection analysis by real-time RT-PCR. Ten bacterial genera and 17 species were identified, and the most prevalent were Escherichia coli and Klebsiella oxytoca. There was no influence of the type of nest in the nestlings' microbiota. All samples tested by ELISA and PCR were negative. There is currently insufficient information available about the health of A. brasiliensis and data of this study provide a reference point for future evaluations and aid in conservation plans. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Organochlorine and heavy metal residues in bald eagle eggs

USGS Publications Warehouse

Krantz, W.C.; Mulhern, B.M.; Bagley, George E.; Sprunt, A.; Ligas, F.J.; Robertson, W.B.

1970-01-01

Bald eagle eggs collected in 1968 from nests in Wisconsin, Maine, and Florida all contained residues of DDE, DDD, dieldrin, heptachlor epoxide, and polychlorinated biphenyls. Many also contained traces of DDT. Eggs from five nonproductive nests sampled in Maine contained much higher residues than did eggs collected from either productive or nonproductive nests in Wisconsin and Florida.

Maximum likelihood estimation for Cox's regression model under nested case-control sampling.

PubMed

Scheike, Thomas H; Juul, Anders

2004-04-01

Nested case-control sampling is designed to reduce the costs of large cohort studies. It is important to estimate the parameters of interest as efficiently as possible. We present a new maximum likelihood estimator (MLE) for nested case-control sampling in the context of Cox's proportional hazards model. The MLE is computed by the EM-algorithm, which is easy to implement in the proportional hazards setting. Standard errors are estimated by a numerical profile likelihood approach based on EM aided differentiation. The work was motivated by a nested case-control study that hypothesized that insulin-like growth factor I was associated with ischemic heart disease. The study was based on a population of 3784 Danes and 231 cases of ischemic heart disease where controls were matched on age and gender. We illustrate the use of the MLE for these data and show how the maximum likelihood framework can be used to obtain information additional to the relative risk estimates of covariates.

Molecular forensics in avian conservation: a DNA-based approach for identifying mammalian predators of ground-nesting birds and eggs.

PubMed

Hopken, Matthew W; Orning, Elizabeth K; Young, Julie K; Piaggio, Antoinette J

2016-01-07

The greater sage-grouse (Centrocercus urophasianus) is a ground-nesting bird from the Northern Rocky Mountains and a species at risk of extinction in in multiple U.S. states and Canada. Herein we report results from a proof of concept that mitochondrial and nuclear DNAs from mammalian predator saliva could be non-invasively collected from depredated greater sage-grouse eggshells and carcasses and used for predator species identification. Molecular forensic approaches have been applied to identify predators from depredated remains as one strategy to better understand predator-prey dynamics and guide management strategies. This can aid conservation efforts by correctly identifying predators most likely to impact threatened and endangered species. DNA isolated from non-invasive samples around nesting sites (e.g. fecal or hair samples) is one method that can increase the success and accuracy of predator species identification when compared to relying on nest remains alone. Predator saliva DNA was collected from depredated eggshells and carcasses using swabs. We sequenced two partial fragments of two mitochondrial genes and obtained microsatellite genotypes using canid specific primers for species and individual identification, respectively. Using this multilocus approach we were able to identify predators, at least down to family, from 11 out of 14 nests (79%) and three out of seven carcasses (47%). Predators detected most frequently were canids (86%), while other taxa included rodents, a striped skunk, and cattle. We attempted to match the genotypes of individual coyotes obtained from eggshells and carcasses with those obtained from fecal samples and coyotes collected in the areas, but no genotype matches were found. Predation is a main cause of nest failure in ground-nesting birds and can impact reproduction and recruitment. To inform predator management for ground-nesting bird conservation, accurate identification of predator species is necessary. Considering predation can have a high impact on recruitment, predation events are very difficult to observe, and predator species are difficult to identify visually from nest remains, molecular approaches that reduce the need to observe or handle animals offer an additional tool to better understand predator-prey dynamics at nesting sites.

Integration of multimodal RNA-seq data for prediction of kidney cancer survival

PubMed Central

Schwartzi, Matt; Parkl, Martin; Phanl, John H.; Wang., May D.

2016-01-01

Kidney cancer is of prominent concern in modern medicine. Predicting patient survival is critical to patient awareness and developing a proper treatment regimens. Previous prediction models built upon molecular feature analysis are limited to just gene expression data. In this study we investigate the difference in predicting five year survival between unimodal and multimodal analysis of RNA-seq data from gene, exon, junction, and isoform modalities. Our preliminary findings report higher predictive accuracy-as measured by area under the ROC curve (AUC)-for multimodal learning when compared to unimodal learning with both support vector machine (SVM) and k-nearest neighbor (KNN) methods. The results of this study justify further research on the use of multimodal RNA-seq data to predict survival for other cancer types using a larger sample size and additional machine learning methods. PMID:27532026

Nosocomial transmission of respiratory syncytial virus in an outpatient cancer center.

PubMed

Chu, Helen Y; Englund, Janet A; Podczervinski, Sara; Kuypers, Jane; Campbell, Angela P; Boeckh, Michael; Pergam, Steven A; Casper, Corey

2014-06-01

Respiratory syncytial virus (RSV) outbreaks in inpatient settings are associated with poor outcomes in cancer patients. The use of molecular epidemiology to document RSV transmission in the outpatient setting has not been well described. We performed a retrospective cohort study of 2 nosocomial outbreaks of RSV at the Seattle Cancer Care Alliance. Subjects included patients seen at the Seattle Cancer Care Alliance with RSV detected in 2 outbreaks in 2007-2008 and 2012 and all employees with respiratory viruses detected in the 2007-2008 outbreak. A subset of samples was sequenced using semi-nested PCR targeting the RSV attachment glycoprotein coding region. Fifty-one cases of RSV were identified in 2007-2008. Clustering of identical viral strains was detected in 10 of 15 patients (67%) with RSV sequenced from 2007 to 2008. As part of a multimodal infection control strategy implemented as a response to the outbreak, symptomatic employees had nasal washes collected. Of 254 employee samples, 91 (34%) tested positive for a respiratory virus, including 14 with RSV. In another RSV outbreak in 2012, 24 cases of RSV were identified; 9 of 10 patients (90%) had the same viral strain, and 1 (10%) had another viral strain. We document spread of clonal strains within an outpatient cancer care setting. Infection control interventions should be implemented in outpatient, as well as inpatient, settings to reduce person-to-person transmission and limit progression of RSV outbreaks. Copyright © 2014 American Society for Blood and Marrow Transplantation. All rights reserved.

Nosocomial Transmission of Respiratory Syncytial Virus in an Outpatient Cancer Center

PubMed Central

Chu, Helen Y.; Englund, Janet A.; Podczervinski, Sara; Kuypers, Jane; Campbell, Angela P.; Boeckh, Michael; Pergam, Steven A.; Casper, Crey

2014-01-01

Background Respiratory syncytial virus (RSV) outbreaks in inpatient settings are associated with poor outcomes in cancer patients. The use of molecular epidemiology to document RSV transmission in the outpatient setting has not been well described. Methods We performed a retrospective cohort study of two nosocomial outbreaks of RSV at the Seattle Cancer Care Alliance (SCCA). Subjects included patients seen at the SCCA with RSV detected in two outbreaks in 2007-2008 and 2012, and all employees with respiratory viruses detected in the 2007-2008 outbreak. A subset of samples was sequenced using semi-nested polymerase chain reaction targeting the RSV attachment glycoprotein coding region. Results Fifty-one cases of RSV were identified in 2007-2008. Clustering of identical viral strains was detected in 10 (67%) of 15 patients with RSV sequenced from 2007-2008. As part of a multimodal infection control strategy implemented as a response to the outbreak, symptomatic employees had nasal washes collected. Of 254 employee samples, 91 (34%) tested positive for a respiratory virus, including 14 with RSV. In another RSV outbreak in 2012, 24 cases of RSV were identified; nine (90%) of 10 patients had the same viral strain, and 1 (10%) had another viral strain. Conclusions We document spread of clonal strains within an outpatient cancer care setting. Infection control interventions should be implemented in outpatient, as well as inpatient, settings to reduce person-to-person transmission and limit progression of RSV outbreaks. PMID:24607551

Job Performance as Multivariate Dynamic Criteria: Experience Sampling and Multiway Component Analysis.

PubMed

Spain, Seth M; Miner, Andrew G; Kroonenberg, Pieter M; Drasgow, Fritz

2010-08-06

Questions about the dynamic processes that drive behavior at work have been the focus of increasing attention in recent years. Models describing behavior at work and research on momentary behavior indicate that substantial variation exists within individuals. This article examines the rationale behind this body of work and explores a method of analyzing momentary work behavior using experience sampling methods. The article also examines a previously unused set of methods for analyzing data produced by experience sampling. These methods are known collectively as multiway component analysis. Two archetypal techniques of multimode factor analysis, the Parallel factor analysis and the Tucker3 models, are used to analyze data from Miner, Glomb, and Hulin's (2010) experience sampling study of work behavior. The efficacy of these techniques for analyzing experience sampling data is discussed as are the substantive multimode component models obtained.

Monitoring and improving the sensitivity of dengue nested RT-PCR used in longitudinal surveillance in Thailand.

PubMed

Klungthong, Chonticha; Manasatienkij, Wudtichai; Phonpakobsin, Thipwipha; Chinnawirotpisan, Piyawan; Rodpradit, Prinyada; Hussem, Kittinun; Thaisomboonsuk, Butsaya; Ong-ajchaowlerd, Prapapun; Nisalak, Ananda; Kalayanarooj, Siripen; Buddhari, Darunee; Gibbons, Robert V; Jarman, Richard G; Yoon, In-Kyu; Fernandez, Stefan

2015-02-01

AFRIMS longitudinal dengue surveillance in Thailand depends on the nested RT-PCR and the dengue IgM/IgG ELISA. To examine and improve the sensitivity of the nested RT-PCR using a panel of archived samples collected during dengue surveillance. A retrospective analysis of 16,454 dengue IgM/IgG ELISA positive cases collected between 2000 and 2013 was done to investigate the sensitivity of the nested RT-PCR. From these cases, 318 acute serum specimens or extracted RNA, previously found to be negative by the nested RT-PCR, were tested using TaqMan real-time RT-PCR (TaqMan rRT-PCR). To improve the sensitivity of nested RT-PCR, we designed a new primer based on nucleotide sequences from contemporary strains found to be positive by the TaqMan rRT-PCR. Sensitivity of the new nested PCR was calculated using a panel of 87 samples collected during 2011-2013. The percentage of dengue IgM/IgG ELISA positive cases that were negative by the nested RT-PCR varied from 17% to 42% for all serotypes depending on the year. Using TaqMan rRT-PCR, dengue RNA was detected in 194 (61%) of the 318 acute sera or extracted RNA previously found to be negative by the nested RT-PCR. The newly designed DENV-1 specific primer increased the sensitivity of DENV-1 detection by the nested RT-PCR from 48% to 88%, and of all 4 serotypes from 73% to 87%. These findings demonstrate the impact of genetic diversity and signal erosion on the sensitivity of PCR-based methods. Published by Elsevier B.V.

Estimating stage-specific daily survival probabilities of nests when nest age is unknown

USGS Publications Warehouse

Stanley, T.R.

2004-01-01

Estimation of daily survival probabilities of nests is common in studies of avian populations. Since the introduction of Mayfield's (1961, 1975) estimator, numerous models have been developed to relax Mayfield's assumptions and account for biologically important sources of variation. Stanley (2000) presented a model for estimating stage-specific (e.g. incubation stage, nestling stage) daily survival probabilities of nests that conditions on “nest type” and requires that nests be aged when they are found. Because aging nests typically requires handling the eggs, there may be situations where nests can not or should not be aged and the Stanley (2000) model will be inapplicable. Here, I present a model for estimating stage-specific daily survival probabilities that conditions on nest stage for active nests, thereby obviating the need to age nests when they are found. Specifically, I derive the maximum likelihood function for the model, evaluate the model's performance using Monte Carlo simulations, and provide software for estimating parameters (along with an example). For sample sizes as low as 50 nests, bias was small and confidence interval coverage was close to the nominal rate, especially when a reduced-parameter model was used for estimation.

Mourning Dove nesting habitat and nest success in Central Missouri

USGS Publications Warehouse

Drobney, R.D.; Schulz, J.H.; Sheriff, S.L.; Fuemmeler, W.J.

1998-01-01

Previous Mourning Dove (Zenaida macroura) nesting studies conducted in areas containing a mixture of edge and continuous habitats have focused on edge habitats. Consequently, little is known about the potential contribution of continuous habitats to dove production. In this study we evaluated the relative importance of these two extensive habitat types by monitoring the habitat use and nest success of 59 radio-marked doves during 1990-1991 in central Missouri. Of 83 nests initiated by our marked sample, most (81.9%) were located in edge habitats. Although continuous habitats were selected less as nest sites, the proportion of successful nests did not differ significantly from that in edge habitats. Our data indicate that continuous habitats should not be considered marginal nesting habitat. If the intensity of use and nest success that we observed are representative regionally or nationally, continuous habitats could contribute substantially to annual Mourning Dove production because of the high availability of these habitats throughout much of the Mourning Dove breeding range.

The Joker: A custom Monte Carlo sampler for binary-star and exoplanet radial velocity data

NASA Astrophysics Data System (ADS)

Price-Whelan, Adrian M.; Hogg, David W.; Foreman-Mackey, Daniel; Rix, Hans-Walter

2017-01-01

Given sparse or low-quality radial-velocity measurements of a star, there are often many qualitatively different stellar or exoplanet companion orbit models that are consistent with the data. The consequent multimodality of the likelihood function leads to extremely challenging search, optimization, and MCMC posterior sampling over the orbital parameters. The Joker is a custom-built Monte Carlo sampler that can produce a posterior sampling for orbital parameters given sparse or noisy radial-velocity measurements, even when the likelihood function is poorly behaved. The method produces correct samplings in orbital parameters for data that include as few as three epochs. The Joker can therefore be used to produce proper samplings of multimodal pdfs, which are still highly informative and can be used in hierarchical (population) modeling.

Nestedness in assemblages of helminth parasites of bats: a function of geography, environment, or host nestedness?

PubMed

Warburton, Elizabeth M; Van Der Mescht, Luther; Khokhlova, Irina S; Krasnov, Boris R; Vonhof, Maarten J

2018-05-01

Nested subsets occur in ecological communities when species-poor communities are subsets of larger, species-rich communities. Understanding this pattern can help elucidate species colonization abilities, extinction risks, and general structuring of biological communities. Here, we evaluate nestedness in a poorly studied host-parasite system, bats and their helminths, across the Japanese archipelago and within its different bioclimatic regions. We hypothesized that (1) if helminth communities are nested across geographic sites at the level of the archipelago, then broad-scale processes, like colonization-extinction dynamics, mainly structure parasite assemblages; (2) if helminth communities are nested across geographic sites at the level of the bioclimatic region, then fine-scale environmental variation plays a significant role in species nestedness; (3) if helminth community nestedness mirrors host species nestedness, then communities are nested because the habitats they occupy are nested; and (4) if nestedness does not occur or if it is not correlated with any geographical or host data, then passive sampling could be responsible for the patterns of parasite assemblage in our sample. We found that helminth communities were nested across host species throughout the archipelago but, when considering each bioclimatic region, helminths in only one region were significantly more nested than the null model. Helminth communities were also nested across sites within all four bioclimatic regions. These results suggest that helminths form nested subsets across the archipelago due to broad-scale processes that reflect the overall lineages of their mammalian hosts; however, at the regional scale, environmental processes related to nestedness of their habitats drive parasite community nestedness.

[Optimized application of nested PCR method for detection of malaria].

PubMed

Yao-Guang, Z; Li, J; Zhen-Yu, W; Li, C

2017-04-28

Objective To optimize the application of the nested PCR method for the detection of malaria according to the working practice, so as to improve the efficiency of malaria detection. Methods Premixing solution of PCR, internal primers for further amplification and new designed primers that aimed at two Plasmodium ovale subspecies were employed to optimize the reaction system, reaction condition and specific primers of P . ovale on basis of routine nested PCR. Then the specificity and the sensitivity of the optimized method were analyzed. The positive blood samples and examination samples of malaria were detected by the routine nested PCR and the optimized method simultaneously, and the detection results were compared and analyzed. Results The optimized method showed good specificity, and its sensitivity could reach the pg to fg level. The two methods were used to detect the same positive malarial blood samples simultaneously, the results indicated that the PCR products of the two methods had no significant difference, but the non-specific amplification reduced obviously and the detection rates of P . ovale subspecies improved, as well as the total specificity also increased through the use of the optimized method. The actual detection results of 111 cases of malarial blood samples showed that the sensitivity and specificity of the routine nested PCR were 94.57% and 86.96%, respectively, and those of the optimized method were both 93.48%, and there was no statistically significant difference between the two methods in the sensitivity ( P > 0.05), but there was a statistically significant difference between the two methods in the specificity ( P < 0.05). Conclusion The optimized PCR can improve the specificity without reducing the sensitivity on the basis of the routine nested PCR, it also can save the cost and increase the efficiency of malaria detection as less experiment links.

Effects of temporally persistent ant nests of soil protozoan communities and the abundance of morphological types of amoeba

USDA-ARS?s Scientific Manuscript database

We compared soil protozoan communities near ant nests with soil protozoans in reference soils 5m from the edge of any mounds. We sampled three species of Chihuahuan Desert ants that construct nests that persist for more than a decade: a seed harvester, Pogonomymex rugosus, a liquid feeding honey-po...

Adaptive Annealed Importance Sampling for Multimodal Posterior Exploration and Model Selection with Application to Extrasolar Planet Detection

NASA Astrophysics Data System (ADS)

Liu, Bin

2014-07-01

We describe an algorithm that can adaptively provide mixture summaries of multimodal posterior distributions. The parameter space of the involved posteriors ranges in size from a few dimensions to dozens of dimensions. This work was motivated by an astrophysical problem called extrasolar planet (exoplanet) detection, wherein the computation of stochastic integrals that are required for Bayesian model comparison is challenging. The difficulty comes from the highly nonlinear models that lead to multimodal posterior distributions. We resort to importance sampling (IS) to estimate the integrals, and thus translate the problem to be how to find a parametric approximation of the posterior. To capture the multimodal structure in the posterior, we initialize a mixture proposal distribution and then tailor its parameters elaborately to make it resemble the posterior to the greatest extent possible. We use the effective sample size (ESS) calculated based on the IS draws to measure the degree of approximation. The bigger the ESS is, the better the proposal resembles the posterior. A difficulty within this tailoring operation lies in the adjustment of the number of mixing components in the mixture proposal. Brute force methods just preset it as a large constant, which leads to an increase in the required computational resources. We provide an iterative delete/merge/add process, which works in tandem with an expectation-maximization step to tailor such a number online. The efficiency of our proposed method is tested via both simulation studies and real exoplanet data analysis.

Detection of small number of Giardia in biological materials prepared from stray dogs.

PubMed

Esmailikia, Leila; Ebrahimzade, Elahe; Shayan, Parviz; Amininia, Narges

2017-12-20

Giardia lamblia is an intestinal protozoa with intermittent and low shedding especially in dogs, and the detection of Giardia is accompanied with problems such as sampling and diagnostic method. The objective of this study was to detection of Giardia in biological materials with low number of parasite using parasitological and molecular methods, and also to determine whether the examined stray dogs harbor known zoonotic genotype of Giardia. For this aim 85 fecal and duodenal samples were studied from which 1 was positive by Trichrome staining of stool, 4 were positive by staining of duodenal samples. The nested PCR analysis with primers derived from 18 SrRNA showed that the specific PCR product could be amplified in 4 stool and 4 duodenal samples. All positive samples in staining analysis were also positive in nested PCR. No amplification could be observed by nested PCR with primers derived from β giardin gene due to the single copy of gene. Interestingly, the extracted DNA from old fixed stained Giardia positive smears could be also amplified with primers derived from 18SrRNA gene. The sequence analysis of nested PCR products showed that they belong to the genotype D. In conclusion, it is to denote that the Trichrome or Giemsa methods were not suitable for the detection of small number of this parasite in stool and the nested PCR with primers derived from 18S rRNA gene can replace the traditional methods successfully. For detection of Giardia in stool, primers derived from β giardin will not be recommended.

Nested Cohort - R software package

Cancer.gov

NestedCohort is an R software package for fitting Kaplan-Meier and Cox Models to estimate standardized survival and attributable risks for studies where covariates of interest are observed on only a sample of the cohort.

Defining a Conceptual Topography of Word Concreteness: Clustering Properties of Emotion, Sensation, and Magnitude among 750 English Words

PubMed Central

Troche, Joshua; Crutch, Sebastian J.; Reilly, Jamie

2017-01-01

Cognitive science has a longstanding interest in the ways that people acquire and use abstract vs. concrete words (e.g., truth vs. piano). One dominant theory holds that abstract and concrete words are subserved by two parallel semantic systems. We recently proposed an alternative account of abstract-concrete word representation premised upon a unitary, high dimensional semantic space wherein word meaning is nested. We hypothesize that a range of cognitive and perceptual dimensions (e.g., emotion, time, space, color, size, visual form) bound this space, forming a conceptual topography. Here we report a normative study where we examined the clustering properties of a sample of English words (N = 750) spanning a spectrum of concreteness in a continuous manner from highly abstract to highly concrete. Participants (N = 328) rated each target word on a range of 14 cognitive dimensions (e.g., color, emotion, valence, polarity, motion, space). The dimensions reduced to three factors: Endogenous factor, Exogenous factor, and Magnitude factor. Concepts were plotted in a unified, multimodal space with concrete and abstract concepts along a continuous continuum. We discuss theoretical implications and practical applications of this dataset. These word norms are freely available for download and use at http://www.reilly-coglab.com/data/. PMID:29075224

Defining a Conceptual Topography of Word Concreteness: Clustering Properties of Emotion, Sensation, and Magnitude among 750 English Words.

PubMed

Troche, Joshua; Crutch, Sebastian J; Reilly, Jamie

2017-01-01

Cognitive science has a longstanding interest in the ways that people acquire and use abstract vs. concrete words (e.g., truth vs. piano). One dominant theory holds that abstract and concrete words are subserved by two parallel semantic systems. We recently proposed an alternative account of abstract-concrete word representation premised upon a unitary, high dimensional semantic space wherein word meaning is nested. We hypothesize that a range of cognitive and perceptual dimensions (e.g., emotion, time, space, color, size, visual form) bound this space, forming a conceptual topography. Here we report a normative study where we examined the clustering properties of a sample of English words ( N = 750) spanning a spectrum of concreteness in a continuous manner from highly abstract to highly concrete. Participants ( N = 328) rated each target word on a range of 14 cognitive dimensions (e.g., color, emotion, valence, polarity, motion, space). The dimensions reduced to three factors: Endogenous factor, Exogenous factor, and Magnitude factor. Concepts were plotted in a unified, multimodal space with concrete and abstract concepts along a continuous continuum. We discuss theoretical implications and practical applications of this dataset. These word norms are freely available for download and use at http://www.reilly-coglab.com/data/.

Sampling considerations for demographic and habitat studies of Northern Goshawks

Treesearch

Richard T. Reynolds; J. David Wiens; Suzanne M. Joy; Susan R. Salafsky

2005-01-01

We used mark-recapture methods to monitor Northern Goshawks (Accipiter gentilis) and their nests over 12 yr in an increasing sample of breeding territories (37 in 1991 to 121 in 2002) in northern Arizona. As many as 8 yr of repeated nest searching were required to identify the population of breeders, as individuals skipped egg-laying on territories...

Arboreal ant colonies as 'hot-points' of cryptic diversity for myrmecophiles: the weaver ant Camponotus sp. aff. textor and its interaction network with its associates.

PubMed

Pérez-Lachaud, Gabriela; Lachaud, Jean-Paul

2014-01-01

Systematic surveys of macrofaunal diversity within ant colonies are lacking, particularly for ants nesting in microhabitats that are difficult to sample. Species associated with ants are generally small and rarely collected organisms, which makes them more likely to be unnoticed. We assumed that this tendency is greater for arthropod communities in microhabitats with low accessibility, such as those found in the nests of arboreal ants that may constitute a source of cryptic biodiversity. We investigated the invertebrate diversity associated with an undescribed, but already threatened, Neotropical Camponotus weaver ant. As most of the common sampling methods used in studies of ant diversity are not suited for evaluating myrmecophile diversity within ant nests, we evaluated the macrofauna within ant nests through exhaustive colony sampling of three nests and examination of more than 80,000 individuals. We identified invertebrates from three classes belonging to 18 taxa, some of which were new to science, and recorded the first instance of the co-occurrence of two brood parasitoid wasp families attacking the same ant host colony. This diversity of ant associates corresponded to a highly complex interaction network. Agonistic interactions prevailed, but the prevalence of myrmecophiles was remarkably low. Our data support the hypothesis of the evolution of low virulence in a variety of symbionts associated with large insect societies. Because most myrmecophiles found in this work are rare, strictly specific, and exhibit highly specialized biology, the risk of extinction for these hitherto unknown invertebrates and their natural enemies is high. The cryptic, far unappreciated diversity within arboreal ant nests in areas at high risk of habitat loss qualifies these nests as 'hot-points' of biodiversity that urgently require special attention as a component of conservation and management programs.

Human herpesvirus infections of the central nervous system: laboratory diagnosis based on DNA detection by nested PCR in plasma and cerebrospinal fluid samples.

PubMed

Rimério, Carla Aparecida Tavares; De Oliveira, Renato Souza; de Almeida Bonatelli, Murilo Queiroz; Nucci, Anamarli; Costa, Sandra Cecília Botelho; Bonon, Sandra Helena Alves

2015-04-01

Infections of the central nervous systems (CNS) present a diagnostic problem for which an accurate laboratory diagnosis is essential. Invasive practices, such as cerebral biopsy, have been replaced by obtaining a polymerase chain reaction (PCR) diagnosis using cerebral spinal fluid (CSF) as a reference method. Tests on DNA extracted from plasma are noninvasive, thus avoiding all of the collateral effects and patient risks associated with CSF collection. This study aimed to determine whether plasma can replace CSF in nested PCR analysis for the detection of CNS human herpesvirus (HHV) diseases by analysing the proportion of patients whose CSF nested PCR results were positive for CNS HHV who also had the same organism identified by plasma nested PCR. In this study, CSF DNA was used as the "gold standard," and nested PCR was performed on both types of samples. Fifty-two patients with symptoms of nervous system infection were submitted to CSF and blood collection. For the eight HHV, one positive DNA result-in plasma and/or CSF nested PCR-was considered an active HHV infection, whereas the occurrence of two or more HHVs in the same sample was considered a coinfection. HHV infections were positively detected in 27/52 (51.9%) of the CSF and in 32/52 (61.5%) of the plasma, difference not significant, thus nested PCR can be performed on plasma instead of CSF. In conclusion, this findings suggest that plasma as a useful material for the diagnosis of cases where there is any difficulty to perform a CSF puncture. © 2015 Wiley Periodicals, Inc.

PCR-based Diagnosis of Toxoplasma Parasite in Ocular Infections Having Clinical Indications of Toxoplasmosis.

PubMed

Farhadi, Atieh; Haniloo, Ali; Fazaeli, Asghar; Moradian, Siamak; Farhadi, Mehdi

2017-01-01

The diagnosis of ocular toxoplasmosis is mainly based on clinical features. However, ocular fluid testing by PCR may be very helpful for approval or rejection of this etiology. In this study, we utilized a nested-PCR technique, targeting the B1 partial sequence to analyze the aqueous and vitreous samples for evaluating the presence of the Toxoplasma DNA. Fifty aqueous or vitreous humor samples were obtained from patients with clinical features of ocular toxoplasmosis admitted to ophthalmology hospitals and clinics in Iran, within 2014. The samples were subsequently subjected to DNA extraction and purification. For nested amplification of the Toxoplasma B1 gene, two primer pairs were used. The outer and inner primers are expected to produce a 193 bp and a 96 bp fragments, respectively. The first-round PCR resulted in the detection of T. gondii in 58% of samples by amplification of the expected 193bp DNA fragment. The nested-PCR using the inner primers, detected 15 additional samples from those with negative amplicons in the first round PCR (overall positivity of 88%). In addition, vitreous samples showed relatively more positive cases than aqueous humor in detection of the infection. The nested-PCR protocol using the B1 gene, with the high detection power, could be a useful complimentary method to clinical diagnose of ocular toxoplasmosis.

Detection of Pneumocystis jirovecii by nested PCR in HIV-negative patients with pulmonary disease.

PubMed

Santos, Cristina Rodrigues; de Assis, Ângela M; Luz, Edson A; Lyra, Luzia; Toro, Ivan F; Seabra, José Claudio C; Daldin, Dira H; Marcalto, Tathiane U; Galasso, Marcos T; Macedo, Ronaldo F; Schreiber, Angélica Z; Aoki, Francisco H

Nested PCR can be used to determine the status of Pneumocystis jirovecii infection in other lung diseases. This study sought to detect a target DNA fragment (mitochondrial large subunit rRNA or mtL SUrRNA) of P. jirovecii in patients with lung disease who underwent bronchoscopy with collection of bronchoalveolar lavage (BAL). The results from toluidine blue staining were compared with those obtained using molecular methods that included an "in house" DNA extraction procedure, PCR and nested PCR. Fifty-five BAL samples from patients with atypical chest X-rays were screened for P. jirovecii. None of the samples was positive for P. jirovecii using toluidine blue staining. In contrast, P. jirovecii DNA was detected by nested PCR in BAL samples from 36 of 55 patients (65.5%). The lung diseases in the patients included cancer, pneumonia, tuberculosis, and chronic obstructive pulmonary disease (COPD). Other chronic problems in the patients included hypertension, diabetes, smoking, and alcoholism. Nested PCR showed high sensitivity for detecting P. jirovecii, especially when compared with toluidine blue staining. Using this method, P. jirovecii infection was detected in HIV-negative patients with lung disease. Copyright © 2016 Asociación Española de Micología. Publicado por Elsevier España, S.L.U. All rights reserved.

Comparison of nested-multiplex, Taqman & SYBR Green real-time PCR in diagnosis of amoebic liver abscess in a tertiary health care institute in India.

PubMed

Dinoop, K P; Parija, Subhash Chandra; Mandal, Jharna; Swaminathan, R P; Narayanan, P

2016-01-01

Amoebiasis is a common parasitic infection caused by Entamoeba histolytica and amoebic liver abscess (ALA) is the most common extraintestinal manifestation of amoebiasis. The aim of this study was to standardise real-time PCR assays (Taqman and SYBR Green) to detect E. histolytica from liver abscess pus and stool samples and compare its results with nested-multiplex PCR. Liver abscess pus specimens were subjected to DNA extraction. The extracted DNA samples were subjected to amplification by nested-multiplex PCR, Taqman (18S rRNA) and SYBR Green real-time PCR (16S-like rRNA assays to detect E. histolytica/E. dispar/E. moshkovskii). The amplification products were further confirmed by DNA sequence analysis. Receiver operator characteristic (ROC) curve analysis was done for nested-multiplex and SYBR Green real-time PCR and the area under the curve was calculated for evaluating the accuracy of the tests to dignose ALA. In all, 17, 19 and 25 liver abscess samples were positive for E. histolytica by nested-multiplex PCR, SYBR Green and Taqman real-time PCR assays, respectively. Significant differences in detection of E. histolytica were noted in the real-time PCR assays evaluated ( P<0.0001). The nested-multiplex PCR, SYBR Green real-time PCR and Taqman real-time PCR evaluated showed a positivity rate of 34, 38 and 50 per cent, respectively. Based on ROC curve analysis (considering Taqman real-time PCR as the gold standard), it was observed that SYBR Green real-time PCR was better than conventional nested-multiplex PCR for the diagnosis of ALA. Taqman real-time PCR targeting the 18S rRNA had the highest positivity rate evaluated in this study. Both nested multiplex and SYBR Green real-time PCR assays utilized were evaluated to give accurate results. Real-time PCR assays can be used as the gold standard in rapid and reliable diagnosis, and appropriate management of amoebiasis, replacing the conventional molecular methods.

Rapid detection of human fecal Eubacterium species and related genera by nested PCR method.

PubMed

Kageyama, A; Benno, Y

2001-01-01

PCR procedures based on 16S rDNA gene sequence specific for seven Eubacterium spp. and Eggerthella lenta that predominate in the human intestinal tract were developed, and used for direct detection of these species in seven human feces samples. Three species of Eggerthella lenta, Eubacterium rectale, and Eubacterium eligens were detected from seven fecal samples. Eubacterium biforme was detected from six samples. It was reported that E. rectale, E. eligens, and E. biforme were difficult to detect by traditional culture method, but the nested PCR method is available for the detection of these species. This result shows that the nested PCR method utilizing a universal primer pair, followed by amplification with species-specific primers, would allow rapid detection of Eubacterium species in human feces.

Single-cell multimodal profiling reveals cellular epigenetic heterogeneity.

PubMed

Cheow, Lih Feng; Courtois, Elise T; Tan, Yuliana; Viswanathan, Ramya; Xing, Qiaorui; Tan, Rui Zhen; Tan, Daniel S W; Robson, Paul; Loh, Yuin-Han; Quake, Stephen R; Burkholder, William F

2016-10-01

Sample heterogeneity often masks DNA methylation signatures in subpopulations of cells. Here, we present a method to genotype single cells while simultaneously interrogating gene expression and DNA methylation at multiple loci. We used this targeted multimodal approach, implemented on an automated, high-throughput microfluidic platform, to assess primary lung adenocarcinomas and human fibroblasts undergoing reprogramming by profiling epigenetic variation among cell types identified through genotyping and transcriptional analysis.

Learning in data-limited multimodal scenarios: Scandent decision forests and tree-based features.

PubMed

Hor, Soheil; Moradi, Mehdi

2016-12-01

Incomplete and inconsistent datasets often pose difficulties in multimodal studies. We introduce the concept of scandent decision trees to tackle these difficulties. Scandent trees are decision trees that optimally mimic the partitioning of the data determined by another decision tree, and crucially, use only a subset of the feature set. We show how scandent trees can be used to enhance the performance of decision forests trained on a small number of multimodal samples when we have access to larger datasets with vastly incomplete feature sets. Additionally, we introduce the concept of tree-based feature transforms in the decision forest paradigm. When combined with scandent trees, the tree-based feature transforms enable us to train a classifier on a rich multimodal dataset, and use it to classify samples with only a subset of features of the training data. Using this methodology, we build a model trained on MRI and PET images of the ADNI dataset, and then test it on cases with only MRI data. We show that this is significantly more effective in staging of cognitive impairments compared to a similar decision forest model trained and tested on MRI only, or one that uses other kinds of feature transform applied to the MRI data. Copyright © 2016. Published by Elsevier B.V.

Age-specific productivity and nest site characteristics of Cooper's hawks (Accipiter cooperii)

USGS Publications Warehouse

Moore, K.R.; Henny, C.J.

1984-01-01

Nesting Cooper's Hawks (Accipiter cooperii) were studied in northeastern Oregon. Second-year (SY) males did not breed, but 22 percent of the breeding females were SY's. Mean clutch size (P = 0.012) and mean number of young fledged per pair that laid eggs (P < 0.10) were lower for SY females than for adult (after second year [ASY}) females; however, an equal percentage of the eggs (excluding a collected sample egg) yielded fledged young for each age class. Stepwise discriminant analysis suggested differences in structural characteristics of the nest site habitat for ASY and SY females, i.e., SY female nest sites were associated with younger successional stages than ASY female nest sites. Nests of both age groups were built in trees with high crown volume, but ASY females utilized mistletoe (Arceuthobium sp.) for nest structures more frequently (P < 0.01) than SY females.

Density and Distribution of Xylocopa Nests (Hymenoptera: Apidae) in Caatinga Areas in the Surroundings of Passion Fruit Crops.

PubMed

Martins, C F; de Siqueira, K M M; Kiill, L H P; Sá, I I S; Aguiar, C M L

2014-08-01

Due to their importance as pollinators of many plant species, this study aimed to know the nest density, spatial distribution, and nesting substrates used by Xylocopa species in the Caatinga, a xerophilous vegetation of Northeastern Brazil. Three areas of Caatinga in the surroundings of passion fruit crops were sampled. The bee species found in these areas were Xylocopa grisescens Lepeletier and Xylocopa frontalis (Olivier). All nests were in Commiphora leptophloeos (Burseraceae) trees (n = 113). Phytosociological analysis showed that this tree species presented the highest absolute density (212.5 individuals/ha) and index of importance value (52.7). The distribution pattern of the C. leptophloeos was aggregated. The nests were located in dead and dried branches with an average diameter of 5.3 ± 2.0 cm (n = 43). The mean number of nests/tree was 3.1 ± 2.8 (n = 113). The less disturbed area showed 6.7 nests/ha and 4.2 nests/tree. In the disturbed areas, 0.9 nests/ha and 2.4 to 2.7 nests/tree were observed. The availability of substrate for nesting in the studied areas and its importance as a limiting factor for nesting are discussed.

Nesting habitat of the Tule Greater White-fronted Goose Anser albifrons elgasi

USGS Publications Warehouse

Densmore, R.V.; Ely, Craig R.; Bollinger, K.S.; Kratzer, S.; Udevitz, M.S.; Fehringer, D.J.; Rothe, T.C.

2006-01-01

This paper presents the first information on the availability and use of nesting habitat by the rare Tule Greater White-fronted Goose Anser albifrons elgasi. The breeding range was sampled by marking geese with radio transmitters on wintering and moulting areas, and tracking them to nest sites in Alaska. Nesting habitat was described at the scales of ecoregion, wetland ecosystem (National Wetlands Inventory (NWI) maps), vegetation type within wetland (Alaska Vegetation Classification (AVC) maps based on satellite imagery), and nest site. Tule Greater White-fronted Goose nests were located in boreal forest wetlands in the upper Cook Inlet Basin ecoregion. Nesting Tule Greater White-fronted Geese selected NWT Palustrine Seasonally Flooded wetlands and used NWI Palustrine Saturated wetlands in proportion to availability. Within these wetlands, Tule Greater White-fronted Geese used Needleleaf Forest, Low Shrub and Herbaceous (mostly graminoid) AVC classes for nest sites in proportion to availability Most (93%) Tule Greater White-fronted Geese nested > 75 m from open water ponds or lakes, and many nested in wetlands with little or no open water. Tule Greater White-fronted Geese nest only in a small breeding area near the most human-impacted area of the state, and continued development may limit the use of suitable nesting habitat.

Baseline plasma corticosterone, haematological and biochemical results in nesting and rehabilitating loggerhead sea turtles (Caretta caretta)

PubMed Central

Flower, Jennifer E.; Norton, Terry M.; Andrews, Kimberly M.; Nelson, Steven E.; Parker, Clare E.; Romero, L. Michael; Mitchell, Mark A.

2015-01-01

The evaluation of hormonal responses to stress in reptiles relies on acquisition of baseline corticosterone concentrations; however, the stress associated with the restraint needed to collect the blood samples can affect the results. The purpose of this study was to determine a time limit for the collection of blood samples to evaluate baseline corticosterone, haematological and biochemical results in nesting (n = 11) and rehabilitating (n = 16) loggerhead sea turtles (Caretta caretta). Blood samples were collected from the dorsal cervical sinus of each turtle immediately after touching the animal (t0; 0–3 min) and 3 (t3; 3–6 min), 6 (t6; 6–9 min; nesting turtles only), 10 (t10; 10–13 min) and 30 min (t30; rehabilitating turtles only) after the initial hands-on time. Consistent between the rehabilitating and nesting turtles, there was a subtle yet significant increase in white blood cell counts over time. Despite the fact that white blood cell counts increased during the sampling period, there was no direct correlation between white blood cell count and corticosterone in the sampled turtles. In the nesting turtles, significant elevations in corticosterone were noted between t0 and t3 (P = 0.014) and between t0 and t6 (P = 0.022). Values at t10 were not significantly different from those at t0 (P = 0.102); however, there was a trend for the corticosterone values to continue to increase. These results suggest that sampling of nesting loggerhead sea turtles within 3 min of handling will provide baseline corticosterone concentrations in their natural environment. Significant elevations in corticosterone were also noted in the rehabilitating loggerhead sea turtles between t0 and t10 (P = 0.02) and between t0 and t30 of sampling (P = 0.0001). These results suggest that sampling of loggerhead sea turtles within 6 min of handling should provide baseline corticosterone concentrations in a rehabilitation setting. The delay in the corticosterone response noted in the rehabilitating turtles may be associated with the daily contact (visual or direct) they have with their human caretakers. PMID:27293688

Nest site characteristics, nesting movements, and lack of long-term nest site fidelity in Agassiz's desert tortoises at a wind energy facility in southern California

USGS Publications Warehouse

Lovich, Jeffrey E.; Agha, Mickey; Yackulic, Charles B.; Meyer-Wilkins, Kathie; Bjurlin, Curtis; Ennen, Joshua R.; Arundel, Terry R.; Austin, Meaghan

2014-01-01

Nest site selection has important consequences for maternal and offspring survival and fitness. Females of some species return to the same nesting areas year after year. We studied nest site characteristics, fidelity, and daily pre-nesting movements in a population of Agassiz’s desert tortoises (Gopherus agassizii) at a wind energy facility in southern California during two field seasons separated by over a decade. No females returned to the same exact nest site within or between years but several nested in the same general area. However, distances between first and second clutches within a year (2000) were not significantly different from distances between nests among years (2000 and 2011) for a small sample of females, suggesting some degree of fidelity within their normal activity areas. Environmental attributes of nest sites did not differ significantly among females but did among years due largely to changes in perennial plant structure as a result of multiple fires. Daily pre-nesting distances moved by females decreased consistently from the time shelled eggs were first visible in X-radiographs until oviposition, again suggesting some degree of nest site selection. Tortoises appear to select nest sites that are within their long-term activity areas, inside the climate-moderated confines of one of their self-constructed burrows, and specifically, at a depth in the burrow that minimizes exposure of eggs and embryos to lethal incubation temperatures. Nesting in “climate-controlled” burrows and nest guarding by females relaxes some of the constraints that drive nest site selection in other oviparous species.

Flexible social organization and high incidence of drifting in the sweat bee, Halictus scabiosae.

PubMed

Ulrich, Yuko; Perrin, Nicolas; Chapuisat, Michel

2009-04-01

The very diverse social systems of sweat bees make them interesting models to study social evolution. Here we focus on the dispersal behaviour and social organization of Halictus scabiosae, a common yet poorly known species of Europe. By combining field observations and genetic data, we show that females have multiple reproductive strategies, which generates a large diversity in the social structure of nests. A detailed microsatellite analysis of 60 nests revealed that 55% of the nests contained the offspring of a single female, whereas the rest had more complex social structures, with three clear cases of multiple females reproducing in the same nest and frequent occurrence of unrelated individuals. Drifting among nests was surprisingly common, as 16% of the 122 nests in the overall sample and 44% of the nests with complex social structure contained females that had genotypes consistent with being full-sisters of females sampled in other nests of the population. Drifters originated from nests with an above-average productivity and were unrelated to their nestmates, suggesting that drifting might be a strategy to avoid competition among related females. The sex-specific comparison of genetic differentiation indicated that dispersal was male-biased, which would reinforce local resource competition among females. The pattern of genetic differentiation among populations was consistent with a dynamic process of patch colonization and extinction, as expected from the unstable, anthropogenic habitat of this species. Overall, our data show that H. scabiosae varies greatly in dispersal behaviour and social organization. The surprisingly high frequency of drifters echoes recent findings in wasps and bees, calling for further investigation of the adaptive basis of drifting in the social insects.

Laser Microdissection and Atmospheric Pressure Chemical Ionization Mass Spectrometry Coupled for Multimodal Imaging

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

Lorenz, Matthias; Ovchinnikova, Olga S; Kertesz, Vilmos

2013-01-01

This paper describes the coupling of ambient laser ablation surface sampling, accomplished using a laser capture microdissection system, with atmospheric pressure chemical ionization mass spectrometry for high spatial resolution multimodal imaging. A commercial laser capture microdissection system was placed in close proximity to a modified ion source of a mass spectrometer designed to allow for sampling of laser ablated material via a transfer tube directly into the ionization region. Rhodamine 6G dye of red sharpie ink in a laser etched pattern as well as cholesterol and phosphatidylcholine in a cerebellum mouse brain thin tissue section were identified and imaged frommore » full scan mass spectra. A minimal spot diameter of 8 m was achieved using the 10X microscope cutting objective with a lateral oversampling pixel resolution of about 3.7 m. Distinguishing between features approximately 13 m apart in a cerebellum mouse brain thin tissue section was demonstrated in a multimodal fashion including co-registered optical and mass spectral chemical images.« less

[A study on identification of edible bird's nests by DNA barcodes].

PubMed

Chen, Yue-Juan; Liu, Wen-Jian; Chen, Dan-Na; Chieng, Sing-Hock; Jiang, Lin

2017-12-01

To provide theoretical basis for the traceability and quality evaluation of edible bird's nests (EBNs), the Cytb sequence was applied to identify the origin of EBNs. A total of 39 experiment samples were collected from Malaysia, Indonesia, Vietnam and Thailand. Genomic DNA was extracted for the PCR reaction. The amplified products were sequenced. 36 sequences were downloaded from Gen Bank including edible nest swiftlet, black nest swiftlet, mascarene swiftlet, pacific swiftlet and germain's swiftlet. MEGA 7.0 was used to analyze the distinction of sequences by the method of calculating the distances in intraspecific and interspecific divergences and constructing NJ and UPMGA phylogenetic tree based on Kimera-2-parameter model. The results showed that 39 samples were from three kinds of EBNs. Interspecific divergences were significantly greater than the intraspecific one. Samples could be successfully distinguished by NJ and UPMGA phylogenetic tree. In conclusion, Cytb sequence could be used to distinguish the origin of EBNs and it is efficient for tracing the origin species of EBNs. Copyright© by the Chinese Pharmaceutical Association.

Multimode optical dermoscopy (SkinSpect) analysis for skin with melanocytic nevus

NASA Astrophysics Data System (ADS)

Vasefi, Fartash; MacKinnon, Nicholas; Saager, Rolf; Kelly, Kristen M.; Maly, Tyler; Chave, Robert; Booth, Nicholas; Durkin, Anthony J.; Farkas, Daniel L.

2016-04-01

We have developed a multimode dermoscope (SkinSpect™) capable of illuminating human skin samples in-vivo with spectrally-programmable linearly-polarized light at 33 wavelengths between 468nm and 857 nm. Diffusely reflected photons are separated into collinear and cross-polarized image paths and images captured for each illumination wavelength. In vivo human skin nevi (N = 20) were evaluated with the multimode dermoscope and melanin and hemoglobin concentrations were compared with Spatially Modulated Quantitative Spectroscopy (SMoQS) measurements. Both systems show low correlation between their melanin and hemoglobin concentrations, demonstrating the ability of the SkinSpect™ to separate these molecular signatures and thus act as a biologically plausible device capable of early onset melanoma detection.

[Contribution of nested PCR in the diagnosis of imported malaria in southern Algeria].

PubMed

Bouiba, L; Gassen, B; Gasmi, M; Hammadi, D; Harrat, Z

2016-12-01

The nested PCR was used to estimate its inputs in malaria diagnosis and in the performance of the microscope operators involved in the surveillance of malaria in remote areas of South Algeria. For the period 2010 to 2015, 112 patients (93 febrile and 19 asymptomatic) coming from sub-Saharan Africa were tested for malaria in the hospital of Tamanrasset. One part of the blood taken from fingertip was used for blood smears and the second part was absorbed in filter paper for molecular diagnosis. Overall, the infection was detected by nested PCR in 63 samples versus 53 by direct examination. In addition, 11 mixed infections and 6 positive asymptomatic cases not detected by microscopy were diagnosed by PCR. Moreover, two negative samples in nested PCR were tested positive by direct examination. The molecular tool is more sensitive than the direct examination in detecting infra-microscopic parasitaemia and mixed infections...

Quantification of periodontal pathogens in vascular, blood, and subgingival samples from patients with peripheral arterial disease or abdominal aortic aneurysms.

PubMed

Figuero, Elena; Lindahl, Christeel; Marín, María José; Renvert, Stefan; Herrera, David; Ohlsson, Ola; Wetterling, Thomas; Sanz, Mariano

2014-09-01

The aim of this investigation is to quantify periodontal pathogens (Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Campylobacter rectus, and Tannerella forsythia) in vascular, blood, and subgingival samples. As a secondary objective, two molecular bacterial identification methods (nested polymerase chain reaction [PCR] and quantitative PCR [qPCR]) are compared. Seventy consecutive patients provided a vascular lesion, a blood sample, and 36 subgingival samples. Bacterial DNA was extracted, and qPCR was used to determine the prevalence and amounts of the target pathogens in each sample. Nested PCR was performed only in the samples from vascular lesions. Periodontal examination was performed in 42 patients. Mann-Whitney U or χ(2) tests were used to compare microbiologic results according to periodontal diagnosis. All targeted periodontal pathogens (A. actinomycetemcomitans, P. gingivalis, T. forsythia, or C. rectus) were detected in subgingival samples, with a prevalence rate of 72.2%, 47.2%, 74.3%, and 82.9%, respectively. In 7.1% and 11.4% of vascular and blood samples, bacterial DNA was detected. One patient was positive for A. actinomycetemcomitans in the three types of samples. No differences were found in the levels of targeted bacteria when comparing patients with and without periodontitis. Prevalence rates obtained with nested PCR were significantly higher than those obtained with qPCR. The presence of A. actinomycetemcomitans was demonstrated in vascular, blood, and subgingival samples in one of 36 patients. These results, although with a very low frequency, may support the hypothesis of a translocation of periodontal pathogens from subgingival microbiota to the bloodstream and then to atheromatous plaques in carotid or other peripheral arteries. Nested PCR is not an adequate method for identifying DNA of periodontal pathogens in low quantities because of the high number of false-negative results.

Nest size is predicted by female identity and the local environment in the blue tit (Cyanistes caeruleus), but is not related to the nest size of the genetic or foster mother

PubMed Central

Parker, Timothy H.; Griffith, Simon C.

2018-01-01

The potential for animals to respond to changing climates has sparked interest in intraspecific variation in avian nest structure since this may influence nest microclimate and protect eggs and offspring from inclement weather. However, there have been relatively few large-scale attempts to examine variation in nests or the determinates of individual variation in nest structure within populations. Using a set of mostly pre-registered analyses, we studied potential predictors of variation in the size of a large sample (803) of blue tit (Cyanistes caeruleus) nests across three breeding seasons at Wytham Woods, UK. While our pre-registered analyses found that individual females built very similar nests across years, there was no evidence in follow-up (post hoc) analyses that their nest size correlated to that of their genetic mother or, in a cross-fostering experiment, to the nest where they were reared. In further pre-registered analyses, spatial environmental variability explained nest size variability at relatively broad spatial scales, and especially strongly at the scale of individual nest boxes. Our study indicates that nest structure is a characteristic of individuals, but is not strongly heritable, indicating that it will not respond rapidly to selection. Explaining the within-individual and within-location repeatability we observed requires further study. PMID:29765658

Cancer-associated autoantibodies to MUC1 and MUC4--a blinded case–control study of colorectal cancer in UK collaborative trial of ovarian cancer screening.

PubMed

Pedersen, Johannes W; Gentry-Maharaj, Aleksandra; Nøstdal, Alexander; Fourkala, Evangelia-Ourania; Dawnay, Anne; Burnell, Matthew; Zaikin, Alexey; Burchell, Joy; Papadimitriou, Joyce Taylor; Clausen, Henrik; Jacobs, Ian; Menon, Usha; Wandall, Hans H

2014-05-01

Recent reports suggest that autoantibodies directed to aberrantly glycosylated mucins, in particular MUC1 and MUC4, are found in patients with colorectal cancer. There is, however, limited information on the autoantibody levels before clinical diagnosis, and their utility in cancer screening in the general population. In our study, we have generated O-glycosylated synthetic MUC1 and MUC4 peptides in vitro, to mimic cancer-associated glycoforms, and displayed these on microarrays. The assay's performance was tested through an initial screening of serum samples taken from patients at the time of colorectal cancer diagnosis and healthy controls. Subsequently, the selected biomarkers were evaluated in a blinded nested case–control study using stored serum samples from among the 50,640 women randomized to the multimodal arm of the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS), where women gave annual blood samples for several years. Cases were 97 postmenopausal women who developed colorectal cancer after recruitment and were age-matched to 97 women without any history of cancer. MUC1-STn and MUC1-Core3 IgG autoantibodies identified cases with 8.2 and 13.4% sensitivity, respectively, at 95% specificity. IgA to MUC4 glycoforms were unable to discriminate between cases and controls in the UKCTOCS sera. Additional analysis was undertaken by combining the data of MUC1-STn and MUC1-Core3 with previously generated data on autoantibodies to p53 peptides, which increased the sensitivity to 32.0% at 95% specificity. These findings suggest that a combination of antibody signatures may have a role as part of a biomarker panel for the early detection of colorectal cancer.

Analysis of sugarcane herbicides in marine turtle nesting areas and assessment of risk using in vitro toxicity assays.

PubMed

Allan, Hannah L; van de Merwe, Jason P; Finlayson, Kimberly A; O'Brien, Jake W; Mueller, Jochen F; Leusch, Frederic D L

2017-10-01

Agricultural processes are associated with many different herbicides that can contaminate surrounding environments. In Queensland, Australia, herbicides applied to agricultural crops may pose a threat to valuable coastal habitats including nesting beaches for threatened loggerhead turtles (Caretta caretta). This study 1) measured concentrations of herbicides in the beach sand of Mon Repos, an important marine turtle nesting beach in Australia that is adjacent to significant sugarcane crops, and 2) investigated the toxicity of these herbicides to marine turtles using a cell-based assay. Samples of sand from turtle nest depth and water from surrounding agricultural drains and wetlands were collected during the wet season when herbicide runoff was expected to be the greatest and turtles were nesting. Samples were extracted using solid phase extraction and extracts were analysed using chemical analysis targeting herbicides, as well as bioanalytical techniques (IPAM-assay and loggerhead turtle skin cell cytotoxicity assay). Twenty herbicides were detected in areas between sugarcane crops and the nesting beach, seven of which were also detected in the sand extracts. Herbicides present in the nearby wetland were also detected in the beach sand, indicating potential contamination of the nesting beach via the river outlet as well as ground water. Although herbicides were detected in nesting sand, bioassays using loggerhead turtle skin cells indicated a low risk of acute toxicity at measured environmental concentrations. Further research should investigate potentially more subtle effects, such as endocrine disruption and mixture effects, to better assess the threat that herbicides pose to this population of marine turtles. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Investigation of Coxiella burnetii contamination in commercial milk and PCR method for the detection of C. burnetii in egg].

PubMed

Hirai, Akihiko; Kaneko, Seiji; Nakama, Akiko; Ishizaki, Naoto; Odagiri, Megumi; Kai, Akemi; Sadamasu, Kenji; Shinkai, Takayuki; Yano, Kazuyoshi; Morozumi, Satoshi

2005-06-01

A total of 244 milk samples collected from supermarkets in Tokyo were examined for contamination with Coxiella burnetii. C. burnetii DNA was detected in 131 (53.7%) of the samples by nested PCR. PCR-positive samples were injected into immunosuppressed A/J strain mice. Of the 22 PCR-positive milk samples tested, none resulted in isolation of C. burnetii from the mice. Heat-treatment was sufficient to inactivate C. burnetii in commercial milk. In addition, a PCR detection method for C. burnetii in chicken egg was developed. Egg yolk was added to an equal volume of 1 mol/L of NaCl phosphate buffer and homogenized for removal of protein and lipid. After centrifugal separation, the supernatant was removed, and template DNA in the precipitate was extracted using SDS, proteinase K and NaI. Using such prepared samples, 3.2 x 10(1) C. burnetii particles in 1 g of egg yolk could be detected by nested PCR. All of 200 chicken egg samples collected from supermarkets in Tokyo were negative for C. burnetii by the nested PCR method.

Nest-site fidelity and dispersal of Gyrfalcons estimated by noninvasive genetic sampling

USGS Publications Warehouse

Booms, T.L.; Talbot, S.L.; Sage, G.K.; McCaffery, B.J.; McCracken, K.G.; Schempf, P.F.

2011-01-01

We used feathers from adult Gyrfalcons (Falco rusticolus) molted in breeding territories and blood samples from nestlings to document nest-site fidelity and dispersal of breeding adults and juveniles at three areas 100- 350 km apart in Yukon Delta National Wildlife Refuge, Alaska, 2003-2007. We used genotypes from seven polymorphic microsatellite loci that provided a mean probability of identity of 0.91 ??10 -5. Breeding Gyrfalcons were highly faithful to study area and territory; we documented no dispersals of breeding birds among study areas and only one dispersal between territories. But their fidelity to nest sites was low; 22% of birds returned to the same nest site the following year. Distance among alternate nests within a territory averaged 750 m and was similar for both sexes. Mean tenure in a territory was 2.8 years, similar for both sexes, and distributed bimodally with peaks at 1 and 4 years. Mean annual turnover rate at the Ingakslugwat Hills (Volcanoes) study area was 20%. We detected three young that established breeding territories at distances ranging from 0 to 254 km from their natal territory, representing 2.5% apparent recruitment. Gyrfalcons in the Askinuk Mountains study area were slightly but statistically significantly differentiated genetically from those in the Volcanoes and Kilbuck Mountain study areas. These data are the first published on the nest-site fidelity, breeding dispersal, and natal dispersal of the Gyrfalcon in North America and demonstrate the utility of noninvasive genetic sampling to greatly improve our understanding of avian dispersal and its underlying mechanisms. ?? The Cooper Ornithological Society 2011.

Changes in gonadal and adrenal steroid levels in the leatherback sea turtle (Dermochelys coriacea) during the nesting cycle.

PubMed

Rostal, D C; Grumbles, J S; Palmer, K S; Lance, V A; Spotila, J R; Paladino, F V

2001-05-01

The reproductive endocrinology of nesting leatherback turtles (Dermochelys coriacea) was studied during the 1996-1997 and 1997-1998 nesting seasons at Los Baulas National Park, Playa Grande, Costa Rica. Blood samples were collected from nesting females throughout the season. Females were observed to nest up to 10 times during the nesting season. Plasma steroids were measured by radioimmunoassay and total plasma calcium was measured by flame atomic absorption spectrophotometry. Plasma testosterone and plasma estradiol levels declined throughout the nesting cycle of the female. Testosterone declined from a mean of 10.18 +/- 0.77 ng/ml at the beginning of the nesting cycle to 1.73 +/- 0.34 ng/ml at the end of the nesting cycle. Estradiol declined in a similar manner, ranging from a mean of 190.95 +/- 16.80 pg/ml at the beginning of the nesting cycle to 76.52 +/- 12.66 pg/ml at the end of the nesting cycle. Plasma progesterone and total calcium levels were relatively constant throughout the nesting cycle. Lack of fluctuation of total calcium levels, ranging from a mean high of 97.46 +/- 11.37 microg/ml to a mean low of 64.85 +/- 11.20 microg/ml, further suggests that vitellogenesis is complete prior to the arrival of the female at the nesting beach. Clutch size (both yolked and yolkless eggs) did not vary over the course of the nesting cycle. Copyright 2001 Academic Press.

ADAPTIVE ANNEALED IMPORTANCE SAMPLING FOR MULTIMODAL POSTERIOR EXPLORATION AND MODEL SELECTION WITH APPLICATION TO EXTRASOLAR PLANET DETECTION

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

Liu, Bin, E-mail: bins@ieee.org

2014-07-01

We describe an algorithm that can adaptively provide mixture summaries of multimodal posterior distributions. The parameter space of the involved posteriors ranges in size from a few dimensions to dozens of dimensions. This work was motivated by an astrophysical problem called extrasolar planet (exoplanet) detection, wherein the computation of stochastic integrals that are required for Bayesian model comparison is challenging. The difficulty comes from the highly nonlinear models that lead to multimodal posterior distributions. We resort to importance sampling (IS) to estimate the integrals, and thus translate the problem to be how to find a parametric approximation of the posterior.more » To capture the multimodal structure in the posterior, we initialize a mixture proposal distribution and then tailor its parameters elaborately to make it resemble the posterior to the greatest extent possible. We use the effective sample size (ESS) calculated based on the IS draws to measure the degree of approximation. The bigger the ESS is, the better the proposal resembles the posterior. A difficulty within this tailoring operation lies in the adjustment of the number of mixing components in the mixture proposal. Brute force methods just preset it as a large constant, which leads to an increase in the required computational resources. We provide an iterative delete/merge/add process, which works in tandem with an expectation-maximization step to tailor such a number online. The efficiency of our proposed method is tested via both simulation studies and real exoplanet data analysis.« less

A rapid single-tube protocol for HAV detection by nested real-time PCR.

PubMed

Hu, Yuan; Arsov, Ivica

2014-09-01

Infections by food-borne viruses such as hepatitis A virus (HAV) and norovirus are significant public health concerns worldwide. Since food-borne viruses are rarely confirmed through direct isolation from contaminated samples, highly sensitive molecular techniques remain the methods of choice for the detection of viral genetic material. Our group has previously developed a specific nested real-time PCR (NRT-PCR) assay for HAV detection that improved overall sensitivity. Furthermore in this study, we have developed a single-tube NRT-PCR approach for HAV detection in food samples that reduces the likelihood of cross contamination between tubes during sample manipulation. HAV RNA was isolated from HAV-spiked food samples and HAV-infected cell cultures. All reactions following HAV RNA isolation, including conventional reverse transcriptase PCR, nested-PCR, and RT-PCR were performed in a single tube. Our results demonstrated that all the samples tested positive by RT-PCR and nested-PCR were also positive by a single-tube NRT-PCR. The detection limits observed for HAV-infected cell cultures and HAV-spiked green onions were 0.1 and 1 PFU, respectively. This novel method retained the specificity and robustness of the original NRT-PCR method, while greatly reducing sample manipulation, turnaround time, and the risk of carry-over contamination. Single-tube NRT-PCR thus represents a promising new tool that can potentially facilitate the detection of HAV in foods thereby improving food safety and public health.

Whole blood Nested PCR and Real-time PCR amplification of Talaromyces marneffei specific DNA for diagnosis.

PubMed

Lu, Sha; Li, Xiqing; Calderone, Richard; Zhang, Jing; Ma, Jianchi; Cai, Wenying; Xi, Liyan

2016-02-01

Talaromyces marneffei is a dimorphic pathogenic fungus, which is a life-threatening invasive mycosis in the immunocompromised host. Prompt diagnosis of T. marneffei infection remains difficult although there has been progress in attempts to expedite the diagnosis of this infection. We previously demonstrated the value of nested polymerase chain reaction (PCR) to detect T. marneffei in paraffin embedded tissue samples with high sensitivity and specificity. In this study, this assay was used to detect the DNA of T. marneffei in whole blood samples. Real-time PCR assay was also evaluated to identify T. marneffei in the same samples. Twenty out of 30 whole blood samples (67%) collected from 23 patients were found positive by using the nested PCR assay, while 23/30 (77%) samples were found positive by using the real-time PCR assay. In order to express accurately the fungal loads, we used a normalized linearized plasmid as an internal control for real-time PCR. The assay results were correlated as the initial quantity (copies/μl) with fungal burden. These data indicate that combination of nested PCR and real-time PCR assay provides an attractive alternative for identification of T. marneffei DNA in whole blood samples of HIV-infected patients. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Impact of human cytomegalovirus infection UL55-nested polymerase chain reaction method in hematopoietic stem cell transplant donors and recipients.

PubMed

Banan, A A; Yaghobi, R; Ramzi, M; Mehrabani, D

2009-09-01

Human cytomegalovirus (HCMV) is one of the most important and critical viral causes of graft rejection among hematopoietic stem cell transplant (HSCT) recipients. Monitoring of this viral infection has a critical role in the management of HSCT clinical complications. In this retrospective cohort, blood (plasma and buffy coat) and urine samples were collected from 110 HSCT patients and 95 donors pretransplantation and weekly for 100 days posttransplantation. An HCMV-optimized UL55-nested polymerase chain reaction (PCR) method was used to detect HCMV infection. Genotyping of the HCMV UL55 gene was performed for all UL55-nested, PCR-positive samples. HSCT donor and recipient laboratory and clinical data were statistically analyzed using SPSS version 15 software. UL55-nested, PCR-positive results were obtained in 3540/4950 (71.5%), 3634/4950 (73.4%), and 3292/4950 (66.5%) of these plasma, buffy coat, and urine samples, respectively. Twenty-five percent of transplant donors were infected with HCMV. An increase in HCMV infection was observed from pre- to post-HSCT conditions. Detection of the gB2 UL55 genotype in most transplant patient samples suggested the need to examine the possible impact of HCMV UL55 genotypes and HCMV infections among stem cell transplant recipients.

Multimode waveguide speckle patterns for compressive sensing.

PubMed

Valley, George C; Sefler, George A; Justin Shaw, T

2016-06-01

Compressive sensing (CS) of sparse gigahertz-band RF signals using microwave photonics may achieve better performances with smaller size, weight, and power than electronic CS or conventional Nyquist rate sampling. The critical element in a CS system is the device that produces the CS measurement matrix (MM). We show that passive speckle patterns in multimode waveguides potentially provide excellent MMs for CS. We measure and calculate the MM for a multimode fiber and perform simulations using this MM in a CS system. We show that the speckle MM exhibits the sharp phase transition and coherence properties needed for CS and that these properties are similar to those of a sub-Gaussian MM with the same mean and standard deviation. We calculate the MM for a multimode planar waveguide and find dimensions of the planar guide that give a speckle MM with a performance similar to that of the multimode fiber. The CS simulations show that all measured and calculated speckle MMs exhibit a robust performance with equal amplitude signals that are sparse in time, in frequency, and in wavelets (Haar wavelet transform). The planar waveguide results indicate a path to a microwave photonic integrated circuit for measuring sparse gigahertz-band RF signals using CS.

Phenology largely explains taller grass at successful nests in greater sage-grouse.

PubMed

Smith, Joseph T; Tack, Jason D; Doherty, Kevin E; Allred, Brady W; Maestas, Jeremy D; Berkeley, Lorelle I; Dettenmaier, Seth J; Messmer, Terry A; Naugle, David E

2018-01-01

Much interest lies in the identification of manageable habitat variables that affect key vital rates for species of concern. For ground-nesting birds, vegetation surrounding the nest may play an important role in mediating nest success by providing concealment from predators. Height of grasses surrounding the nest is thought to be a driver of nest survival in greater sage-grouse ( Centrocercus urophasianus ; sage-grouse), a species that has experienced widespread population declines throughout their range. However, a growing body of the literature has found that widely used field methods can produce misleading inference on the relationship between grass height and nest success. Specifically, it has been demonstrated that measuring concealment following nest fate (failure or hatch) introduces a temporal bias whereby successful nests are measured later in the season, on average, than failed nests. This sampling bias can produce inference suggesting a positive effect of grass height on nest survival, though the relationship arises due to the confounding effect of plant phenology, not an effect on predation risk. To test the generality of this finding for sage-grouse, we reanalyzed existing datasets comprising >800 sage-grouse nests from three independent studies across the range where there was a positive relationship found between grass height and nest survival, including two using methods now known to be biased. Correcting for phenology produced equivocal relationships between grass height and sage-grouse nest survival. Viewed in total, evidence for a ubiquitous biological effect of grass height on sage-grouse nest success across time and space is lacking. In light of these findings, a reevaluation of land management guidelines emphasizing specific grass height targets to promote nest success may be merited.

Numerical modelling of multimode fibre-optic communication lines

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

Sidelnikov, O S; Fedoruk, M P; Sygletos, S

The results of numerical modelling of nonlinear propagation of an optical signal in multimode fibres with a small differential group delay are presented. It is found that the dependence of the error vector magnitude (EVM) on the differential group delay can be reduced by increasing the number of ADC samples per symbol in the numerical implementation of the differential group delay compensation algorithm in the receiver. The possibility of using multimode fibres with a small differential group delay for data transmission in modern digital communication systems is demonstrated. It is shown that with increasing number of modes the strong couplingmore » regime provides a lower EVM level than the weak coupling one. (fibre-optic communication lines)« less

Field Testing New Plot Designs and Methods for Determining Hydrophytic Vegetation during Wetland Delineations in the United States

DTIC Science & Technology

2014-03-01

Trees and woody vines are sampled in large plots with 9 m (30 ft) radii. Saplings, shrubs , and herbs are sampled in nested smaller plots with 2 m (5 ft... woody vines in 9 m (30 ft) radius plots and saplings, shrubs , and herbaceous species in 2 m (5 ft) radius plots. In herbaceous meadows, only the 2 m (5...suggests stratifying vegetation by growth forms of trees, shrubs , herbs, and vines and sampling plant communities by using nested circular plots

Detection of environmental sources of Histoplasma capsulatum in Chiang Mai, Thailand, by nested PCR.

PubMed

Norkaew, Treepradab; Ohno, Hideaki; Sriburee, Pojana; Tanabe, Koichi; Tharavichitkul, Prasit; Takarn, Piyawan; Puengchan, Tanpalang; Bumrungsri, Sara; Miyazaki, Yoshitsugu

2013-12-01

Histoplasmosis is a systemic mycosis caused by inhaling spores of Histoplasma capsulatum, a dimorphic fungus. This fungus grows in soil contaminated with bat and avian excreta. Each year, patients with disseminated histoplasmosis have been diagnosed in Chiang Mai, northern Thailand. No published information is currently available on the environmental sources of this fungus in Chiang Mai or anywhere else in Thailand. The aim of this study was to detect H. capsulatum in soil samples contaminated with bat guano and avian droppings by nested PCR. Two hundred and sixty-five samples were collected from the following three sources: soil contaminated with bat guano, 88 samples; soil contaminated with bird droppings, 86 samples; and soil contaminated with chicken droppings, 91 samples. Genomic DNA was directly extracted from each sample, and H. capsulatum was detected by nested PCR using a primer set specific to a gene encoding 100-kDa-like protein (HcI, HcII and HcIII, HcIV). Histoplasma capsulatum was detected in seven of 88 soil samples contaminated with bat guano, one of 21 soil samples contaminated with pigeon droppings and 10 of 91 soil samples contaminated with chicken droppings. The results indicate the possibility of the association of bat guano and chicken droppings with H. capsulatum in this area of Thailand.

Microplastic at nesting grounds used by the northern Gulf of Mexico loggerhead recovery unit.

PubMed

Beckwith, Valencia K; Fuentes, Mariana M P B

2018-06-01

Microplastics can impact key habitats used by endangered species, such as marine turtles. They impact the environment by transporting toxicants and altering sediment properties affecting temperature and sediment permeability. Our study determined the exposure of the ten most important nesting sites for the Northern Gulf of Mexico Loggerhead Recovery Unit to microplastic. Sand samples were obtained at each nesting site during the 2017 nesting season and analyzed for abundance and characteristics of microplastic. Microplastic was found at all sites, with an average abundance of 61.08 ± 34.61 pieces/m 2 , and 59.9% located at the dunes, where turtles primarily nest. A gradual decrease in microplastics abundance was observed from the most western nesting ground to the east. The results from this study indicate that microplastic accumulation on nesting sites for the Northern Gulf of Mexico may be of great concern, and could negatively affect the incubating environment for marine turtles. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

PubMed

Al-Harthi, Saeed A

2015-12-01

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

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

PubMed

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

2015-07-19

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

AN EVALUATION OF PRIMARY DATA-COLLECTION MODES IN AN ADDRESS-BASED SAMPLING DESIGN.

PubMed

Amaya, Ashley; Leclere, Felicia; Carris, Kari; Liao, Youlian

2015-01-01

As address-based sampling becomes increasingly popular for multimode surveys, researchers continue to refine data-collection best practices. While much work has been conducted to improve efficiency within a given mode, additional research is needed on how multimode designs can be optimized across modes. Previous research has not evaluated the consequences of mode sequencing on multimode mail and phone surveys, nor has significant research been conducted to evaluate mode sequencing on a variety of indicators beyond response rates. We conducted an experiment within the Racial and Ethnic Approaches to Community Health across the U.S. Risk Factor Survey (REACH U.S.) to evaluate two multimode case-flow designs: (1) phone followed by mail (phone-first) and (2) mail followed by phone (mail-first). We compared response rates, cost, timeliness, and data quality to identify differences across case-flow design. Because surveys often differ on the rarity of the target population, we also examined whether changes in the eligibility rate altered the choice of optimal case flow. Our results suggested that, on most metrics, the mail-first design was superior to the phone-first design. Compared with phone-first, mail-first achieved a higher yield rate at a lower cost with equivalent data quality. While the phone-first design initially achieved more interviews compared to the mail-first design, over time the mail-first design surpassed it and obtained the greatest number of interviews.

Detection of oral HPV infection - Comparison of two different specimen collection methods and two HPV detection methods.

PubMed

de Souza, Marjorie M A; Hartel, Gunter; Whiteman, David C; Antonsson, Annika

2018-04-01

Very little is known about the natural history of oral HPV infection. Several different methods exist to collect oral specimens and detect HPV, but their respective performance characteristics are unknown. We compared two different methods for oral specimen collection (oral saline rinse and commercial saliva kit) from 96 individuals and then analyzed the samples for HPV by two different PCR detection methods (single GP5+/6+ PCR and nested MY09/11 and GP5+/6+ PCR). For the oral rinse samples, the oral HPV prevalence was 10.4% (GP+ PCR; 10% repeatability) vs 11.5% (nested PCR method; 100% repeatability). For the commercial saliva kit samples, the prevalences were 3.1% vs 16.7% with the GP+ PCR vs the nested PCR method (repeatability 100% for both detection methods). Overall the agreement was fair or poor between samples and methods (kappa 0.06-0.36). Standardizing methods of oral sample collection and HPV detection would ensure comparability between future oral HPV studies. Copyright © 2017 Elsevier Inc. All rights reserved.

BRAZILIAN CONSENSUS FOR MULTIMODAL TREATMENT OF COLORECTAL LIVER METASTASES. MODULE 3: CONTROVERSIES AND UNRESECTABLE METASTASES.

PubMed

Torres, Orlando Jorge Martins; Marques, Márcio Carmona; Santos, Fabio Nasser; Farias, Igor Correia de; Coutinho, Anelisa Kruschewsky; Oliveira, Cássio Virgílio Cavalcante de; Kalil, Antonio Nocchi; Mello, Celso Abdon Lopes de; Kruger, Jaime Arthur Pirola; Fernandes, Gustavo Dos Santos; Quireze, Claudemiro; Murad, André M; Silva, Milton José de Barros E; Zurstrassen, Charles Edouard; Freitas, Helano Carioca; Cruz, Marcelo Rocha; Weschenfelder, Rui; Linhares, Marcelo Moura; Castro, Leonaldson Dos Santos; Vollmer, Charles; Dixon, Elijah; Ribeiro, Héber Salvador de Castro; Coimbra, Felipe José Fernandez

2016-01-01

In the last module of this consensus, controversial topics were discussed. Management of the disease after progression during first line chemotherapy was the first discussion. Next, the benefits of liver resection in the presence of extra-hepatic disease were debated, as soon as, the best sequence of treatment. Conversion chemotherapy in the presence of unresectable liver disease was also discussed in this module. Lastly, the approach to the unresectable disease was also discussed, focusing in the best chemotherapy regimens and hole of chemo-embolization. RESUMO Neste último módulo do consenso, abordou-se alguns temas controversos. O primeiro tópico discutido foi o manejo da doença após progressão na primeira linha de quimioterapia, com foco em se ainda haveria indicação cirúrgica neste cenário. A seguir, o painel debruçou-se sobre as situações de ressecção da doença hepática na presença de doença extra-hepática, assim como, qual a melhor sequência de tratamento. O tratamento de conversão para doença inicialmente irressecável também foi abordado neste módulo, incluindo as importantes definições de quando se pode esperar que a doença se torne ressecável e quais esquemas terapêuticos seriam mais efetivos à luz dos conhecimentos atuais sobre a biologia tumoral e taxas de resposta objetiva. Por último, o tratamento da doença não passível de ressecção foi discutida, focando-se nos melhores esquemas a serem empregados e seu sequenciamento, bem como o papel da quimioembolização no manejo destes pacientes.

Arboreal Ant Colonies as ‘Hot-Points’ of Cryptic Diversity for Myrmecophiles: The Weaver Ant Camponotus sp. aff. textor and Its Interaction Network with Its Associates

PubMed Central

Pérez-Lachaud, Gabriela; Lachaud, Jean-Paul

2014-01-01

Introduction Systematic surveys of macrofaunal diversity within ant colonies are lacking, particularly for ants nesting in microhabitats that are difficult to sample. Species associated with ants are generally small and rarely collected organisms, which makes them more likely to be unnoticed. We assumed that this tendency is greater for arthropod communities in microhabitats with low accessibility, such as those found in the nests of arboreal ants that may constitute a source of cryptic biodiversity. Materials and Methods We investigated the invertebrate diversity associated with an undescribed, but already threatened, Neotropical Camponotus weaver ant. As most of the common sampling methods used in studies of ant diversity are not suited for evaluating myrmecophile diversity within ant nests, we evaluated the macrofauna within ant nests through exhaustive colony sampling of three nests and examination of more than 80,000 individuals. Results We identified invertebrates from three classes belonging to 18 taxa, some of which were new to science, and recorded the first instance of the co-occurrence of two brood parasitoid wasp families attacking the same ant host colony. This diversity of ant associates corresponded to a highly complex interaction network. Agonistic interactions prevailed, but the prevalence of myrmecophiles was remarkably low. Conclusions Our data support the hypothesis of the evolution of low virulence in a variety of symbionts associated with large insect societies. Because most myrmecophiles found in this work are rare, strictly specific, and exhibit highly specialized biology, the risk of extinction for these hitherto unknown invertebrates and their natural enemies is high. The cryptic, far unappreciated diversity within arboreal ant nests in areas at high risk of habitat loss qualifies these nests as ‘hot-points’ of biodiversity that urgently require special attention as a component of conservation and management programs. PMID:24941047

Development and Validation of an Improved PCR Method Using the 23S-5S Intergenic Spacer for Detection of Rickettsiae in Dermacentor variabilis Ticks and Tissue Samples from Humans and Laboratory Animals

PubMed Central

Kakumanu, Madhavi L.; Ponnusamy, Loganathan; Sutton, Haley T.; Meshnick, Steven R.; Nicholson, William L.

2016-01-01

A novel nested PCR assay was developed to detect Rickettsia spp. in ticks and tissue samples from humans and laboratory animals. Primers were designed for the nested run to amplify a variable region of the 23S-5S intergenic spacer (IGS) of Rickettsia spp. The newly designed primers were evaluated using genomic DNA from 11 Rickettsia species belonging to the spotted fever, typhus, and ancestral groups and, in parallel, compared to other Rickettsia-specific PCR targets (ompA, gltA, and the 17-kDa protein gene). The new 23S-5S IGS nested PCR assay amplified all 11 Rickettsia spp., but the assays employing other PCR targets did not. The novel nested assay was sensitive enough to detect one copy of a cloned 23S-5S IGS fragment from “Candidatus Rickettsia amblyommii.” Subsequently, the detection efficiency of the 23S-5S IGS nested assay was compared to those of the other three assays using genomic DNA extracted from 40 adult Dermacentor variabilis ticks. The nested 23S-5S IGS assay detected Rickettsia DNA in 45% of the ticks, while the amplification rates of the other three assays ranged between 5 and 20%. The novel PCR assay was validated using clinical samples from humans and laboratory animals that were known to be infected with pathogenic species of Rickettsia. The nested 23S-5S IGS PCR assay was coupled with reverse line blot hybridization with species-specific probes for high-throughput detection and simultaneous identification of the species of Rickettsia in the ticks. “Candidatus Rickettsia amblyommii,” R. montanensis, R. felis, and R. bellii were frequently identified species, along with some potentially novel Rickettsia strains that were closely related to R. bellii and R. conorii. PMID:26818674

Development and Validation of an Improved PCR Method Using the 23S-5S Intergenic Spacer for Detection of Rickettsiae in Dermacentor variabilis Ticks and Tissue Samples from Humans and Laboratory Animals.

PubMed

Kakumanu, Madhavi L; Ponnusamy, Loganathan; Sutton, Haley T; Meshnick, Steven R; Nicholson, William L; Apperson, Charles S

2016-04-01

A novel nested PCR assay was developed to detectRickettsiaspp. in ticks and tissue samples from humans and laboratory animals. Primers were designed for the nested run to amplify a variable region of the 23S-5S intergenic spacer (IGS) ofRickettsiaspp. The newly designed primers were evaluated using genomic DNA from 11Rickettsiaspecies belonging to the spotted fever, typhus, and ancestral groups and, in parallel, compared to otherRickettsia-specific PCR targets (ompA,gltA, and the 17-kDa protein gene). The new 23S-5S IGS nested PCR assay amplified all 11Rickettsiaspp., but the assays employing other PCR targets did not. The novel nested assay was sensitive enough to detect one copy of a cloned 23S-5S IGS fragment from "CandidatusRickettsia amblyommii." Subsequently, the detection efficiency of the 23S-5S IGS nested assay was compared to those of the other three assays using genomic DNA extracted from 40 adultDermacentor variabilisticks. The nested 23S-5S IGS assay detectedRickettsiaDNA in 45% of the ticks, while the amplification rates of the other three assays ranged between 5 and 20%. The novel PCR assay was validated using clinical samples from humans and laboratory animals that were known to be infected with pathogenic species ofRickettsia The nested 23S-5S IGS PCR assay was coupled with reverse line blot hybridization with species-specific probes for high-throughput detection and simultaneous identification of the species ofRickettsiain the ticks. "CandidatusRickettsia amblyommii,"R. montanensis,R. felis, andR. belliiwere frequently identified species, along with some potentially novelRickettsiastrains that were closely related toR. belliiandR. conorii. Copyright © 2016 Kakumanu et al.

Comparison of nested-multiplex, Taqman & SYBR Green real-time PCR in diagnosis of amoebic liver abscess in a tertiary health care institute in India

PubMed Central

Dinoop, K.P.; Parija, Subhash Chandra; Mandal, Jharna; Swaminathan, R.P.; Narayanan, P.

2016-01-01

Background & objectives: Amoebiasis is a common parasitic infection caused by Entamoeba histolytica and amoebic liver abscess (ALA) is the most common extraintestinal manifestation of amoebiasis. The aim of this study was to standardise real-time PCR assays (Taqman and SYBR Green) to detect E. histolytica from liver abscess pus and stool samples and compare its results with nested-multiplex PCR. Methods: Liver abscess pus specimens were subjected to DNA extraction. The extracted DNA samples were subjected to amplification by nested-multiplex PCR, Taqman (18S rRNA) and SYBR Green real-time PCR (16S-like rRNA assays to detect E. histolytica/E. dispar/E. moshkovskii). The amplification products were further confirmed by DNA sequence analysis. Receiver operator characteristic (ROC) curve analysis was done for nested-multiplex and SYBR Green real-time PCR and the area under the curve was calculated for evaluating the accuracy of the tests to dignose ALA. Results: In all, 17, 19 and 25 liver abscess samples were positive for E. histolytica by nested-multiplex PCR, SYBR Green and Taqman real-time PCR assays, respectively. Significant differences in detection of E. histolytica were noted in the real-time PCR assays evaluated (P<0.0001). The nested-multiplex PCR, SYBR Green real-time PCR and Taqman real-time PCR evaluated showed a positivity rate of 34, 38 and 50 per cent, respectively. Based on ROC curve analysis (considering Taqman real-time PCR as the gold standard), it was observed that SYBR Green real-time PCR was better than conventional nested-multiplex PCR for the diagnosis of ALA. Interpretation & conclusions: Taqman real-time PCR targeting the 18S rRNA had the highest positivity rate evaluated in this study. Both nested multiplex and SYBR Green real-time PCR assays utilized were evaluated to give accurate results. Real-time PCR assays can be used as the gold standard in rapid and reliable diagnosis, and appropriate management of amoebiasis, replacing the conventional molecular methods. PMID:26997014

Differential parental care by adult Mountain Plovers, Charadrius montanus

USGS Publications Warehouse

Dinsmore, S.J.; Knopf, F.L.

2005-01-01

We studied chick survival of the Mountain Plover (Charadrius montanus) in Montana and found that chicks tended by females had higher survival rates than chicks tended by males, and that chick survival generally increased during the nesting season. Differences in chick survival were most pronounced early in the nesting season, and may be related to a larger sample of nests during this period. When compared to information about the nest survival of male- and female-tended plover nests, our chick data suggest a trade-off for adult plovers between the egg and chick phases of reproduction. Because Mountain Plover pairs have clutches at two nests at two different locations and show differential success between the sexes during the egg and chick phases, we offer that the Mountain Plover breeding system favours optimizing annual recruitment in a dynamic ecologic setting driven by annually unpredictable drought, grazing, and predation pressures.

Use of geostatistics to determine the spatial distribution and infestation rate of leaf-cutting ant nests (Hymenoptera: Formicidae) in eucalyptus plantations.

PubMed

Lasmar, O; Zanetti, R; dos Santos, A; Fernandes, B V

2012-08-01

One of the fundamental steps in pest sampling is the assessment of the population distribution in the field. Several studies have investigated the distribution and appropriate sampling methods for leaf-cutting ants; however, more reliable methods are still required, such as those that use geostatistics. The objective of this study was to determine the spatial distribution and infestation rate of leaf-cutting ant nests in eucalyptus plantations by using geostatistics. The study was carried out in 2008 in two eucalyptus stands in Paraopeba, Minas Gerais, Brazil. All of the nests in the studied area were located and used for the generation of GIS maps, and the spatial pattern of distribution was determined considering the number and size of nests. Each analysis and map was made using the R statistics program and the geoR package. The nest spatial distribution in a savanna area of Minas Gerais was clustered to a certain extent. The models generated allowed the production of kriging maps of areas infested with leaf-cutting ants, where chemical intervention would be necessary, reducing the control costs, impact on humans, and the environment.

Detection of adenoviruses in shellfish by means of conventional-PCR, nested-PCR, and integrated cell culture PCR (ICC/PCR).

PubMed

Rigotto, C; Sincero, T C M; Simões, C M O; Barardi, C R M

2005-01-01

We tested three PCR based methodologies to detect adenoviruses associated with cultivated oysters. Conventional-PCR, nested-PCR, and integrated cell culture-PCR (ICC/PCR) were first optimized using oysters seeded with know amounts of Adenovirus serotype 5 (Ad5). The maximum sensitivity for Ad5 detection was determined for each method, and then used to detect natural adenovirus contamination in oysters from three aquiculture farms in Florianopolis, Santa Catarina State, Brazil, over a period of 6 months. The results showed that the nested-PCR was more sensitive (limit of detection: 1.2 PFU/g of tissue) than conventional-PCR and ICC-PCR (limit of detection for both: 1.2 x 10(2)PFU/g of tissue) for detection of Ad5 in oyster extracts. Nested-PCR was able to detect 90% of Ad5 contamination in harvested oyster samples, while conventional-PCR was unable to detect Ad5 in any of the samples. The present work suggests that detection of human adenoviruses can be used as a tool to monitor the presence of human viruses in marine environments where shellfish grow, and that nested-PCR is the method of choice.

Antennal responses of an oligolectic bee and its cleptoparasite to plant volatiles.

PubMed

Dötterl, Stefan

2008-05-01

Cleptoparasitic or cuckoo bees lay their eggs in nests of other bees, and the parasitic larvae feed the food that had been provided for the host larvae. Nothing is known about the specific signals used by the cuckoo bees for host nest finding, but previous studies have shown that olfactory cues originating from the host bee alone, or the host bee and the larval provision are essential. Here, I compared by using gas chromatography coupled to electroantennographic detection (GC-EAD) the antennal responses of the oligolectic oil-bee Macropis fulvipes and their cleptoparasite, Epeoloides coecutiens, to dynamic headspace scent samples of Lysimachia punctata, a pollen and oil host of Macropis. Both bee species respond to some scent compounds emitted by L. punctata, and two compounds, which were also found in scent samples collected from a Macropis nest entrance, elicited clear signals in the antennae of both species. These compounds may not only play a role for host plant detection by Macropis, but also for host nest detection by Epeoloides. I hypothesise that oligolectic bees and their cleptoparasites use the same compounds for host plant and host nest detection, respectively.

[Pollen analysis of the post-emergence residue of Centris tarsata Smith (Hymenoptera: Apidae, Centridini) nests].

PubMed

Dórea, Marcos da C; Dos Santos, Francisco de A R; Lima, Luciene C de L E; Figueroa, Luís E R

2009-01-01

A new treatment protocol was developed to analyze pollen residues found in nests of Centris tarsata Smith harvested from nest-traps. The study area was located in the Canudos Biological Station in the municipality of Canudos (09 masculine56'34'S; 38 masculine59'17'W), in the northeastern micro-region of Bahia State, Brazil. The local vegetation is an open caatinga (deciduous dryland vegetation), the regional climate is semi-arid, the average annual temperature is 24.1 masculineC, and the annual regional rainfall rate is 454 mm. Ten nests of C. tarsata were collected in trap-nests during the first semester of 2004. Pollen analysis from the nests required the development of a new methodology that combined techniques of palynological sediment analysis with the more common pollinic analysis by acetolysis. Microscopic analyses employed optical microscopy techniques. The pollinic spectrum of the samples from C. tarsata indicated the presence of 17 pollen types from seven plant families, which were present in assemblage of five to eleven pollen types, pointed to the plants used by bees to feed on their offspring. The most represented plant families were Leguminosae (49.3%) and Solanaceae (43.2%). The most frequent pollen types in the samples were from Solanum paniculatum (43.8%) and Senna rizzini (32.1%). The protocol developed provides a new tool for diet assessment of Centris and other groups of solitary bees.

A two-stage adaptive stochastic collocation method on nested sparse grids for multiphase flow in randomly heterogeneous porous media

NASA Astrophysics Data System (ADS)

Liao, Qinzhuo; Zhang, Dongxiao; Tchelepi, Hamdi

2017-02-01

A new computational method is proposed for efficient uncertainty quantification of multiphase flow in porous media with stochastic permeability. For pressure estimation, it combines the dimension-adaptive stochastic collocation method on Smolyak sparse grids and the Kronrod-Patterson-Hermite nested quadrature formulas. For saturation estimation, an additional stage is developed, in which the pressure and velocity samples are first generated by the sparse grid interpolation and then substituted into the transport equation to solve for the saturation samples, to address the low regularity problem of the saturation. Numerical examples are presented for multiphase flow with stochastic permeability fields to demonstrate accuracy and efficiency of the proposed two-stage adaptive stochastic collocation method on nested sparse grids.

Evaluation of nested PCR in diagnosis of fungal rhinosinusitis.

PubMed

Badiee, Parisa; Gandomi, Behrooz; Sabz, Gholamabbass; Khodami, Bijan; Choopanizadeh, Maral; Jafarian, Hadis

2015-02-01

Given the importance of rapid diagnosis for fungal rhinosinusitis, this study aimed to evaluate the use of nested PCR to identify Aspergillus and Mucor species in clinical samples from patients with suspected fungal rhinosinusitis. Functional endoscopic sinus surgery specimens were collected from 98 patients with rhinosinusitis from 2012 to 2013. All samples were ground and cultured on sabouraud dextrose agar. The isolated fungi were identified based on their macroscopic and microscopic features. Fungal DNA was extracted from the tissue samples and nested PCR was performed with two sets of primers for Mucor and Aspergillus. Direct microscopic showed that 5.1% contained fungal components and 9.2% exhibited growth of fungi in culture. The most common agents isolated were Aspergillus fumigatus (n= 3), Aspergillus flavus (n=2), Penicillium sp (n=3) and Alternaria sp. (n=1). Mucor sp. was identified in the pathology smear from 1 patient. Positive results for fungal rhinosinusitis were obtained for a total of 10.2% by culture or pathology smear. Positive PCR results were obtained in 72 samples for Aspergillus and 31 samples for Mucor. Our results suggest that endoscopic sinus surgery specimens are not suitable for nested PCR, probably because of the accumulation of fungi that contaminate the environmental air. This drawback is a limiting factor for diagnosis with nasal cavity specimens. Therefore, molecular methods and conventional culture techniques are helpful complementary diagnostic methods to detect fungal rhinosinusitis and determine appropriate management for these patients.

Sampling animal sign in heterogeneous environments: how much is enough?

USGS Publications Warehouse

Holbrook, Joseph D.; Arkle, Robert S.; Rachlow, Janet L.; Vierling, Kerri T.; Pilliod, David S.

2015-01-01

Animal ecologists often use animal sign as a surrogate for direct observation of organisms, especially when species are secretive or difficult to observe. Spatial heterogeneity in arid environments makes it challenging to consistently detect and precisely characterize animal sign, which can bias estimates of animal abundance or habitat use. Piute ground squirrels (Urocitellus mollis) and Owyhee harvester ants (Pogonomyrmex salinus) live in arid environments and are fossorial, which can make them difficult to observe directly. Their relative abundance can be assessed using sign (i.e., burrows and nests). We implemented an over-sampling framework (i.e., recorded an excessive amount of information) with two observers to 1) identify a sampling intensity that balanced precision with our resource constraints, and 2) assess classification and detection of squirrel burrows and ant nests across vegetation conditions. We sampled 20 1-ha plots for ground squirrel burrows and ant nests using six 4 m × 100 m belt transects. Analyses of precision and sampling effort indicated that three belt transects covering 1200 m2 per ha provided sufficient precision, while minimizing effort. Regardless of vegetation conditions, counts by two observers were strongly correlated for ground squirrel burrows (r = 0.99, P < 0.001, df = 18; slope = 0.92) and harvester ant nests (r = 0.99, P < 0.001, df = 18; slope = 1.01) indicating observer consistency and perhaps high detection probability. These findings illustrate an approach for evaluating sampling designs in many ecological contexts.

Multimodal manifold-regularized transfer learning for MCI conversion prediction.

PubMed

Cheng, Bo; Liu, Mingxia; Suk, Heung-Il; Shen, Dinggang; Zhang, Daoqiang

2015-12-01

As the early stage of Alzheimer's disease (AD), mild cognitive impairment (MCI) has high chance to convert to AD. Effective prediction of such conversion from MCI to AD is of great importance for early diagnosis of AD and also for evaluating AD risk pre-symptomatically. Unlike most previous methods that used only the samples from a target domain to train a classifier, in this paper, we propose a novel multimodal manifold-regularized transfer learning (M2TL) method that jointly utilizes samples from another domain (e.g., AD vs. normal controls (NC)) as well as unlabeled samples to boost the performance of the MCI conversion prediction. Specifically, the proposed M2TL method includes two key components. The first one is a kernel-based maximum mean discrepancy criterion, which helps eliminate the potential negative effect induced by the distributional difference between the auxiliary domain (i.e., AD and NC) and the target domain (i.e., MCI converters (MCI-C) and MCI non-converters (MCI-NC)). The second one is a semi-supervised multimodal manifold-regularized least squares classification method, where the target-domain samples, the auxiliary-domain samples, and the unlabeled samples can be jointly used for training our classifier. Furthermore, with the integration of a group sparsity constraint into our objective function, the proposed M2TL has a capability of selecting the informative samples to build a robust classifier. Experimental results on the Alzheimer's Disease Neuroimaging Initiative (ADNI) database validate the effectiveness of the proposed method by significantly improving the classification accuracy of 80.1 % for MCI conversion prediction, and also outperforming the state-of-the-art methods.

Efficiency of Nested-PCR in Detecting Asymptomatic Cases toward Malaria Elimination Program in an Endemic Area of Iran.

PubMed

Turki, Habibollah; Raeisi, Ahmad; Malekzadeh, Kianoosh; Ghanbarnejad, Amin; Zoghi, Samaneh; Yeryan, Masoud; Abedi Nejad, Masoumeh; Mohseni, Fatemeh; Shekari, Mohammad

2015-01-01

The aim of this study was to detect low parasite and asymptomatic malaria infections by means of three malaria diagnostic tests, in a low transmission region of Minab district, Hormozgan Province, southern Iran. Blood samples of 200 healthy volunteers from Bagh-e-Malek area were evaluated using microscopic, rapid diagnostic tests (RDT) and nested-PCR to inspect malaria parasite. The results showed no Plasmodium parasite in subjects by means of microscopy and RDT. However, 3 P. vivax positive samples (1.5%) were discovered by Nested-PCR while microscopy and RDT missed the cases. Microscopy as the gold standard method and RDT correctly identified 98.5% of cases, and molecular analysis is sensitive and reliable, especially in the detection of "asymptomatic" infections for active case surveillance. Regarding the existence of asymptomatic malaria in endemic area of Hormozgan, Iran, nested-PCR could be considered as a sensitive tool to interrupt malaria transmission in the country, beside the microscopic and RDT methods.

Elevated temperatures are associated with stress in rooftop-nesting Common Nighthawk (Chordeiles minor) chicks.

PubMed

Newberry, Gretchen N; Swanson, David L

2018-01-01

Grasslands and riparian forests in southeastern South Dakota have been greatly reduced since historical times, primarily due to conversion to row-crop agriculture. Common Nighthawk ( Chordeiles minor ) nesting habitat includes grasslands, open woodlands and urban rooftops, but nesting sites in southeastern South Dakota are confined to rooftops, as natural nesting habitat is limited. Nighthawks nesting on exposed rooftop habitats may encounter thermal conditions that increase operative temperatures relative to vegetated land cover types. Mean humidity has increased and mean wind speed and cloud cover have decreased during the nighthawk breeding season from 1948 to 2016 in southeastern South Dakota. These changes might contribute to increasing operative temperatures at exposed rooftop nest sites and this could influence chick condition. We studied nest micro-climate and the plasma stress response for 24 rooftop-nesting nighthawk chicks from 17 nests during 2015 and 2016. High humidity prior to blood collection reduced both baseline and stress-induced plasma corticosterone (CORT). In contrast, high maximum temperatures during the day before sampling increased stress-induced CORT. The magnitude of the chick stress response was significantly negatively related to maximum wind speed for the week prior to CORT measurement. Other weather and micro-climate variables were not significant effectors of CORT metrics. Most chicks had low baseline CORT and were able to mount a stress response, but a subset of chicks ( n = 4) showed elevated baseline CORT and a negative association between the magnitude of stress response and ambient temperature. For this subset, mean ambient temperature for the day before sampling was significantly higher (2.3°C) than for chicks with typical baseline CORT levels. These data suggest that regional climate change trends could affect the ability of nighthawk chicks to mount a stress response, which, in turn, might influence the susceptibility of nighthawk chicks to climate change in the Northern Prairie region.

Contaminants in ospreys from the Pacific Northwest: I. Trends and Patterns in polychlorinated dibenzo-p-dioxins and -dibenzofurans in eggs and plasma

USGS Publications Warehouse

Elliott, J.E.; Machmer, M.M.; Henny, Charles J.; Wilson, L.K.; Norstrom, R.J.

1998-01-01

Osprey (Pandion haliaetus) eggs were collected from 1991 to 1997 at nests (na??=a??121) upstream and downstream of bleached kraft pulp mills and at reference sites in the Fraser and Columbia River drainage systems of British Columbia, Washington, and Oregon. Blood samples were collected from nestling ospreys during the 1992 breeding season on the Thompson River. Samples were analyzed for polychlorinated dibenzo-p-dioxins (PCDDs) and -dibenzofurans (PCDFs). Mean concentrations of 2,3,7,8-TCDD were significantly higher in eggs collected in 1991 at downstream compared to upstream nests near pulp mills at Kamloops and Castlegar, British Columbia. There were no significant temporal trends in 2,3,7,8-TCDD, -TCDF or other measured compounds at a sample of nests monitored between 1991 and 1994 downstream of the Castlegar pulp mill, despite changes in bleaching technology (CIO2 substitution). However, by 1997 concentrations of 2,3,7,8-TCDD and -TCDF were significantly lower than previous years in nests sampled downstream at both Castlegar and Kamloops. An unusual pattern of higher chlorinated PCDDs and PCDFs was found in many of the osprey eggs collected in this study, and considerable individual variation in the pattern existed among eggs from the same site. For example, eggs from four different nests at one study area (Quesnel) on the Fraser River had concentrations of 1,2,3,4,6,7,8-HpCDD ranging from <1 to 1,100 ng/kg and OCDD from <1 to 7,000 ng/kg wet weight. Higher mean concentrations of HpCDD and OCDD were found in eggs from the Thompson River, a tributary of the Fraser, compared to the Columbia River, and concentrations were generally higher at nests upstream of pulp mills. In plasma samples, 1,2,3,4,6,7,8-HpCDD and OCDD were the main compounds detected, with no significant differences measured between samples upstream versus downstream or earlier versus later in the breeding season. Use of chlorophenolic wood preservatives by lumber processors was considered the main source of higher chlorinated PCDD/Fs throughout the systems, based on patterns of trace PCDFs in eggs and significant correlations between egg concentrations of pentachlorophenol and both HpCDD (ra??=a??0.891, pa??

Contaminants in ospreys from the Pacific Northwest: I. Trends and patterns in polychlorinated dibenzo-p-dioxins and -dibenzofurans in eggs and plasma.

PubMed

Elliott, J E; Machmer, M M; Henny, C J; Wilson, L K; Norstrom, R J

1998-11-01

Osprey (Pandion haliaetus) eggs were collected from 1991 to 1997 at nests (n = 121) upstream and downstream of bleached kraft pulp mills and at reference sites in the Fraser and Columbia River drainage systems of British Columbia, Washington, and Oregon. Blood samples were collected from nestling ospreys during the 1992 breeding season on the Thompson River. Samples were analyzed for polychlorinated dibenzo-p-dioxins (PCDDs) and -dibenzofurans (PCDFs). Mean concentrations of 2,3,7,8-TCDD were significantly higher in eggs collected in 1991 at downstream compared to upstream nests near pulp mills at Kamloops and Castlegar, British Columbia. There were no significant temporal trends in 2,3,7,8-TCDD, -TCDF or other measured compounds at a sample of nests monitored between 1991 and 1994 downstream of the Castlegar pulp mill, despite changes in bleaching technology (CIO2 substitution). However, by 1997 concentrations of 2, 3,7,8-TCDD and -TCDF were significantly lower than previous years in nests sampled downstream at both Castlegar and Kamloops. An unusual pattern of higher chlorinated PCDDs and PCDFs was found in many of the osprey eggs collected in this study, and considerable individual variation in the pattern existed among eggs from the same site. For example, eggs from four different nests at one study area (Quesnel) on the Fraser River had concentrations of 1,2,3,4,6,7,8-HpCDD ranging from <1 to 1,100 ng/kg and OCDD from <1 to 7,000 ng/kg wet weight. Higher mean concentrations of HpCDD and OCDD were found in eggs from the Thompson River, a tributary of the Fraser, compared to the Columbia River, and concentrations were generally higher at nests upstream of pulp mills. In plasma samples, 1,2,3,4,6,7,8-HpCDD and OCDD were the main compounds detected, with no significant differences measured between samples upstream versus downstream or earlier versus later in the breeding season. Use of chlorophenolic wood preservatives by lumber processors was considered the main source of higher chlorinated PCDD/Fs throughout the systems, based on patterns of trace PCDFs in eggs and significant correlations between egg concentrations of pentachlorophenol and both HpCDD (r = 0.891, p < 0.01) and OCDD (r = 0.870, p < 0.01).

Simultaneous fluorescence and quantitative phase microscopy with single-pixel detectors

NASA Astrophysics Data System (ADS)

Liu, Yang; Suo, Jinli; Zhang, Yuanlong; Dai, Qionghai

2018-02-01

Multimodal microscopy offers high flexibilities for biomedical observation and diagnosis. Conventional multimodal approaches either use multiple cameras or a single camera spatially multiplexing different modes. The former needs expertise demanding alignment and the latter suffers from limited spatial resolution. Here, we report an alignment-free full-resolution simultaneous fluorescence and quantitative phase imaging approach using single-pixel detectors. By combining reference-free interferometry with single-pixel detection, we encode the phase and fluorescence of the sample in two detection arms at the same time. Then we employ structured illumination and the correlated measurements between the sample and the illuminations for reconstruction. The recovered fluorescence and phase images are inherently aligned thanks to single-pixel detection. To validate the proposed method, we built a proof-of-concept setup for first imaging the phase of etched glass with the depth of a few hundred nanometers and then imaging the fluorescence and phase of the quantum dot drop. This method holds great potential for multispectral fluorescence microscopy with additional single-pixel detectors or a spectrometer. Besides, this cost-efficient multimodal system might find broad applications in biomedical science and neuroscience.

Sparse Representation Based Frequency Detection and Uncertainty Reduction in Blade Tip Timing Measurement for Multi-Mode Blade Vibration Monitoring

PubMed Central

Pan, Minghao; Yang, Yongmin; Guan, Fengjiao; Hu, Haifeng; Xu, Hailong

2017-01-01

The accurate monitoring of blade vibration under operating conditions is essential in turbo-machinery testing. Blade tip timing (BTT) is a promising non-contact technique for the measurement of blade vibrations. However, the BTT sampling data are inherently under-sampled and contaminated with several measurement uncertainties. How to recover frequency spectra of blade vibrations though processing these under-sampled biased signals is a bottleneck problem. A novel method of BTT signal processing for alleviating measurement uncertainties in recovery of multi-mode blade vibration frequency spectrum is proposed in this paper. The method can be divided into four phases. First, a single measurement vector model is built by exploiting that the blade vibration signals are sparse in frequency spectra. Secondly, the uniqueness of the nonnegative sparse solution is studied to achieve the vibration frequency spectrum. Thirdly, typical sources of BTT measurement uncertainties are quantitatively analyzed. Finally, an improved vibration frequency spectra recovery method is proposed to get a guaranteed level of sparse solution when measurement results are biased. Simulations and experiments are performed to prove the feasibility of the proposed method. The most outstanding advantage is that this method can prevent the recovered multi-mode vibration spectra from being affected by BTT measurement uncertainties without increasing the probe number. PMID:28758952

Multimode Acoustic Research

NASA Technical Reports Server (NTRS)

Barmatz, M.

1985-01-01

There is a need for high temperature containerless processing facilities that can efficiently position and manipulate molten samples in the reduced gravity environment of space. The goal of the research is to develop sophisticated high temperature manipulation capabilities such as selection of arbitrary axes rotation and rapid sample cooling. This program will investigate new classes of acoustic levitation in rectangular, cylindrical and spherical geometries. The program tasks include calculating theoretical expressions of the acoustic forces in these geometries for the excitation of up to three acoustic modes (multimodes). These calculations are used to: (1) determine those acoustic modes that produce stable levitation, (2) isolate the levitation and rotation capabilities to produce more than one axis of rotation, and (3) develop methods to translate samples down long tube cylindrical chambers. Experimental levitators will then be constructed to verify the stable levitation and rotation predictions of the models.

Detection of Histoplasma capsulatum in Organic Fertilizers by Hc100 Nested Polymerase Chain Reaction and Its Correlation with the Physicochemical and Microbiological Characteristics of the Samples.

PubMed

Gómez, Luisa F; Torres, Isaura P; Jiménez-A, María Del Pilar; McEwen, Juan Gmo; de Bedout, Catalina; Peláez, Carlos A; Acevedo, José M; Taylor, María L; Arango, Myrtha

2018-05-01

Histoplasma capsulatum is the causative agent of histoplasmosis and this fungus inhabits soils rich in phosphorus and nitrogen that are enriched with bird and bat manure. The replacement of organic matter in agroecosystems is necessary in the tropics, and the use of organic fertilizers has increased. Cases and outbreaks due to the presence of the fungus in these components have been reported. The Instituto Colombiano Agropecuario resolution 150 of 2003 contains the parameters set by the Colombian Technical Standard (NTC 5167) on the physicochemical and microbiological features of fertilizers, but it does not regulate the search for H. capsulatum . The aim of this study was to demonstrate H. capsulatum presence in organic fertilizers by nested polymerase chain reaction (PCR). A total of 239 samples were collected: 201 (84.1%) corresponded to organic fertilizers, 30 (12.5%) to bird excrement, and 8 (3.4%) to cave soils. The Hc100 nested PCR had a detection limit of 0.1 pg/µL and a specificity of 100%. A total of 25 (10.5%) samples were positive and validated by sequencing. Seven of the positive samples represented locations where H. capsulatum was previously detected, suggesting the persistence of the fungus. No significant correlations were detected between the physicochemical and microbiological parameters with the presence of H. capsulatum by nested PCR, indicating the fungus existence in organic fertilizers that complied with the NTC 5167. The Hc100 nested PCR targeting H. capsulatum standardized in this work will improve the evaluation of organic fertilizers and ensure the prevention of outbreaks and cases due to manufacturing, marketing, and use of fertilizers contaminated with H. capsulatum .

Direct detection of Mycobacterium tuberculosis complex in bovine and bubaline tissues through nested-PCR.

PubMed

Araújo, Cristina P; Osório, Ana Luiza A R; Jorge, Klaudia S G; Ramos, Carlos A N; Souza Filho, Antonio F; Vidal, Carlos E S; Vargas, Agueda P C; Roxo, Eliana; Rocha, Adalgiza S; Suffys, Philip N; Fonseca, Antônio A; Silva, Marcio R; Barbosa Neto, José D; Cerqueira, Valíria D; Araújo, Flábio R

2014-01-01

Post-mortem bacterial culture and specific biochemical tests are currently performed to characterize the etiologic agent of bovine tuberculosis. Cultures take up to 90 days to develop. A diagnosis by molecular tests such as PCR can provide fast and reliable results while significantly decreasing the time of confirmation. In the present study, a nested-PCR system, targeting rv2807, with conventional PCR followed by real-time PCR, was developed to detect Mycobacterium tuberculosis complex (MTC) organisms directly from bovine and bubaline tissue homogenates. The sensitivity and specificity of the reactions were assessed with DNA samples extracted from tuberculous and non-tuberculous mycobacteria, as well as other Actinomycetales species and DNA samples extracted directly from bovine and bubaline tissue homogenates. Regarding the analytical sensitivity, DNA of the M. bovis AN5 strain was detected up to 1.5 pg by nested-PCR, whereas DNA of M. tuberculosis H37Rv strain was detected up to 6.1 pg. The nested-PCR system showed 100% analytical specificity for MTC when tested with DNA of reference strains of non-tuberculous mycobacteria and closely-related Actinomycetales. A clinical sensitivity level of 76.7% was detected with tissues samples positive for MTC by means of the culture and conventional PCR. A clinical specificity of 100% was detected with DNA from tissue samples of cattle with negative results in the comparative intradermal tuberculin test. These cattle exhibited no visible lesions and were negative in the culture for MTC. The use of the nested-PCR assay to detect M. tuberculosis complex in tissue homogenates provided a rapid diagnosis of bovine and bubaline tuberculosis.

Direct detection of Mycobacterium tuberculosis complex in bovine and bubaline tissues through nested-PCR

PubMed Central

Araújo, Cristina P.; Osório, Ana Luiza A.R.; Jorge, Klaudia S.G.; Ramos, Carlos A.N.; Souza Filho, Antonio F.; Vidal, Carlos E.S.; Vargas, Agueda P.C.; Roxo, Eliana; Rocha, Adalgiza S.; Suffys, Philip N.; Fonseca, Antônio A.; Silva, Marcio R.; Barbosa Neto, José D.; Cerqueira, Valíria D.; Araújo, Flábio R.

2014-01-01

Post-mortem bacterial culture and specific biochemical tests are currently performed to characterize the etiologic agent of bovine tuberculosis. Cultures take up to 90 days to develop. A diagnosis by molecular tests such as PCR can provide fast and reliable results while significantly decreasing the time of confirmation. In the present study, a nested-PCR system, targeting rv2807, with conventional PCR followed by real-time PCR, was developed to detect Mycobacterium tuberculosis complex (MTC) organisms directly from bovine and bubaline tissue homogenates. The sensitivity and specificity of the reactions were assessed with DNA samples extracted from tuberculous and non-tuberculous mycobacteria, as well as other Actinomycetales species and DNA samples extracted directly from bovine and bubaline tissue homogenates. Regarding the analytical sensitivity, DNA of the M. bovis AN5 strain was detected up to 1.5 pg by nested-PCR, whereas DNA of M. tuberculosis H37Rv strain was detected up to 6.1 pg. The nested-PCR system showed 100% analytical specificity for MTC when tested with DNA of reference strains of non-tuberculous mycobacteria and closely-related Actinomycetales. A clinical sensitivity level of 76.7% was detected with tissues samples positive for MTC by means of the culture and conventional PCR. A clinical specificity of 100% was detected with DNA from tissue samples of cattle with negative results in the comparative intradermal tuberculin test. These cattle exhibited no visible lesions and were negative in the culture for MTC. The use of the nested-PCR assay to detect M. tuberculosis complex in tissue homogenates provided a rapid diagnosis of bovine and bubaline tuberculosis. PMID:25242951

Real-time PCR assay in differentiating Entamoeba histolytica, Entamoeba dispar, and Entamoeba moshkovskii infections in Orang Asli settlements in Malaysia.

PubMed

Lau, Yee Ling; Anthony, Claudia; Fakhrurrazi, Siti Aminah; Ibrahim, Jamaiah; Ithoi, Init; Mahmud, Rohela

2013-08-28

Amebiasis caused by Entamoeba histolytica is the third leading cause of death worldwide. This pathogenic amoeba is morphologically indistinguishable from E. dispar and E. moshkovskii, the non-pathogenic species. Polymerase chain reaction is the current method of choice approved by World Health Organization. Real-time PCR is another attractive molecular method for diagnosis of infectious diseases as post-PCR analyses are eliminated and turnaround times are shorter. The present work aimed to compare the results of Entamoeba species identification using the real-time assay against the established nested PCR method. In this study, a total of 334 human faecal samples were collected from different Orang Asli settlements. Faecal samples were processed by direct wet smear and formalin ethyl acetate concentration methods followed by iodine staining and was microscopically examined for Entamoeba species and other intestinal parasites. Microscopically positive samples were then subject to nested PCR and real-time PCR. The overall prevalence of Entamoeba infection was 19.5% (65/334). SK Posh Piah recorded highest Entamoeba prevalence (63.3%) while Kampung Kemensah had the lowest prevalence (3.7%) of Entamoeba. Microscopically positive samples were then tested by real-time PCR and nested PCR for the presence of Entamoeba histolytica, Entamoeba dispar, and Entamoeba moshkovskii infection. Real-time PCR showed higher Entamoeba detection (86.2%) compared to nested PCR (80%), although the McNemar test value showed no significant difference between the two methods (p = 0.221). This study is the first in Malaysia to report the use of real-time PCR in identifying and differentiating the three Entamoeba infections. It is also proven to be more effective compared to the conventional nested PCR molecular method.

Real-time PCR assay in differentiating Entamoeba histolytica, Entamoeba dispar, and Entamoeba moshkovskii infections in Orang Asli settlements in Malaysia

PubMed Central

2013-01-01

Background Amebiasis caused by Entamoeba histolytica is the third leading cause of death worldwide. This pathogenic amoeba is morphologically indistinguishable from E. dispar and E. moshkovskii, the non-pathogenic species. Polymerase chain reaction is the current method of choice approved by World Health Organization. Real-time PCR is another attractive molecular method for diagnosis of infectious diseases as post-PCR analyses are eliminated and turnaround times are shorter. The present work aimed to compare the results of Entamoeba species identification using the real-time assay against the established nested PCR method. Methods In this study, a total of 334 human faecal samples were collected from different Orang Asli settlements. Faecal samples were processed by direct wet smear and formalin ethyl acetate concentration methods followed by iodine staining and was microscopically examined for Entamoeba species and other intestinal parasites. Microscopically positive samples were then subject to nested PCR and real-time PCR. Results The overall prevalence of Entamoeba infection was 19.5% (65/334). SK Posh Piah recorded highest Entamoeba prevalence (63.3%) while Kampung Kemensah had the lowest prevalence (3.7%) of Entamoeba. Microscopically positive samples were then tested by real-time PCR and nested PCR for the presence of Entamoeba histolytica, Entamoeba dispar, and Entamoeba moshkovskii infection. Real-time PCR showed higher Entamoeba detection (86.2%) compared to nested PCR (80%), although the McNemar test value showed no significant difference between the two methods (p = 0.221). Conclusions This study is the first in Malaysia to report the use of real-time PCR in identifying and differentiating the three Entamoeba infections. It is also proven to be more effective compared to the conventional nested PCR molecular method. PMID:23985047

A simple and rapid method for detection of Trypanosoma evansi in the dromedary camel using a nested polymerase chain reaction

PubMed Central

Aradaib, Imadeldin E; Majid, Ali A

2006-01-01

A nested polymerase chain reaction (nPCR)-based assay, was developed and evaluated for rapid detection of Trypanosoma evansi in experimentally infected mice and naturally infected camels (Camelus dromedarius). Four oligonucleotide primers (TE1, TE2, TE3 and TE4), selected from nuclear repetitive gene of T. evansi, were designed and used for PCR amplifications. The first amplification, using a pair of outer primers TE1 and TE2, produced a 821-bp primary PCR product from T. evansi DNA. The second amplification, using nested (internal) pair of primers TE3 and TE4, produced a 270-bp PCR product. T. evansi DNAs extracted from blood samples of experimentally infected mice and naturally infected Sudanese breed of dromedary camels were detected by this nested PCR-based assay. The nested primers TE3 and TE4 increased the sensitivity of the PCR assay and as little as 10 fg of T. evansi DNA (equivalent to a single copy of the putative gene of the parasite) was amplified and visualized onto ethidium bromide-stained agarose gels. Amplification products were not detected when the PCR-based assay was applied to DNA from other blood parasites including Thieleria annulata, Babesia bigemina or nucleic acid free samples. Application of this nPCR-based assay to clinical samples resulted in direct detection of T. evansi from a variety of tissue samples collected from experimentally infected mice and blood from naturally infected camels. The described nPCR-based assay provides a valuable tool to study the epidemiology of T. evansi infection in camels and other susceptible animal populations. PMID:16712737

Test plan for evaluating the operational performance of the prototype nested, fixed-depth fluidic sampler

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

REICH, F.R.

The PHMC will provide Low Activity Wastes (LAW) tank wastes for final treatment by a privatization contractor from two double-shell feed tanks, 241-AP-102 and 241-AP-104. Concerns about the inability of the baseline ''grab'' sampling to provide large volume samples within time constraints has led to the development of a nested, fixed-depth sampling system. This sampling system will provide large volume, representative samples without the environmental, radiation exposure, and sample volume impacts of the current base-line ''grab'' sampling method. A plan has been developed for the cold testing of this nested, fixed-depth sampling system with simulant materials. The sampling system willmore » fill the 500-ml bottles and provide inner packaging to interface with the Hanford Sites cask shipping systems (PAS-1 and/or ''safe-send''). The sampling system will provide a waste stream that will be used for on-line, real-time measurements with an at-tank analysis system. The cold tests evaluate the performance and ability to provide samples that are representative of the tanks' content within a 95 percent confidence interval, to sample while mixing pumps are operating, to provide large sample volumes (1-15 liters) within a short time interval, to sample supernatant wastes with over 25 wt% solids content, to recover from precipitation- and settling-based plugging, and the potential to operate over the 20-year expected time span of the privatization contract.« less

Euschoengastia suzukii (Acari: Trombiculidae): A new species of chigger mite collected from soil samples in the nest burrows of streaked shearwater in Japan.

PubMed

Takahashi, Mamoru; Fukaya, Hajime; Takahashi, Hisae

2005-07-01

Euschoengastia suzukii Takahashi, Fukaya & Takahashi is described and illustrated. The type material was collected from soil samples in the nest burrows of the sea bird streaked shearwater, Calonectris leucomelas (Temminck), living on Mikurajima Island in Tokyo; Oomorijima Island, Oki, Shimane Prefecture; and Awashima Island, Niigata Prefecture, in Japan, indicating that C. leucomelas is the main parasitic host of E. suzukii new species.

Multimodal Perception and Multicriterion Control of Nested Systems. 2; Constraints on Crew Members During Space Vehicle Abort, Entry, and Landing

NASA Technical Reports Server (NTRS)

Riccio, Gary E.; McDonald, P. Vernon; Irvin, Gregg E.; Bloomberg, Jacob J.

1998-01-01

This report reviews the operational demands made of a Shuttle pilot or commander within the context of a proven empirical methodology for describing human sensorimotor performance and whole-body coordination in mechanically and perceptually complex environments. The conclusions of this review pertain to a) methods for improving our understanding of the psychophysics and biomechanics of visual/manual control and whole-body coordination in space vehicle cockpits; b) the application of scientific knowledge about human perception and performance in dynamic inertial conditions to the development of technology, procedures, and training for personnel in space vehicle cockpits; c) recommendations for mitigation of safety and reliability concerns about human performance in space vehicle cockpits; and d) in-flight evaluation of flight crew performance during nominal and off-nominal launch and reentry scenarios.

Evaluating nest supplementation as a recovery strategy for the endangered rodents of the Florida Keys

USGS Publications Warehouse

Cove, Michael V.; Simons, Theodore R.; Gardner, Beth; Maurer, Andrew S.; O'Connell, Allan F.

2017-01-01

The Key Largo woodrat (Neotoma floridana smalli) and Key Largo cotton mouse (Peromyscus gossypinus allapaticola) are federally endangered subspecies endemic to the tropical hardwood hammocks of Key Largo, Florida. Woodrats are considered generalists in habitat and diet, yet a steady decline in natural stick nests and capture rates over the past several decades suggests that they are limited by the availability of nesting habitat due to habitat loss and fragmentation. The more specialized Key Largo cotton mouse appears to rely on old growth hammock, a habitat type that is rare following past land clearing. In 2004, the U.S. Fish and Wildlife Service started building supplemental nest structures to restore habitat quality and connectivity for these endangered rodents, but nest use requires evaluation. We used camera traps and occupancy models to evaluate the factors influencing woodrat and cotton mouse use of the supplemental nests. We detected woodrats at 65 and cotton mice at 175 of 284 sampled nest structures, with co-occurrence at 38 nests. Woodrat nest use followed a gradient from low nest use in the north to high nest use in the south, which might relate to the proximity of free-ranging domestic cat (Felis catus) colonies in residential developments. Cotton mouse nest use, however, was related positively to mature hammock and related negatively to disturbed areas (e.g. scarified lands). The two species occurred independently of each other. Stick-stacking behavior was observed at supplemental nests and, although it was correlated with detection of woodrats, it was not a strong predictor of their occurrence. We suggest that nest supplementation can be an important tool for species recovery as habitat quality continues to improve with succession.

The ART of mating: alternative reproductive tactics and mating success in a nest-guarding fish.

PubMed

Mascolino, S; Benvenuto, C; Gubili, C; Sacchi, C; Boufana, B; Mariani, S

2016-12-01

Behavioural observations in the field of male Mediterranean damselfish Chromis chromis were combined with molecular analyses, using bi-parentally and maternally inherited markers, to investigate reproductive success patterns of alternative reproductive tactics (ARTs) in terms of number of eggs sired and number of females contributing to each nest. Cuckoldry was observed in every nest sampled, with at least two and up to seven sneaker males per nest. The nesting male, however, always significantly fertilized the greater number of eggs (on average 49%) in each clutch, whereas each sneaker fertilized around 7% of the clutch. The average number of females whose eggs were fertilized by nesting males was 6·76 (range 2-13), while each sneaker on average fertilized the eggs of 1·74 (range 1-8) females. Using this sibship reconstruction, some of the factors involved in the regulation of the dynamic equilibrium of reproductive success were investigated between the two ARTs shown by C. chromis males. Results show that the sneakers' reproductive success was positively linked to egg clutch size; the density of individuals in the nesting area negatively affected the size of egg clutches; the rate of defence behaviours performed by nesting males negatively influenced the number of females contributing to each nest. © 2016 The Fisheries Society of the British Isles.

Exploring the Energy Landscapes of Protein Folding Simulations with Bayesian Computation

PubMed Central

Burkoff, Nikolas S.; Várnai, Csilla; Wells, Stephen A.; Wild, David L.

2012-01-01

Nested sampling is a Bayesian sampling technique developed to explore probability distributions localized in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence (marginal likelihood) of the model. The nested sampling algorithm also provides an efficient way to calculate free energies and the expectation value of thermodynamic observables at any temperature, through a simple post processing of the output. Previous applications of the algorithm have yielded large efficiency gains over other sampling techniques, including parallel tempering. In this article, we describe a parallel implementation of the nested sampling algorithm and its application to the problem of protein folding in a Gō-like force field of empirical potentials that were designed to stabilize secondary structure elements in room-temperature simulations. We demonstrate the method by conducting folding simulations on a number of small proteins that are commonly used for testing protein-folding procedures. A topological analysis of the posterior samples is performed to produce energy landscape charts, which give a high-level description of the potential energy surface for the protein folding simulations. These charts provide qualitative insights into both the folding process and the nature of the model and force field used. PMID:22385859

Exploring the energy landscapes of protein folding simulations with Bayesian computation.

PubMed

Burkoff, Nikolas S; Várnai, Csilla; Wells, Stephen A; Wild, David L

2012-02-22

Nested sampling is a Bayesian sampling technique developed to explore probability distributions localized in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence (marginal likelihood) of the model. The nested sampling algorithm also provides an efficient way to calculate free energies and the expectation value of thermodynamic observables at any temperature, through a simple post processing of the output. Previous applications of the algorithm have yielded large efficiency gains over other sampling techniques, including parallel tempering. In this article, we describe a parallel implementation of the nested sampling algorithm and its application to the problem of protein folding in a Gō-like force field of empirical potentials that were designed to stabilize secondary structure elements in room-temperature simulations. We demonstrate the method by conducting folding simulations on a number of small proteins that are commonly used for testing protein-folding procedures. A topological analysis of the posterior samples is performed to produce energy landscape charts, which give a high-level description of the potential energy surface for the protein folding simulations. These charts provide qualitative insights into both the folding process and the nature of the model and force field used. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Identifying Kittlitz's Murrelet nesting habitat in North America at the landscape scale

USGS Publications Warehouse

Felis, Jonathan J.; Kissling, Michelle L.; Kaler, Robb S.A.; Kenney, Leah A.; Lawonn, Matthew J.

2016-01-01

The Kittlitz's Murrelet (Brachyramphus brevirostris) is a small, non-colonial seabird endemic to marine waters of Alaska and eastern Russia that may have experienced significant population decline in recent decades, in part because of low reproductive success and terrestrial threats. Although recent studies have shed new light on Kittlitz's Murrelet nesting habitat in a few discrete areas, the location and extent of suitable nesting habitat throughout most of its range remains unclear. Here, we have compiled all existing nest records and locations to identify landscape-scale parameters (distance to coast, elevation, slope, and land cover) that provide potential nesting habitat in four regions: northern Alaska, Aleutian Islands, Alaska Peninsula Mountains and Kodiak Island, and Pacific Coastal Mountains (including nearshore interior Canada). We produced a final map classifying 12% (70,411 km2) of the lands assessed as potential Kittlitz's Murrelet nesting habitat, with dense but distinct patches in northern Alaska and a more uninterrupted, narrow band extending across the Pacific Coastal Mountains, Alaska Peninsula Mountains, and Aleutian Islands. The extent of habitat-capable parameter values varied regionally, indicating that the Kittlitz's Murrelet may be able to use a variety of habitats for nesting, depending on availability. Future nesting habitat studies could employ spatially random sampling designs to allow for quantitatively robust modeling of nesting habitat and predictive extrapolation to areas where nests have not been located but likely exist.

Development of a species-diagnostic marker and its application for population genetics studies of the stingless bee Trigona collina in Thailand.

PubMed

Theeraapisakkun, M; Klinbunga, S; Sittipraneed, S

2010-05-18

A molecular maker for authenticating species origin of the stingless bee (Trigona collina) was developed. Initially, amplified fragment length polymorphism analysis was made of 11 stingless bee species using 64 primer combinations. A 316-bp band found only in T. collina was cloned and sequenced. A primer pair (CUTc1-F/R) was designed and tested for species-specificity in 15 stingless bee species (239 nests). The expected 259-bp fragment was consistently amplified in all T. collina individuals (134/134 nests, 100%). Cross-species amplification was observed in T. pagdeni (43/51 nests; 84.3%), but not in other species. SSCP analysis of CUTc1 unambiguously differentiated T. collina from T. pagdeni. CUTc1 generated three genotypes in Thai T. collina (134 nests). An AA (259/259 bp) genotype was found in all stingless bees from the north (21 nests) and northeast (32 nests), and 23/28 nests from the Central region, whereas a BB (253/253 bp) genotype was observed in most samples from peninsular Thailand (42/53 nests). Heterozygotes exhibiting the AB (253/259 bp) genotype were observed in 5 of 28 nests from Prachuap Khiri Khan located slightly above the Kra ecotone and 11 of 53 nests originated further south of the Kra ecotone. Genotype distribution patterns of CUTc1 clearly indicated intraspecific population differentiation of Thai T. collina.

Power lines, roads, and avian nest survival: effects on predator identity and predation intensity

PubMed Central

DeGregorio, Brett A; Weatherhead, Patrick J; Sperry, Jinelle H

2014-01-01

1 Anthropogenic alteration of landscapes can affect avian nest success by influencing the abundance, distribution, and behavior of predators. Understanding avian nest predation risk necessitates understanding how landscapes affect predator distribution and behavior. 2 From a sample of 463 nests of 17 songbird species, we evaluated how landscape features (distance to forest edge, unpaved roads, and power lines) influenced daily nest survival. We also used video cameras to identify nest predators at 137 nest predation events and evaluated how landscape features influenced predator identity. Finally, we determined the abundance and distribution of several of the principal predators using surveys and radiotelemetry. 3 Distance to power lines was the best predictor of predator identity: predation by brown-headed cowbirds (Molothrus ater), corvids (Corvus sp. and Cyanocitta cristata), racers (Coluber constrictor), and coachwhips (Masticophis flagellum) increased with proximity to power lines, whereas predation by rat snakes (Elaphe obsoleta) and raptors decreased. In some cases, predator density may reliably indicate nest predation risk because racers, corvids, and cowbirds frequently used power line right-of-ways. 4 Of five bird species with enough nests to analyze individually, daily nest survival of only indigo buntings (Passerina cyanea) decreased with proximity to power lines, despite predation by most predators at our site being positively associated with power lines. For all nesting species combined, distance to unpaved road was the model that most influenced daily nest survival. This pattern is likely a consequence of rat snakes, the locally dominant nest predator (28% of predation events), rarely using power lines and associated areas. Instead, rat snakes were frequently associated with road edges, indicating that not all edges are functionally similar. 5 Our results suggest that interactions between predators and landscape features are likely to be specific to both the local predators and landscape. Thus, predicting how anthropogenic changes to landscapes affect nesting birds requires that we know more about how landscape changes affect the behavior of nest predators and which nest predators are locally important. PMID:24967077

Power lines, roads, and avian nest survival: effects on predator identity and predation intensity.

PubMed

DeGregorio, Brett A; Weatherhead, Patrick J; Sperry, Jinelle H

2014-05-01

1 Anthropogenic alteration of landscapes can affect avian nest success by influencing the abundance, distribution, and behavior of predators. Understanding avian nest predation risk necessitates understanding how landscapes affect predator distribution and behavior. 2 From a sample of 463 nests of 17 songbird species, we evaluated how landscape features (distance to forest edge, unpaved roads, and power lines) influenced daily nest survival. We also used video cameras to identify nest predators at 137 nest predation events and evaluated how landscape features influenced predator identity. Finally, we determined the abundance and distribution of several of the principal predators using surveys and radiotelemetry. 3 Distance to power lines was the best predictor of predator identity: predation by brown-headed cowbirds (Molothrus ater), corvids (Corvus sp. and Cyanocitta cristata), racers (Coluber constrictor), and coachwhips (Masticophis flagellum) increased with proximity to power lines, whereas predation by rat snakes (Elaphe obsoleta) and raptors decreased. In some cases, predator density may reliably indicate nest predation risk because racers, corvids, and cowbirds frequently used power line right-of-ways. 4 Of five bird species with enough nests to analyze individually, daily nest survival of only indigo buntings (Passerina cyanea) decreased with proximity to power lines, despite predation by most predators at our site being positively associated with power lines. For all nesting species combined, distance to unpaved road was the model that most influenced daily nest survival. This pattern is likely a consequence of rat snakes, the locally dominant nest predator (28% of predation events), rarely using power lines and associated areas. Instead, rat snakes were frequently associated with road edges, indicating that not all edges are functionally similar. 5 Our results suggest that interactions between predators and landscape features are likely to be specific to both the local predators and landscape. Thus, predicting how anthropogenic changes to landscapes affect nesting birds requires that we know more about how landscape changes affect the behavior of nest predators and which nest predators are locally important.

Breeding ecology and nesting habitat associations of five marsh bird species in western New York

USGS Publications Warehouse

Lor, S.; Malecki, R.A.

2006-01-01

Nesting habitats and nest success of five species of marsh birds were studied during 1997 and 1998 at the Iroquois National Wildlife Refuge (NWR) and the adjacent Oak Orchard and Tonawanda State Wildlife Management Areas (WMA) located in western New York. Nest searches located 18 American Bittern (Botaurus lentiginosus), 117 Least Bittern (Ixobrychus exilis), 189 Pied-billed Grebe (Podilymbus podiceps), 23 Sora (Porzana carolina), and 72 Virginia Rail (Rallus limicola) nests. Average nest densities in 1998, our best nest searching year, ranged from 0.01/ha for Soras (N = 8) to 0.28/ha for Pied-billed Grebes (N = 160). Mayfield nest success estimates for Least Bittern were 80% (N = 16) in 1997 and 46% (N = 37) in 1998. Nest success estimates were 72% (N = 55) for Pied-billed Grebe, 43% (N = 6) for Sora, and 38% (N = 20) for Virginia Rail. Nests of all five species were located in ???70% emergent vegetation with a mean water depth of 24-56 cm and an average vegetation height that ranged from 69-133 cm. Logistic regression models were developed for each species using habitat variables at nest and random site locations. Each model was ranked with Akaike's Information Criterion for small sample size (AICc). In general, our best models indicated that increased emergent vegetation and horizontal cover with shallow water depths improved the odds of encountering marsh bird nests in the wetlands of western New York. We suggest that managing wetlands as a complex, at different stages of succession, would best benefit marsh bird species.

A two-stage adaptive stochastic collocation method on nested sparse grids for multiphase flow in randomly heterogeneous porous media

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

Liao, Qinzhuo, E-mail: liaoqz@pku.edu.cn; Zhang, Dongxiao; Tchelepi, Hamdi

A new computational method is proposed for efficient uncertainty quantification of multiphase flow in porous media with stochastic permeability. For pressure estimation, it combines the dimension-adaptive stochastic collocation method on Smolyak sparse grids and the Kronrod–Patterson–Hermite nested quadrature formulas. For saturation estimation, an additional stage is developed, in which the pressure and velocity samples are first generated by the sparse grid interpolation and then substituted into the transport equation to solve for the saturation samples, to address the low regularity problem of the saturation. Numerical examples are presented for multiphase flow with stochastic permeability fields to demonstrate accuracy and efficiencymore » of the proposed two-stage adaptive stochastic collocation method on nested sparse grids.« less

A multiplex nested PCR for the detection and identification of Candida species in blood samples of critically ill paediatric patients

PubMed Central

2014-01-01

Background Nosocomial candidaemia is associated with high mortality rates in critically ill paediatric patients; thus, the early detection and identification of the infectious agent is crucial for successful medical intervention. The PCR-based techniques have significantly increased the detection of Candida species in bloodstream infections. In this study, a multiplex nested PCR approach was developed for candidaemia detection in neonatal and paediatric intensive care patients. Methods DNA samples from the blood of 54 neonates and children hospitalised in intensive care units with suspected candidaemia were evaluated by multiplex nested PCR with specific primers designed to identify seven Candida species, and the results were compared with those obtained from blood cultures. Results The multiplex nested PCR had a detection limit of four Candida genomes/mL of blood for all Candida species. Blood cultures were positive in 14.8% of patients, whereas the multiplex nested PCR was positive in 24.0% of patients, including all culture-positive patients. The results obtained with the molecular technique were available within 24 hours, and the assay was able to identify Candida species with 100% of concordance with blood cultures. Additionally, the multiplex nested PCR detected dual candidaemia in three patients. Conclusions Our proposed PCR method may represent an effective tool for the detection and identification of Candida species in the context of candidaemia diagnosis in children, showing highly sensitive detection and the ability to identify the major species involved in this infection. PMID:25047415

A multiplex nested PCR for the detection and identification of Candida species in blood samples of critically ill paediatric patients.

PubMed

Taira, Cleison Ledesma; Okay, Thelma Suely; Delgado, Artur Figueiredo; Ceccon, Maria Esther Jurfest Rivero; de Almeida, Margarete Teresa Gottardo; Del Negro, Gilda Maria Barbaro

2014-07-21

Nosocomial candidaemia is associated with high mortality rates in critically ill paediatric patients; thus, the early detection and identification of the infectious agent is crucial for successful medical intervention. The PCR-based techniques have significantly increased the detection of Candida species in bloodstream infections. In this study, a multiplex nested PCR approach was developed for candidaemia detection in neonatal and paediatric intensive care patients. DNA samples from the blood of 54 neonates and children hospitalised in intensive care units with suspected candidaemia were evaluated by multiplex nested PCR with specific primers designed to identify seven Candida species, and the results were compared with those obtained from blood cultures. The multiplex nested PCR had a detection limit of four Candida genomes/mL of blood for all Candida species. Blood cultures were positive in 14.8% of patients, whereas the multiplex nested PCR was positive in 24.0% of patients, including all culture-positive patients. The results obtained with the molecular technique were available within 24 hours, and the assay was able to identify Candida species with 100% of concordance with blood cultures. Additionally, the multiplex nested PCR detected dual candidaemia in three patients. Our proposed PCR method may represent an effective tool for the detection and identification of Candida species in the context of candidaemia diagnosis in children, showing highly sensitive detection and the ability to identify the major species involved in this infection.

Rapid and sensitive detection of mink circovirus by recombinase polymerase amplification.

PubMed

Ge, Junwei; Shi, Yunjia; Cui, Xingyang; Gu, Shanshan; Zhao, Lili; Chen, Hongyan

2018-06-01

To date, the pathogenic role of mink circovirus (MiCV) remains unclear, and its prevalence and economic importance are unknown. Therefore, a rapid and sensitive molecular diagnosis is necessary for disease management and epidemiological surveillance. However, only PCR methods can identify MiCV infection at present. In this study, we developed a nested PCR and established a novel recombinase polymerase amplification (RPA) assay for MiCV detection. Sensitivity analysis showed that the detection limit of nested PCR and RPA assay was 10 1 copies/reaction, and these methods were more sensitive than conventional PCR, which has a detection limit of 10 5 copies/reaction. The RPA assay had no cross-reactivity with other related viral pathogens, and amplification was completed in less than 20 min with a simple device. Further assessment of clinical samples showed that the two assays were accurate in identifying positive and negative conventional PCR samples. The detection rate of MiCV by the RPA assay in clinical samples was 38.09%, which was 97% consistent with that by the nested PCR. The developed nested PCR is a highly sensitive tool for practical use, and the RPA assay is a simple, sensitive, and potential alternative method for rapid and accurate MiCV diagnosis. Copyright © 2018 Elsevier B.V. All rights reserved.

Prevalence of equine herpesvirus-1 and equine herpesvirus-4 infections in equidae species in Turkey as determined by ELISA and multiplex nested PCR.

PubMed

Ataseven, Veysel S; Dağalp, Seval B; Güzel, Murat; Başaran, Zeynep; Tan, Mehmet T; Geraghty, Bob

2009-04-01

In this report we examined the presence of specific antibodies against equine herpesvirus type 1 (EHV-1), and equine herpesvirus type 4 (EHV-4) in several equidae, including mules, donkeys, horses. The presence of EHV-1 and EHV-4 in respiratory diseases of equids, and ability of multiplex nested polymerase chain reaction (PCR) screening in simultaneous diagnosis of horses acutely infected by EHV-1 and EHV-4 were also investigated. Sera from 504 horses, mules and donkeys sampled were tested for the presence of EHV-1 and EHV-4 specific antibodies. Blood samples taken from 21 symptomatic horses and nasal swabs taken from 40 symptomatic horses were tested for the presence of EHV-1 and EHV-4 by a multiplex nested PCR. A total of 14.3% (3/21) of buffy coat samples and 32.5% (13/40) nasal swab samples were found to contain EHV-1 DNA, while 19% (4/21) buffy coat samples and 22.5% (9/40) nasal swab samples were found to be positive for EHV-4 DNA. By species, 14.5% of horses, 37.2% of mules and 24.2% of donkeys tested were EHV-1 seropositive. EHV-4 specific antibodies were detected in 237 (81.7%) of 290 horse sera tested. Results from this investigation demonstrate that EHV-1 and EHV-4 are prevalent throughout the equid population, and that donkeys and mules might also represent an important source of infection for other equids. We also showed that the multiplex nested PCR assay might be useful for diagnosis of mixed respiratory infections in horses due to EHV-1 and EHV-4.

Evaluation of the efficiency of nested q-PCR in the detection of Mycobacterium tuberculosis complex directly from tuberculosis-suspected lesions in post-mortem macroscopic inspections of bovine carcasses slaughtered in the state of Mato Grosso, Brazil.

PubMed

Carvalho, Ricardo César Tavares; Furlanetto, Leone Vinícius; Maruyama, Fernanda Harumy; Araújo, Cristina Pires de; Barros, Sílvia Letícia Bomfim; Ramos, Carlos Alberto do Nascimento; Dutra, Valéria; Araújo, Flábio Ribeiro de; Paschoalin, Vânia Margaret Flosi; Nakazato, Luciano; Figueiredo, Eduardo Eustáquio de Souza

2015-08-01

Bovine tuberculosis (BTB) is a zoonotic disease caused by Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex (MTC). The quick and specific detection of this species is of extreme importance, since BTB may cause economic impacts, in addition to presenting imminent risks to human health. In the present study a nested real-time PCR test (nested q-PCR) was used in post-mortem evaluations to assess cattle carcasses with BTB-suspected lesions. A total of 41,193 cattle slaughtered in slaughterhouses located in the state of Mato Grosso, were examined. Of the examined animals, 198 (0.48%) showed BTB-suspected lesions. M. bovis was isolated in 1.5% (3/198) of the samples. Multiplex-PCR detected MTC in 7% (14/198) of the samples. The nested q-PCR test detected MTC in 28% (56/198) of the BTB-suspected lesions, demonstrating higher efficiency when compared to the multiplex-PCR and conventional microbiology. Nested q-PCR can therefore be used as a complementary test in the national program for control and eradication of bovine tuberculosis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Improved assay to detect Plasmodium falciparum using an uninterrupted, semi-nested PCR and quantitative lateral flow analysis

PubMed Central

2013-01-01

Background A rapid, non-invasive, and inexpensive point-of-care (POC) diagnostic for malaria followed by therapeutic intervention would improve the ability to control infection in endemic areas. Methods A semi-nested PCR amplification protocol is described for quantitative detection of Plasmodium falciparum and is compared to a traditional nested PCR. The approach uses primers that target the P. falciparum dihydrofolate reductase gene. Results This study demonstrates that it is possible to perform an uninterrupted, asymmetric, semi-nested PCR assay with reduced assay time to detect P. falciparum without compromising the sensitivity and specificity of the assay using saliva as a testing matrix. Conclusions The development of this PCR allows nucleic acid amplification without the need to transfer amplicon from the first PCR step to a second reaction tube with nested primers, thus reducing both the chance of contamination and the time for analysis to < two hours. Analysis of the PCR amplicon yield was adapted to lateral flow detection using the quantitative up-converting phosphor (UCP) reporter technology. This approach provides a basis for migration of the assay to a POC microfluidic format. In addition the assay was successfully evaluated with oral samples. Oral fluid collection provides a simple non-invasive method to collect clinical samples. PMID:23433252

Development of an instrumentation system for measurement of degradation of lubricating oil using optical fiber sensor

NASA Astrophysics Data System (ADS)

Laskar, S.; Bordoloi, S.

2016-01-01

This paper presents an instrumentation system to measure the degradation in lubricating oil using a bare, tapered and bent multi-mode optical fiber (BTBMOF) sensor probe and a temperature probe. The sensor system consists of (i) a bare, tapered and bent multi-mode optical fiber (BTBMOF) as optical sensor along with a laser source and a LDR (Light Dependent Resistor) as detector (ii) a temperature sensor (iii) a ATmega microcontroller based data acquisition system and (iv) a trained ANN for processing and calibration. The BTBMOF sensor and the temperature sensor are used to provide the measure of refractive index (RI) and the temperature of a lubricating oil sample. A microcontroller based instrumentation system with trained ANN algorithm has been developed to determine the degradation of the lubricating oil sample by sampling the readings of the optical fiber sensor, and the temperature sensor.

Comparison of statistical sampling methods with ScannerBit, the GAMBIT scanning module

NASA Astrophysics Data System (ADS)

Martinez, Gregory D.; McKay, James; Farmer, Ben; Scott, Pat; Roebber, Elinore; Putze, Antje; Conrad, Jan

2017-11-01

We introduce ScannerBit, the statistics and sampling module of the public, open-source global fitting framework GAMBIT. ScannerBit provides a standardised interface to different sampling algorithms, enabling the use and comparison of multiple computational methods for inferring profile likelihoods, Bayesian posteriors, and other statistical quantities. The current version offers random, grid, raster, nested sampling, differential evolution, Markov Chain Monte Carlo (MCMC) and ensemble Monte Carlo samplers. We also announce the release of a new standalone differential evolution sampler, Diver, and describe its design, usage and interface to ScannerBit. We subject Diver and three other samplers (the nested sampler MultiNest, the MCMC GreAT, and the native ScannerBit implementation of the ensemble Monte Carlo algorithm T-Walk) to a battery of statistical tests. For this we use a realistic physical likelihood function, based on the scalar singlet model of dark matter. We examine the performance of each sampler as a function of its adjustable settings, and the dimensionality of the sampling problem. We evaluate performance on four metrics: optimality of the best fit found, completeness in exploring the best-fit region, number of likelihood evaluations, and total runtime. For Bayesian posterior estimation at high resolution, T-Walk provides the most accurate and timely mapping of the full parameter space. For profile likelihood analysis in less than about ten dimensions, we find that Diver and MultiNest score similarly in terms of best fit and speed, outperforming GreAT and T-Walk; in ten or more dimensions, Diver substantially outperforms the other three samplers on all metrics.

Detection and Resolution of Cryptosporidium Species and Species Mixtures by Genus-Specific Nested PCR-Restriction Fragment Length Polymorphism Analysis, Direct Sequencing, and Cloning ▿

PubMed Central

Ruecker, Norma J.; Hoffman, Rebecca M.; Chalmers, Rachel M.; Neumann, Norman F.

2011-01-01

Molecular methods incorporating nested PCR-restriction fragment length polymorphism (RFLP) analysis of the 18S rRNA gene of Cryptosporidium species were validated to assess performance based on limit of detection (LoD) and for detecting and resolving mixtures of species and genotypes within a single sample. The 95% LoD was determined for seven species (Cryptosporidium hominis, C. parvum, C. felis, C. meleagridis, C. ubiquitum, C. muris, and C. andersoni) and ranged from 7 to 11 plasmid template copies with overlapping 95% confidence limits. The LoD values for genomic DNA from oocysts on microscope slides were 7 and 10 template copies for C. andersoni and C. parvum, respectively. The repetitive nested PCR-RFLP slide protocol had an LoD of 4 oocysts per slide. When templates of two species were mixed in equal ratios in the nested PCR-RFLP reaction mixture, there was no amplification bias toward one species over another. At high ratios of template mixtures (>1:10), there was a reduction or loss of detection of the less abundant species by RFLP analysis, most likely due to heteroduplex formation in the later cycles of the PCR. Replicate nested PCR was successful at resolving many mixtures of Cryptosporidium at template concentrations near or below the LoD. The cloning of nested PCR products resulted in 17% of the cloned sequences being recombinants of the two original templates. Limiting-dilution nested PCR followed by the sequencing of PCR products resulted in no sequence anomalies, suggesting that this method is an effective and accurate way to study the species diversity of Cryptosporidium, particularly for environmental water samples, in which mixtures of parasites are common. PMID:21498746

Origin and Alteration of Organic Matter in Termite Mounds from Different Feeding Guilds of the Amazon Rainforests

PubMed Central

Siebers, Nina; Martius, Christopher; Eckhardt, Kai-Uwe; Garcia, Marcos V. B.; Leinweber, Peter; Amelung, Wulf

2015-01-01

The impact of termites on nutrient cycling and tropical soil formation depends on their feeding habits and related material transformation. The identification of food sources, however, is difficult, because they are variable and changed by termite activity and nest construction. Here, we related the sources and alteration of organic matter in nests from seven different termite genera and feeding habits in the Terra Firme rainforests to the properties of potential food sources soil, wood, and microepiphytes. Chemical analyses comprised isotopic composition of C and N, cellulosic (CPS), non-cellulosic (NCPS), and N-containing saccharides, and molecular composition screening using pyrolysis-field ionization mass spectrometry (Py-FIMS). The isotopic analysis revealed higher soil δ13C (-27.4‰) and δ15N (6.6‰) values in nests of wood feeding Nasutitermes and Cornitermes than in wood samples (δ13C = -29.1‰, δ15N = 3.4‰), reflecting stable-isotope enrichment with organic matter alterations during or after nest construction. This result was confirmed by elevated NCPS:CPS ratios, indicating a preferential cellulose decomposition in the nests. High portions of muramic acid (MurAc) pointed to the participation of bacteria in the transformation processes. Non-metric multidimensional scaling (NMDS) revealed increasing geophagy in the sequence Termes < Embiratermes < Anoplotermes and increasing xylophagy for Cornitermes < Nasutitermes, and that the nest material of Constrictotermes was similar to the microepiphytes sample, confirming the report that Constrictotermes belongs to the microepiphyte-feeders. We therewith document that nest chemistry of rainforest termites shows variations and evidence of modification by microbial processes, but nevertheless it primarily reflects the trophic niches of the constructors. PMID:25909987

Origin and alteration of organic matter in termite mounds from different feeding guilds of the Amazon rainforests.

PubMed

Siebers, Nina; Martius, Christopher; Eckhardt, Kai-Uwe; Garcia, Marcos V B; Leinweber, Peter; Amelung, Wulf

2015-01-01

The impact of termites on nutrient cycling and tropical soil formation depends on their feeding habits and related material transformation. The identification of food sources, however, is difficult, because they are variable and changed by termite activity and nest construction. Here, we related the sources and alteration of organic matter in nests from seven different termite genera and feeding habits in the Terra Firme rainforests to the properties of potential food sources soil, wood, and microepiphytes. Chemical analyses comprised isotopic composition of C and N, cellulosic (CPS), non-cellulosic (NCPS), and N-containing saccharides, and molecular composition screening using pyrolysis-field ionization mass spectrometry (Py-FIMS). The isotopic analysis revealed higher soil δ13C (-27.4‰) and δ15N (6.6‰) values in nests of wood feeding Nasutitermes and Cornitermes than in wood samples (δ13C = -29.1‰, δ15N = 3.4‰), reflecting stable-isotope enrichment with organic matter alterations during or after nest construction. This result was confirmed by elevated NCPS:CPS ratios, indicating a preferential cellulose decomposition in the nests. High portions of muramic acid (MurAc) pointed to the participation of bacteria in the transformation processes. Non-metric multidimensional scaling (MDS) revealed increasing geophagy in the sequence Termes < Embiratermes < Anoplotermes and increasing xylophagy for Cornitermes < Nasutitermes., and that the nest material of Constrictotermes was similar to the microepiphytes sample, confirming the report that Constrictotermes belongs to the microepiphyte-feeders. We therewith document that nest chemistry of rainforest termites shows variations and evidence of modification by microbial processes, but nevertheless it primarily reflects the trophic niches of the constructors.

Multimodal system for the planning and guidance of bronchoscopy

NASA Astrophysics Data System (ADS)

Higgins, William E.; Cheirsilp, Ronnarit; Zang, Xiaonan; Byrnes, Patrick

2015-03-01

Many technical innovations in multimodal radiologic imaging and bronchoscopy have emerged recently in the effort against lung cancer. Modern X-ray computed-tomography (CT) scanners provide three-dimensional (3D) high-resolution chest images, positron emission tomography (PET) scanners give complementary molecular imaging data, and new integrated PET/CT scanners combine the strengths of both modalities. State-of-the-art bronchoscopes permit minimally invasive tissue sampling, with vivid endobronchial video enabling navigation deep into the airway-tree periphery, while complementary endobronchial ultrasound (EBUS) reveals local views of anatomical structures outside the airways. In addition, image-guided intervention (IGI) systems have proven their utility for CT-based planning and guidance of bronchoscopy. Unfortunately, no IGI system exists that integrates all sources effectively through the complete lung-cancer staging work flow. This paper presents a prototype of a computer-based multimodal IGI system that strives to fill this need. The system combines a wide range of automatic and semi-automatic image-processing tools for multimodal data fusion and procedure planning. It also provides a flexible graphical user interface for follow-on guidance of bronchoscopy/EBUS. Human-study results demonstrate the system's potential.

Multimodal Neuroimaging in Schizophrenia: Description and Dissemination.

PubMed

Aine, C J; Bockholt, H J; Bustillo, J R; Cañive, J M; Caprihan, A; Gasparovic, C; Hanlon, F M; Houck, J M; Jung, R E; Lauriello, J; Liu, J; Mayer, A R; Perrone-Bizzozero, N I; Posse, S; Stephen, J M; Turner, J A; Clark, V P; Calhoun, Vince D

2017-10-01

In this paper we describe an open-access collection of multimodal neuroimaging data in schizophrenia for release to the community. Data were acquired from approximately 100 patients with schizophrenia and 100 age-matched controls during rest as well as several task activation paradigms targeting a hierarchy of cognitive constructs. Neuroimaging data include structural MRI, functional MRI, diffusion MRI, MR spectroscopic imaging, and magnetoencephalography. For three of the hypothesis-driven projects, task activation paradigms were acquired on subsets of ~200 volunteers which examined a range of sensory and cognitive processes (e.g., auditory sensory gating, auditory/visual multisensory integration, visual transverse patterning). Neuropsychological data were also acquired and genetic material via saliva samples were collected from most of the participants and have been typed for both genome-wide polymorphism data as well as genome-wide methylation data. Some results are also presented from the individual studies as well as from our data-driven multimodal analyses (e.g., multimodal examinations of network structure and network dynamics and multitask fMRI data analysis across projects). All data will be released through the Mind Research Network's collaborative informatics and neuroimaging suite (COINS).

Nesting habitat relationships of sympatric Crested Caracaras, Red-tailed Hawks, and White-tailed Hawks in South Texas

USGS Publications Warehouse

Actkinson, M.A.; Kuvlesky, W.P.; Boal, C.W.; Brennan, L.A.; Hernandez, F.

2007-01-01

We quantified nesting-site habitats for sympatric White-tailed Hawks (Buteo albicaudatus) (n = 40), Red-tailed Hawks (B. jamaicensis) (n = 39), and Crested Caracaras (Caracara cheriway) (n = 24) in the Coastal Sand Plain of south Texas. White-tailed Hawks and Crested Caracara nest sites occurred in savannas, whereas Red-tailed Hawk nest sites occurred in woodlands on the edge of savannas. White-tailed Hawk nest sites were in shrubs and trees that were shorter (3.5 ?? 1.0 m) and had smaller canopy diameters (5.5 ?? 2.1 m) than those of Red-tailed Hawks (10.1 ?? 2.0 m, 13.7 ?? 5.8 m) and Crested Caracaras (5.6 ?? 1.7 m, 8.5 ?? 3.5 m). Red-tailed Hawk nest sites had higher woody densities (15.7 ?? 9.6 plants) and more woody cover (84 ?? 19%) than those of White-tailed Hawks (5.6 ?? 5.8 plants, 20 ?? 21%) and Crested Caracaras (9.9 ?? 6.7 plants, 55 ?? 34%). Crested Caracara nest sites were in dense, multi-branched shrubs composed of more living material (97 ?? 3%) than those of White-tailed (88 ?? 18%) and Red-tailed hawks (88 ?? 18%). Nest sites of White-tailed Hawks, Red-tailed Hawks, and Crested Caracaras were similar to random samples from the surrounding habitat indicating that preferred nesting habitat was available for each of these species at least within 60 m of active nest sites. Nest tree height, along with woody plant and native grass cover best discriminated nest sites among the three raptor species. There was no overlap at Red-tailed and White-tailed hawk nest sites in vegetation structure, while Crested Caracara nests were in habitat intermediate between the two other species. Partitioning of nesting habitat may be how these raptor species co-exist at the broader landscape scale of our study area in the Coastal Sand Plain of Texas.

Using full-cohort data in nested case-control and case-cohort studies by multiple imputation.

PubMed

Keogh, Ruth H; White, Ian R

2013-10-15

In many large prospective cohorts, expensive exposure measurements cannot be obtained for all individuals. Exposure-disease association studies are therefore often based on nested case-control or case-cohort studies in which complete information is obtained only for sampled individuals. However, in the full cohort, there may be a large amount of information on cheaply available covariates and possibly a surrogate of the main exposure(s), which typically goes unused. We view the nested case-control or case-cohort study plus the remainder of the cohort as a full-cohort study with missing data. Hence, we propose using multiple imputation (MI) to utilise information in the full cohort when data from the sub-studies are analysed. We use the fully observed data to fit the imputation models. We consider using approximate imputation models and also using rejection sampling to draw imputed values from the true distribution of the missing values given the observed data. Simulation studies show that using MI to utilise full-cohort information in the analysis of nested case-control and case-cohort studies can result in important gains in efficiency, particularly when a surrogate of the main exposure is available in the full cohort. In simulations, this method outperforms counter-matching in nested case-control studies and a weighted analysis for case-cohort studies, both of which use some full-cohort information. Approximate imputation models perform well except when there are interactions or non-linear terms in the outcome model, where imputation using rejection sampling works well. Copyright © 2013 John Wiley & Sons, Ltd.

Nested-PCR real time as alternative molecular tool for detection of Borrelia burgdorferi compared to the classical serological diagnosis of the blood.

PubMed

Sroka-Oleksiak, Agnieszka; Ufir, Krzysztof; Salamon, Dominika; Bulanda, Malgorzata; Gosiewski, Tomasz

Lyme disease, caused by Borrelia burgdorferi, is a multisystem disease that often makes difficulties to recognize caused by their genetic heterogenity. Currently, the gold standard for the detection of Lyme disease (LD) is serologic diagnostics based mainly on tests: ELISA and Western blot (WB). These methods, however, are subject to consider- able defect, especially in the initial phase of infection due to the occurrence of so-called serological window period and low specificity. For this reason, they might be replaced by molecular methods, for example polymerase chain reaction (PCR), which should be more sensitivity and specificity. In the present study we attempt to optimize the PCR reaction conditions and enhance existing test sensitivity by applying the equivalent of real time PCR - nested PCR for detection B. burgdorferi DNA in the patient's blood. The study involved 94 blood samples of patients with suspected LD. From each sample, 1.5 ml of blood was used for the isolation of bacterial DNA and PCR real time am- plification and its equivalent, in nested version. The remaining part earmarked for serologi- cal testing. Optimization of the reaction conditions made experimentally, using gradient of the temperature and gradient of the magnesium ions concentration for reaction real time in nested-PCR and PCR version. The results show that the nested-PCR real time, has a much higher sensitivity 45 (47.8%) of positive results for the detection of B. burgdorferi compared to the single- variety, without a preceding pre-amplification 2 (2.1%). Serological methods allowed the detection of infection in 41 (43.6%) samples. These results support of the nested PCR method as a better molecular tool for the detection of B. burgdorferi infection than classical PCR real time reaction. The nested-PCR real time method may be considered as a complement to ELISA and WB mainly in the early stages of infection, when in the blood circulating B. burgdorferi cells. By contrast, the results of serological and molecular tests should always be carried out tak- ing into account the patient's clinical status.

Simultaneous detection of Plasmodium vivax and Plasmodium falciparum gametocytes in clinical isolates by multiplex-nested RT-PCR

PubMed Central

2012-01-01

Background Gametocyte carriage is essential for malaria transmission and endemicity of disease; thereby it is a target for malaria control strategies. Malaria-infected individuals may harbour gametocytes below the microscopic detection threshold that can be detected by reverse transcription polymerase chain reaction (RT-PCR) targeting gametocyte-specific mRNA. To date, RT-PCR has mainly been applied to the diagnosis of Plasmodium falciparum gametocytes but very limited for that of Plasmodium vivax. Methods A multiplex-nested RT-PCR targeting Pfs25 and Pvs25 mRNA specific to mature gametocytes of P. falciparum and P. vivax, respectively, was developed. The assay was evaluated using blood samples collected in rainy and dry seasons from febrile patients,in a malaria-endemic area in Thailand. Malaria diagnosis was performed by Giemsa-stained blood smears and 18S rRNA PCR. Results The multiplex-nested RT-PCR detected Pfs25 mRNA in 75 of 86 (87.2%) P. falciparum-infected individuals and Pvs25 mRNA in 82 of 90 (91.1%) P. vivax malaria patients diagnosed by 18S rRNA PCR. Gametocytes were detected in 38 (eight P. falciparum and 30 P. vivax) of 157 microscopy positive samples, implying that a large number of patients harbour sub-microscopic gametocytaemia. No seasonal differences in gametocyte carriage were observed for both malaria species diagnosed by multiplex-nested RT-PCR. With single-nested RT-PCR targeting Pfs25 or Pvs25 mRNA as standard, the multiplex-nested RT-PCR offered sensitivities of 97.4% and 98.9% and specificities of 100% and 98.8% for diagnosing mature gametocytes of P. falciparum and P. vivax, respectively. The minimum detection limit of the multiplex-nested PCR was 10 copies of templates. Conclusions The multiplex-nested RT-PCR developed herein is useful for simultaneous assessment of both P. falciparum and P. vivax gametocyte carriage that is prevalent and generally sympatric in several malaria-endemic areas outside Africa. PMID:22682065

Simultaneous detection of Plasmodium vivax and Plasmodium falciparum gametocytes in clinical isolates by multiplex-nested RT-PCR.

PubMed

Kuamsab, Napaporn; Putaporntip, Chaturong; Pattanawong, Urassaya; Jongwutiwes, Somchai

2012-06-10

Gametocyte carriage is essential for malaria transmission and endemicity of disease; thereby it is a target for malaria control strategies. Malaria-infected individuals may harbour gametocytes below the microscopic detection threshold that can be detected by reverse transcription polymerase chain reaction (RT-PCR) targeting gametocyte-specific mRNA. To date, RT-PCR has mainly been applied to the diagnosis of Plasmodium falciparum gametocytes but very limited for that of Plasmodium vivax. A multiplex-nested RT-PCR targeting Pfs25 and Pvs25 mRNA specific to mature gametocytes of P. falciparum and P. vivax, respectively, was developed. The assay was evaluated using blood samples collected in rainy and dry seasons from febrile patients,in a malaria-endemic area in Thailand. Malaria diagnosis was performed by Giemsa-stained blood smears and 18S rRNA PCR. The multiplex-nested RT-PCR detected Pfs25 mRNA in 75 of 86 (87.2%) P. falciparum-infected individuals and Pvs25 mRNA in 82 of 90 (91.1%) P. vivax malaria patients diagnosed by 18S rRNA PCR. Gametocytes were detected in 38 (eight P. falciparum and 30 P. vivax) of 157 microscopy positive samples, implying that a large number of patients harbour sub-microscopic gametocytaemia. No seasonal differences in gametocyte carriage were observed for both malaria species diagnosed by multiplex-nested RT-PCR. With single-nested RT-PCR targeting Pfs25 or Pvs25 mRNA as standard, the multiplex-nested RT-PCR offered sensitivities of 97.4% and 98.9% and specificities of 100% and 98.8% for diagnosing mature gametocytes of P. falciparum and P. vivax, respectively. The minimum detection limit of the multiplex-nested PCR was 10 copies of templates. The multiplex-nested RT-PCR developed herein is useful for simultaneous assessment of both P. falciparum and P. vivax gametocyte carriage that is prevalent and generally sympatric in several malaria-endemic areas outside Africa.

Use of nested PCR to detect Ceratocystis fagacearum in sapwood of diseased northern oak species

USDA-ARS?s Scientific Manuscript database

Early and accurate diagnosis of oak wilt, caused by Ceratocystis fagacearum (Cf), is important when disease control action is planned. When laboratory diagnosis is needed, standard isolation protocols that are used rely on high quality samples and require > 14 days for incubation. Use of a nested P...

Flying the Nest: How the Home Department Shapes Researchers' Career Paths

ERIC Educational Resources Information Center

Hottenrott, Hanna; Lawson, Cornelia

2017-01-01

This paper studies the importance of the socialization environment--nest--for the career destinations of early career researchers. In a sample of research groups in the fields of science and engineering at universities in Germany, we identify research orientation, output, funding as well as openness to industry and commercialization as relevant…

Parental Representations and Attachment Security in Young Israeli Mothers' Bird's Nest Drawings

ERIC Educational Resources Information Center

Goldner, Limor; Golan, Yifat

2016-01-01

The Bird's Nest Drawing (BND; Kaiser, 1996) is an art-based technique developed to assess attachment security. In an attempt to expand the BND's validity, the authors explored the possible associations between parental representations and the BND's dimensions and attachment classifications in a sample of 80 young Israeli mothers. Positive…

Isolation and confirmation of viral nervous necrosis (VNN) disease in golden grey mullet (Liza aurata) and leaping mullet (Liza saliens) in the Iranian waters of the Caspian Sea.

PubMed

Zorriehzahra, M E J; Ghasemi, M; Ghiasi, M; Karsidani, S Haghighi; Bovo, G; Nazari, A; Adel, M; Arizza, V; Dhama, K

2016-07-15

The present study was conducted on 428 moribund mullet fish samples to isolate and identify the causative agent of a mysterious acute mortality which recently occurred in wild mullets in Iranian waters of Caspian Sea, suspected to be due to viral nervous necrosis (VNN) disease. Disease investigation was carried out employing various diagnostic procedures such as virology, bacteriology, parasitology, haematology, histopathology, IFAT, IHC and nested RT-PCR. Brain and eye samples of affected fishes were collected in sterile conditions and then kept at -80°C for cell culture isolation and nested RT-PCR detection of the causative agent. Other tissue samples were also collected and fixed for histopathology, IHC and EM examinations. CPE was observed in cell cultures at 6days after inoculation. Nine samples were found positive with virological assay. Nested RT-PCR, performed on suspected tissues and CPE positive samples, showed that about 21 tissue samples and all the CPE positive samples were positive for VNN virus (VNNV). IFAT was selected as a confirmatory method for detecting the presence of Betanodavirus antigen, cell culture isolation results and nested RT-PCR findings. Moreover, VNNV particles with 25-30nm in diameter were also visualized in the infected brain and retina. In pathogenicity studies, guppy fishes bathed in VNNV-infected tissue culture (10(-4) TCID50) showed clinical signs similar to naturally infected mullet after 15days post infection (dpi), with mortality rates reaching up to 100% at 30dpi. Affected organ samples as examined by cell culture isolation, IFAT, IHC and histopathology, revealed the presence of VNNV in the guppy fishes. In conclusion, it was confirmed that VNNV was the main causative agent for the disease outbreak in mullet fish in the Caspian Sea, and this is such first official report of VNN disease from Iran. Copyright © 2016 Elsevier B.V. All rights reserved.

Facile synthesis of bird's nest-like TiO2 microstructure with exposed (001) facets for photocatalytic degradation of methylene blue

NASA Astrophysics Data System (ADS)

Zhang, Guozhong; Zhang, Shuqu; Wang, Longlu; Liu, Ran; Zeng, Yunxiong; Xia, Xinnian; Liu, Yutang; Luo, Shenglian

2017-01-01

The scrupulous design of hierarchical structure and highly active crystal facets exposure is essential for the creation of photocatalytic system. However, it is still a big challenge for scrupulous design of TiO2 architectures. In this paper, bird's nest-like anatase TiO2 microstructure with exposed highly active (001) surface has been successfully synthesized by a facile one-step solvothermal method. Methylene blue (MB) is chosen as a model pollutant to evaluate photocatalytic activity of as-obtained TiO2 samples. The results show that the photocatalytic activity of the bird's nest-like sample is more excellent than P25 in the degradation of MB due to high specific surface area and highly active (001) crystal facets exposure when tested under simulated solar light. Besides, it can be readily separated from the photocatalytic system by sedimentation after photocatalytic reaction, which is a significant advantage against conventional powder photocatalyst. The bird's nest-like microspheres with novel structure may have potential application in photocatalysis and other fields.

Development of a rapid and sensitive one-step reverse transcription-nested polymerase chain reaction in a single tube using the droplet-polymerase chain reaction machine.

PubMed

Yamaguchi, Akemi; Matsuda, Kazuyuki; Sueki, Akane; Taira, Chiaki; Uehara, Masayuki; Saito, Yasunori; Honda, Takayuki

2015-08-25

Reverse transcription (RT)-nested polymerase chain reaction (PCR) is a time-consuming procedure because it has several handling steps and is associated with the risk of cross-contamination during each step. Therefore, a rapid and sensitive one-step RT-nested PCR was developed that could be performed in a single tube using a droplet-PCR machine. The K562 BCR-ABL mRNA-positive cell line as well as bone marrow aspirates from 5 patients with chronic myelogenous leukemia (CML) and 5 controls without CML were used. We evaluated one-step RT-nested PCR using the droplet-PCR machine. One-step RT-nested PCR performed in a single tube using the droplet-PCR machine enabled the detection of BCR-ABL mRNA within 40min, which was 10(3)-fold superior to conventional RT nested PCR using three steps in separate tubes. The sensitivity of the one-step RT-nested PCR was 0.001%, with sample reactivity comparable to that of the conventional assay. One-step RT-nested PCR was developed using the droplet-PCR machine, which enabled all reactions to be performed in a single tube accurately and rapidly and with high sensitivity. This one-step RT-nested PCR may be applicable to a wide spectrum of genetic tests in clinical laboratories. Copyright © 2015 Elsevier B.V. All rights reserved.

Impact of pest control strategies on the arthropodofauna living in bird nests built in nestboxes in pear and apple orchards.

PubMed

Roy, Lise; Bouvier, Jean-Charles; Lavigne, Claire; Galès, Mathieu; Buronfosse, Thierry

2013-08-01

Pesticide applications have a strong impact on biodiversity in agroecosystems. The present study aimed to assess the impact of pest control strategies on the arthropodofauna of Parus major nests built within nestboxes installed in orchards. Unlike many studied groups, these arthropod communities are not in direct contact with pesticide sprays (on account of their being sheltered by nestboxes) and are also unable to move away from the treated area. In this pilot study, we estimated the prevalence and the taxonomic and ecological diversities of arthropodofauna sampled in the nests and assessed the extent to which the whole and nest-specific arthropodofauna were affected by pest control strategies. Sixteen different insect and arachnid Primary Taxonomic Groups (PTGs, order level or below) were found in nests. The best represented PTGs (≥10% occurrence in years 2007 and 2008) were Psocoptera (Insecta, detritivorous/saprophagous), detritivorous/saprophagous Astigmata (Acari) and hematophagous Mesostigmata (Acari). Pest control strategies had a large impact on the prevalence of arthropods in nests, with higher proportions of nests hosting arthropods in organic orchards than in conventional orchards and with intermediate proportions in nests in Integrated Pest Management orchards. In contrast, pest control strategies had no significant effect on the composition of the arthropod communities when only nests hosting nidicolous arthropods were considered.

Patch size and edge proximity are useful predictors of brood parasitism but not nest survival of grassland birds.

PubMed

Benson, Thomas J; Chiavacci, Scott J; Ward, Michael P

2013-06-01

Declines of migratory birds have led to increased focus on causative factors for these declines, including the potential adverse effects of habitat fragmentation on reproductive success. Although numerous studies have addressed how proximity to a habitat edge, patch size, or landscape context influence nest survival or brood parasitism, many have failed to find the purported effects. Furthermore, many have sought to generalize patterns across large geographic areas and habitats. Here, we examined evidence for effects of edge proximity, patch size, and landscape context on nest survival and brood parasitism of grassland birds, a group of conservation concern. The only consistent effect was a positive association between edge proximity and brood parasitism. We examined effects of patch size on nest survival (37 studies) and brood parasitism (30 studies) representing 170 and 97 different estimates, respectively, with a total sample size of > 14000 nests spanning eastern North America. Nest survival weakly increased with patch size in the Great Plains, but not in the Midwestern or Eastern United States, and brood parasitism was inversely related to patch size and consistently greater in the Great Plains. The consistency in brood parasitism relative to nest survival patterns is likely due to parasitism being caused by one species, while nest survival is driven by a diverse and variable suite of nest predators. Often, studies assume that predators responsible for nest predation, the main driver of nest success, either are the same or exhibit the same behaviors across large geographic areas. These results suggest that a better mechanistic understanding of nest predation is needed to provide meaningful conservation recommendations for improving grassland bird productivity, and that the use of general recommendations across large geographic areas should only be undertaken when sufficient data are available from all regions.

Diagnostic value of nested-PCR for identification of Malassezia species in dandruff

NASA Astrophysics Data System (ADS)

Jusuf, N. K.; Nasution, T. A.; Ullyana, S.

2018-03-01

Dandruff or pityriasis simplex is a condition of abnormal occurrence of formation of yellowish white scales from the scalp. Many factors play a role in the pathogenesis of dandruff, i.e.colonization of Malassezia species. Examination of Malassezia species previously done by culture as the gold standard. However, there are various difficulties in doing the culture. Identification method with anested-polymerase chain reaction (nested-PCR) is expected to provide quickly and easily detected. This study aimedto determine the diagnostic value of nested-PCR in the identification of Malassezia species in dandruff. From 21 subjects, scales from the scalp were taken and sent to the laboratory for nested-PCR identification. Statistical analysis of diagnostic test carried out to determine sensitivity, specificity, positive predictive value, and negative predictive value. The results showed nested-PCR detected 10 sample (47.6%) positive for Malassezia species consist of M. sympodialis (23.8%); M. slooffiae (9.5%); M. furfur (4.8%); M. globosa and M. furfur (4.8%); and M. restricta and M. sympodialis (4.8%). Detection of Malassezia species by nested-PCR has 100% in sensitivity whereas the specificity was 55%. Nested-PCR test has high sensitivity. Therefore nested-PCR may be considered for a faster and simpler alternative examination in identification for Malassezia species in dandruff.

Multimodal label-free ex vivo imaging using a dual-wavelength microscope with axial chromatic aberration compensation.

PubMed

Filippi, Andrea; Dal Sasso, Eleonora; Iop, Laura; Armani, Andrea; Gintoli, Michele; Sandri, Marco; Gerosa, Gino; Romanato, Filippo; Borile, Giulia

2018-03-01

Label-free microscopy is a very powerful technique that can be applied to study samples with no need for exogenous fluorescent probes, keeping the main benefits of multiphoton microscopy, such as longer penetration depths and intrinsic optical sectioning while enabling serial multitechniques examinations on the same specimen. Among the many label-free microscopy methods, harmonic generation (HG) is one of the most intriguing methods due to its generally low photo-toxicity and relative ease of implementation. Today, HG and common two-photon microscopy (TPM) are well-established techniques, and are routinely used in several research fields. However, they require a significant amount of fine-tuning to be fully exploited, making them quite difficult to perform in parallel. Here, we present our designed multimodal microscope, capable of performing simultaneously TPM and HG without any kind of compromise thanks to two, separate, individually optimized laser sources with axial chromatic aberration compensation. We also apply our setup to the examination of a plethora of ex vivo samples to prove its capabilities and the significant advantages of a multimodal approach. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Comparison of Antigen Detection and Nested PCR in CSF Samples of HIV Positive and Negative Patients with Suspected Cryptococcal Meningitis in a Tertiary Care Hospital.

PubMed

Kumari, Sunita; Verma, Rajesh Kumar; Singh, Dharmendra Prasad; Yadav, Ramakant

2016-04-01

The cases of cryptococcal meningitis and other forms of cryptococcosis have increased in recent time and the present scenario of the condition with significant morbidity and mortality is actually posing a serious threat to the community, so an early and prompt diagnosis is necessary to prevent serious complications and thus improving the overall disease outcome. Comparison of diagnostic efficacy of nested Polymerase Chain Reaction (PCR) with Latex Agglutination Test (LAT) in the Cerebro Spinal Fluid (CSF) samples of the cases of meningitis in HIV positive and negative cases. We have compared the diagnostic efficacy of Latex Agglutination Test (LAT) with nested Polymerase Chain Reaction (PCR) in 200 Cerebrospinal Fluid (CSF) samples, including 14 HIV positive also, in the cases of suspected cryptococcal meningitis. Nested PCR was done in all cases reporting positive by LAT and results were then compared with that of India ink and culture on Sabouraud Dextrose Agar (SDA), and the isolates were further identified by urease, nitrate and sugar assimilation tests. Of the 200 cases, including 14 HIV positive, LAT was positive in 46 cases while 154 were negative. Out of these 46 LAT positive cases, nested PCR was positive in 40 cases only, while culture and India ink was positive in 38 and 33 cases respectively. Majority of the cases, 30 (65.2%) were between age group 21-50 years, while 2 (4.3%) in 0-20, and 14 (30.4%) in 51-80 years age group. Although negative staining like India ink and nigrosin are most widely used techniques, but these suffer with subjective error. Rapid method like LAT is available but it always has the scope of false positive and negative results. In such cases nested PCR can help in establishing final diagnosis.

Optimization of the elution buffer and concentration method for detecting hepatitis E virus in swine liver using a nested reverse transcription-polymerase chain reaction and real-time reverse transcription-polymerase chain reaction.

PubMed

Son, Na Ry; Seo, Dong Joo; Lee, Min Hwa; Seo, Sheungwoo; Wang, Xiaoyu; Lee, Bog-Hieu; Lee, Jeong-Su; Joo, In-Sun; Hwang, In-Gyun; Choi, Changsun

2014-09-01

The aim of this study was to develop an optimal technique for detecting hepatitis E virus (HEV) in swine livers. Here, three elution buffers and two concentration methods were compared with respect to enhancing recovery of HEV from swine liver samples. Real-time reverse transcription-polymerase chain reaction (RT-PCR) and nested RT-PCR were performed to detect HEV RNA. When phosphate-buffered saline (PBS, pH 7.4) was used to concentrate HEV in swine liver samples using ultrafiltration, real-time RT-PCR detected HEV in 6 of the 26 samples. When threonine buffer was used to concentrate HEV using polyethylene glycol (PEG) precipitation and ultrafiltration, real-time RT-PCR detected HEV in 1 and 3 of the 26 samples, respectively. When glycine buffer was used to concentrate HEV using ultrafiltration and PEG precipitation, real-time RT-PCR detected HEV in 1 and 3 samples of the 26 samples, respectively. When nested RT-PCR was used to detect HEV, all samples tested negative regardless of the type of elution buffer or concentration method used. Therefore, the combination of real-time RT-PCR and ultrafiltration with PBS buffer was the most sensitive and reliable method for detecting HEV in swine livers. Copyright © 2014 Elsevier B.V. All rights reserved.

Detection of Giardia intestinalis in water samples collected from natural water reservoirs and wells in northern and north-eastern Poland using LAMP, real-time PCR and nested PCR.

PubMed

Lass, Anna; Szostakowska, Beata; Korzeniewski, Krzysztof; Karanis, Panagiotis

2017-10-01

Giardia intestinalis is a protozoan parasite, transmitted to humans and animals by the faecal-oral route, mainly through contaminated water and food. Knowledge about the distribution of this parasite in surface water in Poland is fragmentary and incomplete. Accordingly, 36 environmental water samples taken from surface water reservoirs and wells were collected in Pomerania and Warmia-Masuria provinces, Poland. The 50 L samples were filtered and subsequently analysed with three molecular detection methods: loop-mediated isothermal amplification (LAMP), real-time polymerase chain reaction (real-time PCR) and nested PCR. Of the samples examined, Giardia DNA was found in 15 (42%) samples with the use of LAMP; in 12 (33%) of these samples, Giardia DNA from this parasite was also detected using real-time PCR; and in 9 (25%) using nested PCR. Sequencing of selected positive samples confirmed that the PCR products were fragments of the Giardia intestinalis small subunit rRNA gene. Genotyping using multiplex real-time PCR indicated the presence of assemblages A and B, with the latter predominating. The results indicate that surface water in Poland, as well as water taken from surface wells, may be a source of Giardia strains which are potentially pathogenic for humans. It was also demonstrated that LAMP assay is more sensitive than the other two molecular assays.

First record of interspecific breeding of Least Bell's Vireo and White-eyed Vireo

USGS Publications Warehouse

Blundell, Melissa A.; Kus, Barbara E.

2011-01-01

We provide the first known documentation of a male Least Bell's Vireo (Vireo bellii pusillus) breeding with a female White-eyed Vireo (V. griseus) and the first report of a White-eyed Vireo breeding in California at the San Luis Rey River, Oceanside, San Diego County. We discovered the pair building a nest on 12 May 2010. The female laid four eggs, and the pair successfully raised and fledged four nestlings. We collected DNA samples from each nestling and the female during the nestling stage and banded them with a numbered federal leg band for future identification. We obtained detailed nest measurements after fledging and monitored the territory for further nesting attempts. No additional nesting attempts were detected.

Multimodal nonlinear imaging of arabidopsis thaliana root cell

NASA Astrophysics Data System (ADS)

Jang, Bumjoon; Lee, Sung-Ho; Woo, Sooah; Park, Jong-Hyun; Lee, Myeong Min; Park, Seung-Han

2017-07-01

Nonlinear optical microscopy has enabled the possibility to explore inside the living organisms. It utilizes ultrashort laser pulse with long wavelength (greater than 800nm). Ultrashort pulse produces high peak power to induce nonlinear optical phenomenon such as two-photon excitation fluorescence (TPEF) and harmonic generations in the medium while maintaining relatively low average energy pre area. In plant developmental biology, confocal microscopy is widely used in plant cell imaging after the development of biological fluorescence labels in mid-1990s. However, fluorescence labeling itself affects the sample and the sample deviates from intact condition especially when labelling the entire cell. In this work, we report the dynamic images of Arabidopsis thaliana root cells. This demonstrates the multimodal nonlinear optical microscopy is an effective tool for long-term plant cell imaging.

Multimodal Image-Based Virtual Reality Presurgical Simulation and Evaluation for Trigeminal Neuralgia and Hemifacial Spasm.

PubMed

Yao, Shujing; Zhang, Jiashu; Zhao, Yining; Hou, Yuanzheng; Xu, Xinghua; Zhang, Zhizhong; Kikinis, Ron; Chen, Xiaolei

2018-05-01

To address the feasibility and predictive value of multimodal image-based virtual reality in detecting and assessing features of neurovascular confliction (NVC), particularly regarding the detection of offending vessels, degree of compression exerted on the nerve root, in patients who underwent microvascular decompression for nonlesional trigeminal neuralgia and hemifacial spasm (HFS). This prospective study includes 42 consecutive patients who underwent microvascular decompression for classic primary trigeminal neuralgia or HFS. All patients underwent preoperative 1.5-T magnetic resonance imaging (MRI) with T2-weighted three-dimensional (3D) sampling perfection with application-optimized contrasts by using different flip angle evolutions, 3D time-of-flight magnetic resonance angiography, and 3D T1-weighted gadolinium-enhanced sequences in combination, whereas 2 patients underwent extra experimental preoperative 7.0-T MRI scans with the same imaging protocol. Multimodal MRIs were then coregistered with open-source software 3D Slicer, followed by 3D image reconstruction to generate virtual reality (VR) images for detection of possible NVC in the cerebellopontine angle. Evaluations were performed by 2 reviewers and compared with the intraoperative findings. For detection of NVC, multimodal image-based VR sensitivity was 97.6% (40/41) and specificity was 100% (1/1). Compared with the intraoperative findings, the κ coefficients for predicting the offending vessel and the degree of compression were >0.75 (P < 0.001). The 7.0-T scans have a clearer view of vessels in the cerebellopontine angle, which may have significant impact on detection of small-caliber offending vessels with relatively slow flow speed in cases of HFS. Multimodal image-based VR using 3D sampling perfection with application-optimized contrasts by using different flip angle evolutions in combination with 3D time-of-flight magnetic resonance angiography sequences proved to be reliable in detecting NVC and in predicting the degree of root compression. The VR image-based simulation correlated well with the real surgical view. Copyright © 2018 Elsevier Inc. All rights reserved.

Image-guided plasma therapy of cutaneous wound

NASA Astrophysics Data System (ADS)

Zhang, Zhiwu; Ren, Wenqi; Yu, Zelin; Zhang, Shiwu; Yue, Ting; Xu, Ronald

2014-02-01

The wound healing process involves the reparative phases of inflammation, proliferation, and remodeling. Interrupting any of these phases may result in chronically unhealed wounds, amputation, or even patient death. Despite the clinical significance in chronic wound management, no effective methods have been developed for quantitative image-guided treatment. We integrated a multimodal imaging system with a cold atmospheric plasma probe for image-guided treatment of chronic wound. Multimodal imaging system offers a non-invasive, painless, simultaneous and quantitative assessment of cutaneous wound healing. Cold atmospheric plasma accelerates the wound healing process through many mechanisms including decontamination, coagulation and stimulation of the wound healing. The therapeutic effect of cold atmospheric plasma is studied in vivo under the guidance of a multimodal imaging system. Cutaneous wounds are created on the dorsal skin of the nude mice. During the healing process, the sample wound is treated by cold atmospheric plasma at different controlled dosage, while the control wound is healed naturally. The multimodal imaging system integrating a multispectral imaging module and a laser speckle imaging module is used to collect the information of cutaneous tissue oxygenation (i.e. oxygen saturation, StO2) and blood perfusion simultaneously to assess and guide the plasma therapy. Our preliminary tests show that cold atmospheric plasma in combination with multimodal imaging guidance has the potential to facilitate the healing of chronic wounds.

Rapid Screening of Cancer Margins in Tissue with Multimodal Confocal Microscopy

PubMed Central

Gareau, Daniel S.; Jeon, Hana; Nehal, Kishwer S.; Rajadhyaksha, Milind

2012-01-01

Background Complete and accurate excision of cancer is guided by the examination of histopathology. However, preparation of histopathology is labor intensive and slow, leading to insufficient sampling of tissue and incomplete and/or inaccurate excision of margins. We demonstrate the potential utility of multimodal confocal mosaicing microscopy for rapid screening of cancer margins, directly in fresh surgical excisions, without the need for conventional embedding, sectioning or processing. Materials/Methods A multimodal confocal mosaicing microscope was developed to image basal cell carcinoma margins in surgical skin excisions, with resolution that shows nuclear detail. Multimodal contrast is with fluorescence for imaging nuclei and reflectance for cellular cytoplasm and dermal collagen. Thirtyfive excisions of basal cell carcinomas from Mohs surgery were imaged, and the mosaics analyzed by comparison to the corresponding frozen pathology. Results Confocal mosaics are produced in about 9 minutes, displaying tissue in fields-of-view of 12 mm with 2X magnification. A digital staining algorithm transforms black and white contrast to purple and pink, which simulates the appearance of standard histopathology. Mosaicing enables rapid digital screening, which mimics the examination of histopathology. Conclusions Multimodal confocal mosaicing microscopy offers a technology platform to potentially enable real-time pathology at the bedside. The imaging may serve as an adjunct to conventional histopathology, to expedite screening of margins and guide surgery toward more complete and accurate excision of cancer. PMID:22721570

Territory and nest site selection patterns by Grasshopper Sparrows in southeastern Arizona

USGS Publications Warehouse

Ruth, Janet M.; Skagen, Susan K.

2017-01-01

Grassland bird populations are showing some of the greatest rates of decline of any North American birds, prompting measures to protect and improve important habitat. We assessed how vegetation structure and composition, habitat features often targeted for management, affected territory and nest site selection by Grasshopper Sparrows (Ammodramus savannarum ammolegus) in southeastern Arizona. To identify features important to males establishing territories, we compared vegetation characteristics of known territories and random samples on 2 sites over 5 years. We examined habitat selection patterns of females by comparing characteristics of nest sites with territories over 3 years. Males selected territories in areas of sparser vegetation structure and more tall shrubs (>2 m) than random plots on the site with low shrub densities. Males did not select territories based on the proportion of exotic grasses. Females generally located nest sites in areas with lower small shrub (1–2 m tall) densities than territories overall when possible and preferentially selected native grasses for nest construction. Whether habitat selection was apparent depended upon the range of vegetation structure that was available. We identified an upper threshold above which grass structure seemed to be too high and dense for Grasshopper Sparrows. Our results suggest that some management that reduces vegetative structure may benefit this species in desert grasslands at the nest and territory scale. However, we did not assess initial male habitat selection at a broader landscape scale where their selection patterns may be different and could be influenced by vegetation density and structure outside the range of values sampled in this study.

A nested real-time PCR assay for the quantification of Plasmodium falciparum DNA extracted from dried blood spots.

PubMed

Tran, Tuan M; Aghili, Amirali; Li, Shanping; Ongoiba, Aissata; Kayentao, Kassoum; Doumbo, Safiatou; Traore, Boubacar; Crompton, Peter D

2014-10-04

As public health efforts seek to eradicate malaria, there has been an emphasis on eliminating low-density parasite reservoirs in asymptomatic carriers. As such, diagnosing submicroscopic Plasmodium infections using PCR-based techniques has become important not only in clinical trials of malaria vaccines and therapeutics, but also in active malaria surveillance campaigns. However, PCR-based quantitative assays that rely on nucleic acid extracted from dried blood spots (DBS) have demonstrated lower sensitivity than assays that use cryopreserved whole blood as source material. The density of Plasmodium falciparum asexual parasites was quantified using genomic DNA extracted from dried blood spots (DBS) and the sensitivity of two approaches was compared: quantitative real-time PCR (qPCR) targeting the P. falciparum 18S ribosomal RNA gene, either with an initial conventional PCR amplification prior to qPCR (nested qPCR), or without an initial amplification (qPCR only). Parasite densities determined by nested qPCR, qPCR only, and light microscopy were compared. Nested qPCR results in 10-fold higher sensitivity (0.5 parasites/μl) when compared to qPCR only (five parasites/ul). Among microscopy-positive samples, parasite densities calculated by nested qPCR correlated strongly with microscopy for both asymptomatic (Pearson's r=0.58, P<0.001) and symptomatic (Pearson's r=0.70, P<0.0001) P. falciparum infections. Nested qPCR improves the sensitivity for the detection of P. falciparum blood-stage infection from clinical DBS samples. This approach may be useful for active malaria surveillance in areas where submicroscopic asymptomatic infections are prevalent.

Diagnosis of theileria equi infections in horses in the Azores using cELISA and nested PCR

USDA-ARS?s Scientific Manuscript database

Equine piroplasmosis is a tick-borne disease of equids that is often caused by the parasite Theileria equi. We applied competitive ELISA (cELISA) and nested PCR diagnostic methods to detect this parasite in horses by screening 162 samples from mainland Portugal where the parasite is endemic, and 143...

Genome-wide association study of carbon and nitrogen metabolism in the maize nested association mapping population

USDA-ARS?s Scientific Manuscript database

Carbon (C) and nitrogen (N) metabolism are critical to plant growth and development and at the basis of yield and adaptation. We have applied high throughput metabolite analyses to over 12,000 diverse field grown samples from the maize nested association mapping population. This allowed us to identi...

Effects of industrial and investigator disturbance on Arctic-nesting geese

USGS Publications Warehouse

Meixell, Brandt W.; Flint, Paul L.

2017-01-01

Oil and gas development on the Arctic Coastal Plain (ACP) of Alaska, USA may have effects on Arctic-nesting birds. To estimate effects of industrial activity and investigator disturbance on avian productivity, we monitored nests of greater white-fronted geese (Anser albifrons) with digital cameras and periodic nest visits during 2013–2014 at 2 sites on the ACP. A disturbed site was adjacent to human-made infrastructure and industrial clean-up activities initiated at the onset of the study and a control site was >2 km from sources of industrial disturbance. We assessed variation in estimates of incubation constancy, nest survival, and predator behavior relative to site, year, and distance from industrial activity using nest photographs obtained at 1-minute intervals. We compared analysis of hourly nest survival informed by intensive monitoring with cameras to analysis of daily nest survival informed by traditional nest visit data obtained at intervals of 5–7 days to assess how method and time scale of sampling affect ecological inference. Geese in both sites exhibited high levels of nest attendance and initiated incubation breaks less than once per day. Observer-caused incubation breaks associated with nest visits ( = 37.8 min) were longer than other types of incubation breaks ( = 8.7 min), demonstrating a differential response by nesting geese to direct human encroachment versus indirect vehicular and aircraft traffic. During both years, geese were absent from nests more frequently in the disturbed ( = 0.9 breaks/day) than control ( = 0.6 breaks/day) site, and this break frequency was slightly higher for nests closer to industrial activity. In the year with high rates of depredation, nest survival was positively related to distance from industrial activity and abandoned infrastructure, consistent with predictions of industry-caused effects. This relationship, however, was not evident in the year with reduced predation pressure, likely because of annual variation in arctic fox (Vulpes lagopus) behavior. Analysis of nest survival probability informed by camera data allowed for detection of detailed patterns of variation that were not supported when using only visit data for the same nests. Observer visits were responsible for reductions of 7–35% in nest survival probability, highlighting the importance of minimizing, and controlling for, observer effects in studies of avian productivity. Indirect vehicular and aircraft disturbance posed less risk to nest survival than direct encroachment by observers at nest sites. Therefore, effects of industrial activities on avian productivity in the Arctic can be minimized through practices that limit direct encounters with nests. 

Improvement of DGGE analysis by modifications of PCR protocols for analysis of microbial community members with low abundance.

PubMed

Wang, Yong-Feng; Zhang, Fang-Qiu; Gu, Ji-Dong

2014-06-01

Denaturing gradient gel electrophoresis (DGGE) is a powerful technique to reveal the community structures and composition of microorganisms in complex natural environments and samples. However, positive and reproducible polymerase chain reaction (PCR) products, which are difficult to acquire for some specific samples due to low abundance of the target microorganisms, significantly impair the effective applications of DGGE. Thus, nested PCR is often introduced to generate positive PCR products from the complex samples, but one problem is also introduced: The total number of thermocycling in nested PCR is usually unacceptably high, which results in skewed community structures by generation of random or mismatched PCR products on the DGGE gel, and this was demonstrated in this study. Furthermore, nested PCR could not resolve the uneven representative issue with PCR products of complex samples with unequal richness of microbial population. In order to solve the two problems in nested PCR, the general protocol was modified and improved in this study. Firstly, a general PCR procedure was used to amplify the target genes with the PCR primers without any guanine cytosine (GC) clamp, and then, the resultant PCR products were purified and diluted to 0.01 μg ml(-1). Subsequently, the diluted PCR products were utilized as templates to amplify again with the same PCR primers with the GC clamp for 17 cycles, and the products were finally subjected to DGGE analysis. We demonstrated that this is a much more reliable approach to obtain a high quality DGGE profile with high reproducibility. Thus, we recommend the adoption of this improved protocol in analyzing microorganisms of low abundance in complex samples when applying the DGGE fingerprinting technique to avoid biased results.

Do weather conditions correlate with findings in failed, provision-filled nest cells of Megachile rotundata (Hymenoptera: Megachilidae) in western North America?

PubMed

Pitts-Singer, Theresa L; James, Rosalind R

2008-06-01

Cavity-nesting alfalfa leafcutting bees, Megachile rotundata (F.) (Hymenoptera: Megachilidae), are excellent pollinators of alfalfa, Medicago savita L., for seed production. In commercial settings, artificial cavities are placed in field domiciles for nesting and, thereby, bee populations are sustained for future use. For this study, cells from leafcutting bee nests were collected in late summer from commercial seed fields. Over 3 yr (2003-2005), 39 samples in total of approximately equal to 1,000 cells each were taken from several northwestern U.S. states and from Manitoba, Canada. X-radiography of 500 cells from each sample was used to identify "pollen balls" (i.e., cells in which the pollen-nectar provision remained, but the egg or larva, if present, was not detectable on an x-radiograph). Most U.S. samples seemed to have higher proportions of pollen ball cells than Manitoba samples. Pollen ball cells were dissected to determine the moisture condition of the mass provision and true contents of each cell. Most pollen ball cells from Manitoba samples contained fungus, the frequency of which was positively correlated with cool, wet weather. In the United States, most pollen ball cells had moist provisions, and many of them lacked young brood. Correlation analysis revealed that pollen ball cells occurred in greater proportions in fields with more hot days (above 38 degrees C). Broodless pollen ball cells occurred in greater proportions under cool conditions, but dead small larvae (second-third instars) seemed to occur in greater proportions under hot conditions. Pollen ball cells with unhatched eggs and first instars (in the chorion) occurred in lesser proportions under hot conditions.

Diagnostic potential of nested PCR, galactomannan EIA, and beta-D-glucan for invasive aspergillosis in pediatric patients.

PubMed

Badiee, Parisa; Alborzi, Abdolvahab; Karimi, Mahammad; Pourabbas, Bahman; Haddadi, Pedram; Mardaneh, Jalal; Moieni, Mahsa

2012-04-13

Limited specific data and investigations are available for invasive aspergillosis (IA) in pediatric patients. We evaluated the diagnostic potential of three noninvasive tests including the Platelia Aspergillus EIA kit for using galactomannan antigen, (1,3)-β-D-glucan Detection Reagent Kit, and nested-PCR for Aspergillus DNA in sera. We evaluated the diagnostic potential of three noninvasive tests including EIA for galactomannan antigen  (Platelia Aspergillus), nested  PCR assay for Aspergillus DNA and test for (1→3)-β-D-glucan (Glucatell assay Kit). All pediatric patients treated at the hematology/oncology unit who were at increased risk of developing invasive aspergillosis were enrolled. Clinical samples were examined for Aspergillus infections by mycological methods. Serial blood samples were collected twice weekly and evaluated by noninvasive tests. We analyzed 230 consecutive blood samples from 62 pediatric patients. The incidence rate of invasive aspergillosis in the patients was found to be 27.4%, and the etiologic agents were Aspergillus flavus, Aspergillus fumigatus, and Aspergillus spp.  The sensitivity, specificity, positive and negative predictive values, and likelihood ratios for positive and negative results of galactomannan in patients with proven and probable IA were 90%, 92%, 81.8%, 96%, 11.25, and 0.1; for beta-D-glucan they were 50%, 46%, 26%, 70.6%, 0.9, 0.9; and for nested-PCR they were 80%, 96.2%, 88.9%, 92.6%, 21, and 0.2, respectively. The conventional methods are not able to detect IA, due to the lack of valid and proper sampling. Galactomannan and nested-PCR tests in serum, with enough accuracy and reliability, can serve as noninvasive methods for the detection of IA in pediatric patients. However, the beta-D-glucan test cannot serve as an efficient diagnostic tool in those with hematologic disorders. 

Analysis of Clinical Cohort Data Using Nested Case-control and Case-cohort Sampling Designs. A Powerful and Economical Tool.

PubMed

Ohneberg, K; Wolkewitz, M; Beyersmann, J; Palomar-Martinez, M; Olaechea-Astigarraga, P; Alvarez-Lerma, F; Schumacher, M

2015-01-01

Sampling from a large cohort in order to derive a subsample that would be sufficient for statistical analysis is a frequently used method for handling large data sets in epidemiological studies with limited resources for exposure measurement. For clinical studies however, when interest is in the influence of a potential risk factor, cohort studies are often the first choice with all individuals entering the analysis. Our aim is to close the gap between epidemiological and clinical studies with respect to design and power considerations. Schoenfeld's formula for the number of events required for a Cox' proportional hazards model is fundamental. Our objective is to compare the power of analyzing the full cohort and the power of a nested case-control and a case-cohort design. We compare formulas for power for sampling designs and cohort studies. In our data example we simultaneously apply a nested case-control design with a varying number of controls matched to each case, a case cohort design with varying subcohort size, a random subsample and a full cohort analysis. For each design we calculate the standard error for estimated regression coefficients and the mean number of distinct persons, for whom covariate information is required. The formula for the power of a nested case-control design and the power of a case-cohort design is directly connected to the power of a cohort study using the well known Schoenfeld formula. The loss in precision of parameter estimates is relatively small compared to the saving in resources. Nested case-control and case-cohort studies, but not random subsamples yield an attractive alternative for analyzing clinical studies in the situation of a low event rate. Power calculations can be conducted straightforwardly to quantify the loss of power compared to the savings in the num-ber of patients using a sampling design instead of analyzing the full cohort.

A multiplex reverse transcription-nested polymerase chain reaction for detection and differentiation of wild-type and vaccine strains of canine distemper virus

PubMed Central

2010-01-01

A multiplex reverse transcription-nested polymerase chain reaction (RT-nPCR) method was developed for the detection and differentiation of wild-type and vaccine strains of canine distemper virus (CDV). A pair of primers (P1 and P4) specific for CDV corresponding to the highly conserved region of the CDV genome were used as a common primer pair in the first-round PCR of the nested PCR. Primers P2 specific for CDV wild-type strains, were used as the forward primer together with the common reverse primer P4 in the second round of nested PCR. Primers P3, P5 specific for CDV wild-type strain or vaccine strain, were used as the forward primer together with the common reverse primer P4+P6 in the second round of nested PCR. A fragment of 177 bp was amplified from vaccine strain genomic RNA, and a fragment of 247 bp from wild-type strain genomic RNA in the RT-nPCR, and two fragments of 247 bp and 177 bp were amplified from the mixed samples of vaccine and wild-type strains. No amplification was achieved for uninfected cells, or cells infected with Newcastle disease virus (NDV), canine parvovirus (CPV), canine coronavirus (CCV), rabies virus (RV), or canine adenovirus (CAV). The RT-nPCR method was used to detect 30 field samples suspected of canine distemper from Heilongjiang and Jilin Provinces, and 51 samples in Shandong province. As a result of 30 samples, were found to be wild-type-like, and 5 to be vaccine-strain-like. The RT-nPCR method can be used to effectively detect and differentiate wild-type CDV-infected dogs from dogs vaccinated with CDV vaccine, and thus can be used in clinical detection and epidemiological surveillance. PMID:20433759

Multimodal MSI in Conjunction with Broad Coverage Spatially Resolved MS 2 Increases Confidence in Both Molecular Identification and Localization

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

Veličković, Dušan; Chu, Rosalie K.; Carrell, Alyssa A.

One critical aspect of mass spectrometry imaging (MSI) is the need to confidently identify detected analytes. While orthogonal tandem MS (e.g., LC-MS 2) experiments from sample extracts can assist in annotating ions, the spatial information about these molecules is lost. Accordingly, this could cause mislead conclusions, especially in cases where isobaric species exhibit different distributions within a sample. In this Technical Note, we employed a multimodal imaging approach, using matrix assisted laser desorption/ionization (MALDI)-MSI and liquid extraction surface analysis (LESA)-MS 2I, to confidently annotate and One critical aspect of mass spectrometry imaging (MSI) is the need to confidently identify detectedmore » analytes. While orthogonal tandem MS (e.g., LC-MS2) experiments from sample extracts can assist in annotating ions, the spatial information about these molecules is lost. Accordingly, this could cause mislead conclusions, especially in cases where isobaric species exhibit different distributions within a sample. In this Technical Note, we employed a multimodal imaging approach, using matrix assisted laser desorption/ionization (MALDI)-MSI and liquid extraction surface analysis (LESA)-MS 2I, to confidently annotate and localize a broad range of metabolites involved in a tripartite symbiosis system of moss, cyanobacteria, and fungus. We found that the combination of these two imaging modalities generated very congruent ion images, providing the link between highly accurate structural information onfered by LESA and high spatial resolution attainable by MALDI. These results demonstrate how this combined methodology could be very useful in differentiating metabolite routes in complex systems.« less

Body Size Correlates with Fertilization Success but not Gonad Size in Grass Goby Territorial Males

PubMed Central

Pujolar, Jose Martin; Locatello, Lisa; Zane, Lorenzo; Mazzoldi, Carlotta

2012-01-01

In fish species with alternative male mating tactics, sperm competition typically occurs when small males that are unsuccessful in direct contests steal fertilization opportunities from large dominant males. In the grass goby Zosterisessor ophiocephalus, large territorial males defend and court females from nest sites, while small sneaker males obtain matings by sneaking into nests. Parentage assignment of 688 eggs from 8 different nests sampled in the 2003–2004 breeding season revealed a high level of sperm competition. Fertilization success of territorial males was very high but in all nests sneakers also contributed to the progeny. In territorial males, fertilization success correlated positively with male body size. Gonadal investment was explored in a sample of 126 grass gobies collected during the period 1995–1996 in the same area (61 territorial males and 65 sneakers). Correlation between body weight and testis weight was positive and significant for sneaker males, while correlation was virtually equal to zero in territorial males. That body size in territorial males is correlated with fertilization success but not gonad size suggests that males allocate much more energy into growth and relatively little into sperm production once the needed size to become territorial is attained. The increased paternity of larger territorial males might be due to a more effective defense of the nest in comparison with smaller territorial males. PMID:23056415

Body size correlates with fertilization success but not gonad size in grass goby territorial males.

PubMed

Pujolar, Jose Martin; Locatello, Lisa; Zane, Lorenzo; Mazzoldi, Carlotta

2012-01-01

In fish species with alternative male mating tactics, sperm competition typically occurs when small males that are unsuccessful in direct contests steal fertilization opportunities from large dominant males. In the grass goby Zosterisessor ophiocephalus, large territorial males defend and court females from nest sites, while small sneaker males obtain matings by sneaking into nests. Parentage assignment of 688 eggs from 8 different nests sampled in the 2003-2004 breeding season revealed a high level of sperm competition. Fertilization success of territorial males was very high but in all nests sneakers also contributed to the progeny. In territorial males, fertilization success correlated positively with male body size. Gonadal investment was explored in a sample of 126 grass gobies collected during the period 1995-1996 in the same area (61 territorial males and 65 sneakers). Correlation between body weight and testis weight was positive and significant for sneaker males, while correlation was virtually equal to zero in territorial males. That body size in territorial males is correlated with fertilization success but not gonad size suggests that males allocate much more energy into growth and relatively little into sperm production once the needed size to become territorial is attained. The increased paternity of larger territorial males might be due to a more effective defense of the nest in comparison with smaller territorial males.

Infections of nervous necrosis virus in wild and cage-reared marine fish from South China Sea with unexpected wide host ranges.

PubMed

Liu, X D; Huang, J N; Weng, S P; Hu, X Q; Chen, W J; Qin, Z D; Dong, X X; Liu, X L; Zhou, Y; Asim, M; Wang, W M; He, J G; Lin, L

2015-06-01

The concerns about the impact of the nervous necrosis virus (NNV) infections in wild fish have been raised. This paper presents the results of quarterly surveys of NNV in wild and cage-reared marine fish from South China Sea. Samples of 892 wild fish belonging to 69 species and 381 cage-reared fish belonging to 11 species were collected and were detected by seminested PCR and nested PCR. In the case of seminested PCR, the positive signal was detected in 3.0% and 3.1% samples of wild and cage-reared fish, respectively. However, by nested RT-PCR, the positive signal was observed in 42.3% and 63.0% samples of wild and cage-reared fish, respectively. If the fish species were considered, the positive signal was detected in 21.7% and 72.7% species of wild and cage-reared fish by seminested PCR assay, respectively. However, by nested RT-PCR, the positive signal was observed in 65.2% and 100% species of wild and cage-reared fish, respectively. The nucleotide sequences of the nested PCR products were determined. Phylogenetic tree showed that all the obtained viral isolates belonged to the red-spotted grouper nervous necrosis virus (RGNNV) genotype. Thirty-five species of the marine fish were the new hosts of NNV. © 2014 John Wiley & Sons Ltd.

Weather radar data correlate to hail-induced mortality in grassland birds

USGS Publications Warehouse

Carver, Amber; Ross, Jeremy D.; Augustine, David J.; Skagen, Susan K.; Dwyer, Angela M.; Tomback, Diana F.; Wunder, Michael B.

2017-01-01

Small-bodied terrestrial animals such as songbirds (Order Passeriformes) are especially vulnerable to hail-induced mortality; yet, hail events are challenging to predict, and they often occur in locations where populations are not being studied. Focusing on nesting grassland songbirds, we demonstrate a novel approach to estimate hail-induced mortality. We quantify the relationship between the probability of nests destroyed by hail and measured Level-III Next Generation Radar (NEXRAD) data, including atmospheric base reflectivity, maximum estimated size of hail and maximum estimated azimuthal wind shear. On 22 June 2014, a hailstorm in northern Colorado destroyed 102 out of 203 known nests within our research site. Lark bunting (Calamospiza melanocorys) nests comprised most of the sample (n = 186). Destroyed nests were more likely to be found in areas of higher storm intensity, and distributions of NEXRAD variables differed between failed and surviving nests. For 133 ground nests where nest-site vegetation was measured, we examined the ameliorative influence of woody vegetation, nest cover and vegetation density by comparing results for 13 different logistic regression models incorporating the independent and additive effects of weather and vegetation variables. The most parsimonious model used only the interactive effect of hail size and wind shear to predict the probability of nest survival, and the data provided no support for any of the models without this predictor. We conclude that vegetation structure may not mitigate mortality from severe hailstorms and that weather radar products can be used remotely to estimate potential for hail mortality of nesting grassland birds. These insights will improve the efficacy of grassland bird population models under predicted climate change scenarios.

Predation on seabirds by red foxes at Shaiak Island, Alaska

USGS Publications Warehouse

Petersen, M.R.

1982-01-01

Two Red Foxes (Vulpes fulva) that invaded Shaiak Island before the 1976 nesting season had a marked impact on the nesting success of five of seven species of seabirds breeding on the island that year. Common Eiders (Somateria mollissima), Glaucous-winged Gulls (Larus glaucescens), and Common Murres (Uria aalge), that nest in areas accessible to foxes, did not raise any young to fledging. Double-crested Cormorants (Phalacrocorax auritus) were only slightly more successful; 13 (4.3%) of 300 pairs raised one or more young to fledging. Evidence suggested that 21 (35.6%) of 62 pairs of Tufted Puffins (Lunda cirrhata) lost eggs or chicks to foxes, and foxes killed at least 13 (8.3%) of 156 adult puffins on ten sample plots. Conversely, Black-Legged Kittiwakes (Rissa tridactyla) and Pelagic Cormorants (Phalacrocorax pelagicus), which nested primarily on cliffs inaccessible to foxes, lost very few nests. There was no apparent change in general nest site selections by seabirds the following year, when foxes were no longer present. Any avoidance by birds of areas vulnerable to fox predation would probably be discernible only after several years of continuous predation.

Avian growth and development rates and age-specific mortality: the roles of nest predation and adult mortality.

PubMed

Remes, V

2007-01-01

Previous studies have shown that avian growth and development covary with juvenile mortality. Juveniles of birds under strong nest predation pressure grow rapidly, have short incubation and nestling periods, and leave the nest at low body mass. Life-history theory predicts that parental investment increases with adult mortality rate. Thus, developmental traits that depend on the parental effort exerted (pre- and postnatal growth rate) should scale positively with adult mortality, in contrast to those that do not have a direct relationship with parental investment (timing of developmental events, e.g. nest leaving). I tested this prediction on a sample of 84 North American songbirds. Nestling growth rate scaled positively and incubation period duration negatively with annual adult mortality rates even when controlled for nest predation and other covariates, including phylogeny. On the contrary, neither the duration of the nestling period nor body mass at fledging showed any relationship. Proximate mechanisms generating the relationship of pre- and postnatal growth rates to adult mortality may include increased feeding, nest attentiveness during incubation and/or allocation of hormones, and deserve further attention.

Ghrelin and leptin modulate the feeding behaviour of the hawksbill turtle Eretmochelys imbricata during nesting season

PubMed Central

Goldberg, Daphne Wrobel; Leitão, Santiago Alonso Tobar; Godfrey, Matthew H.; Lopez, Gustave Gilles; Santos, Armando José Barsante; Neves, Fabiana Alves; de Souza, Érica Patrícia Garcia; Moura, Anibal Sanchez; Bastos, Jayme da Cunha; Bastos, Vera Lúcia Freire da Cunha

2013-01-01

Female sea turtles have rarely been observed foraging during the nesting season. This suggests that prior to their migration to nesting beaches the females must store sufficient energy and nutrients at their foraging grounds and must be physiologically capable of undergoing months without feeding. Leptin (an appetite-suppressing protein) and ghrelin (a hunger-stimulating peptide) affect body weight by influencing energy intake in all vertebrates. We investigated the levels of these hormones and other physiological and nutritional parameters in nesting hawksbill sea turtles in Rio Grande do Norte State, Brazil, by collecting consecutive blood samples from 41 turtles during the 2010–2011 and 2011–2012 reproductive seasons. We found that levels of serum leptin decreased over the nesting season, which potentially relaxed suppression of food intake and stimulated females to begin foraging either during or after the post-nesting migration. Concurrently, we recorded an increasing trend in ghrelin, which may have stimulated food intake towards the end of the nesting season. Both findings are consistent with the prediction that post-nesting females will begin to forage, either during or immediately after their post-nesting migration. We observed no seasonal trend for other physiological parameters (values of packed cell volume and serum levels of alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, γ-glutamyl transferase, low-density lipoprotein, and high-density lipoprotein). The observed downward trends in general serum biochemistry levels were probably due to the physiological challenge of vitellogenesis and nesting in addition to limited energy resources and probable fasting. PMID:27293600

Ghrelin and leptin modulate the feeding behaviour of the hawksbill turtle Eretmochelys imbricata during nesting season.

PubMed

Goldberg, Daphne Wrobel; Leitão, Santiago Alonso Tobar; Godfrey, Matthew H; Lopez, Gustave Gilles; Santos, Armando José Barsante; Neves, Fabiana Alves; de Souza, Érica Patrícia Garcia; Moura, Anibal Sanchez; Bastos, Jayme da Cunha; Bastos, Vera Lúcia Freire da Cunha

2013-01-01

Female sea turtles have rarely been observed foraging during the nesting season. This suggests that prior to their migration to nesting beaches the females must store sufficient energy and nutrients at their foraging grounds and must be physiologically capable of undergoing months without feeding. Leptin (an appetite-suppressing protein) and ghrelin (a hunger-stimulating peptide) affect body weight by influencing energy intake in all vertebrates. We investigated the levels of these hormones and other physiological and nutritional parameters in nesting hawksbill sea turtles in Rio Grande do Norte State, Brazil, by collecting consecutive blood samples from 41 turtles during the 2010-2011 and 2011-2012 reproductive seasons. We found that levels of serum leptin decreased over the nesting season, which potentially relaxed suppression of food intake and stimulated females to begin foraging either during or after the post-nesting migration. Concurrently, we recorded an increasing trend in ghrelin, which may have stimulated food intake towards the end of the nesting season. Both findings are consistent with the prediction that post-nesting females will begin to forage, either during or immediately after their post-nesting migration. We observed no seasonal trend for other physiological parameters (values of packed cell volume and serum levels of alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, γ-glutamyl transferase, low-density lipoprotein, and high-density lipoprotein). The observed downward trends in general serum biochemistry levels were probably due to the physiological challenge of vitellogenesis and nesting in addition to limited energy resources and probable fasting.

Raman Plus X: Biomedical Applications of Multimodal Raman Spectroscopy.

PubMed

Das, Nandan K; Dai, Yichuan; Liu, Peng; Hu, Chuanzhen; Tong, Lieshu; Chen, Xiaoya; Smith, Zachary J

2017-07-07

Raman spectroscopy is a label-free method of obtaining detailed chemical information about samples. Its compatibility with living tissue makes it an attractive choice for biomedical analysis, yet its translation from a research tool to a clinical tool has been slow, hampered by fundamental Raman scattering issues such as long integration times and limited penetration depth. In this review we detail the how combining Raman spectroscopy with other techniques yields multimodal instruments that can help to surmount the translational barriers faced by Raman alone. We review Raman combined with several optical and non-optical methods, including fluorescence, elastic scattering, OCT, phase imaging, and mass spectrometry. In each section we highlight the power of each combination along with a brief history and presentation of representative results. Finally, we conclude with a perspective detailing both benefits and challenges for multimodal Raman measurements, and give thoughts on future directions in the field.

Enhanced EDX images by fusion of multimodal SEM images using pansharpening techniques.

PubMed

Franchi, G; Angulo, J; Moreaud, M; Sorbier, L

2018-01-01

The goal of this paper is to explore the potential interest of image fusion in the context of multimodal scanning electron microscope (SEM) imaging. In particular, we aim at merging the backscattered electron images that usually have a high spatial resolution but do not provide enough discriminative information to physically classify the nature of the sample, with energy-dispersive X-ray spectroscopy (EDX) images that have discriminative information but a lower spatial resolution. The produced images are named enhanced EDX. To achieve this goal, we have compared the results obtained with classical pansharpening techniques for image fusion with an original approach tailored for multimodal SEM fusion of information. Quantitative assessment is obtained by means of two SEM images and a simulated dataset produced by a software based on PENELOPE. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Raman Plus X: Biomedical Applications of Multimodal Raman Spectroscopy

PubMed Central

Das, Nandan K.; Dai, Yichuan; Liu, Peng; Hu, Chuanzhen; Tong, Lieshu; Chen, Xiaoya

2017-01-01

Raman spectroscopy is a label-free method of obtaining detailed chemical information about samples. Its compatibility with living tissue makes it an attractive choice for biomedical analysis, yet its translation from a research tool to a clinical tool has been slow, hampered by fundamental Raman scattering issues such as long integration times and limited penetration depth. In this review we detail the how combining Raman spectroscopy with other techniques yields multimodal instruments that can help to surmount the translational barriers faced by Raman alone. We review Raman combined with several optical and non-optical methods, including fluorescence, elastic scattering, OCT, phase imaging, and mass spectrometry. In each section we highlight the power of each combination along with a brief history and presentation of representative results. Finally, we conclude with a perspective detailing both benefits and challenges for multimodal Raman measurements, and give thoughts on future directions in the field. PMID:28686212

Ecological factors related to the widespread distribution of sylvatic Rhodnius ecuadoriensis populations in southern Ecuador

PubMed Central

2012-01-01

Background Chagas disease transmission risk is a function of the presence of triatomines in domestic habitats. Rhodnius ecuadoriensis is one of the main vectors implicated in transmission of Trypanosoma cruzi in Ecuador. This triatomine species is present in domestic, peridomestic and sylvatic habitats in the country. To determine the distribution of sylvatic populations of R. ecuadoriensis and the factors related to this distribution, triatomine searches were conducted between 2005 and 2009 in southern Ecuador. Methods Manual triatomine searches were conducted by skilled bug collectors in 23 communities. Sylvatic searched sites were selected by a) directed sampling, where microhabitats were selected by the searchers and b) random sampling, where sampling points where randomly generated. Domiciliary triatomine searches were conducted using the one man-hour method. Natural trypanosome infection was determined by microscopic examination and PCR. Generalized linear models were used to test the effect of environmental factors on the presence of sylvatic triatomines. Results In total, 1,923 sylvatic individuals were collected representing a sampling effort of 751 man-hours. Collected sylvatic triatomines were associated with mammal and bird nests. The 1,219 sampled nests presented an infestation index of 11.9%, a crowding of 13 bugs per infested nest, and a colonization of 80% of the nests. Triatomine abundance was significantly higher in squirrel (Sciurus stramineus) nests located above five meters from ground level and close to the houses. In addition, 8.5% of the 820 examined houses in the same localities were infested with triatomines. There was a significant correlation between R. ecuadoriensis infestation rates found in sylvatic and synanthropic environments within communities (p = 0.012). Parasitological analysis revealed that 64.7% and 15.7% of the sylvatic bugs examined (n = 300) were infected with Trypanosoma cruzi and T. rangeli respectively, and 8% of the bugs presented mixed infections. Conclusions The wide distribution of sylvatic R. ecuadoriensis populations may jeopardize the effectiveness of control campaigns conducted to eliminate domestic populations of this species. Also, the high T. cruzi infection rates found in sylvatic R. ecuadoriensis populations in southern Ecuador could constitute a risk for house re-infestation and persistent long-term Chagas disease transmission in the region. PMID:22243930

Ecological factors related to the widespread distribution of sylvatic Rhodnius ecuadoriensis populations in southern Ecuador.

PubMed

Grijalva, Mario J; Suarez-Davalos, Victoria; Villacis, Anita G; Ocaña-Mayorga, Sofia; Dangles, Olivier

2012-01-13

Chagas disease transmission risk is a function of the presence of triatomines in domestic habitats. Rhodnius ecuadoriensis is one of the main vectors implicated in transmission of Trypanosoma cruzi in Ecuador. This triatomine species is present in domestic, peridomestic and sylvatic habitats in the country. To determine the distribution of sylvatic populations of R. ecuadoriensis and the factors related to this distribution, triatomine searches were conducted between 2005 and 2009 in southern Ecuador. Manual triatomine searches were conducted by skilled bug collectors in 23 communities. Sylvatic searched sites were selected by a) directed sampling, where microhabitats were selected by the searchers and b) random sampling, where sampling points where randomly generated. Domiciliary triatomine searches were conducted using the one man-hour method. Natural trypanosome infection was determined by microscopic examination and PCR. Generalized linear models were used to test the effect of environmental factors on the presence of sylvatic triatomines. In total, 1,923 sylvatic individuals were collected representing a sampling effort of 751 man-hours. Collected sylvatic triatomines were associated with mammal and bird nests. The 1,219 sampled nests presented an infestation index of 11.9%, a crowding of 13 bugs per infested nest, and a colonization of 80% of the nests. Triatomine abundance was significantly higher in squirrel (Sciurus stramineus) nests located above five meters from ground level and close to the houses. In addition, 8.5% of the 820 examined houses in the same localities were infested with triatomines. There was a significant correlation between R. ecuadoriensis infestation rates found in sylvatic and synanthropic environments within communities (p = 0.012). Parasitological analysis revealed that 64.7% and 15.7% of the sylvatic bugs examined (n = 300) were infected with Trypanosoma cruzi and T. rangeli respectively, and 8% of the bugs presented mixed infections. The wide distribution of sylvatic R. ecuadoriensis populations may jeopardize the effectiveness of control campaigns conducted to eliminate domestic populations of this species. Also, the high T. cruzi infection rates found in sylvatic R. ecuadoriensis populations in southern Ecuador could constitute a risk for house re-infestation and persistent long-term Chagas disease transmission in the region.

A Newly Developed Nested PCR Assay for the Detection of Helicobacter pylori in the Oral Cavity.

PubMed

Ismail, Hawazen; Morgan, Claire; Griffiths, Paul; Williams, John; Jenkins, Gareth

2016-01-01

To develop a new nested polymerase chain reaction (PCR) assay for identifying Helicobacter pylori DNA from dental plaque. H. pylori is one of the most common chronic bacterial pathogens in humans. The accurate detection of this organism is essential for proper patient management and for the eradication of the bacteria following treatment. Forty-nine patients (24 males and 25 females; mean age: 51; range, 19 to 94 y) were investigated for the presence of H. pylori in dental plaque by single-step PCR and nested PCR and in the stomach by single-step PCR, nested PCR, and histologic examination. The newly developed nested PCR assay identified H. pylori DNA in gastric biopsies of 18 patients who were histologically classified as H. pylori-positive and 2 additional biopsies of patients who were H. pylori-negative by histologic examination (20/49; 40.8%). Dental plaque samples collected before and after endoscopy from the 49 patients revealed that single-step PCR did not detect H. pylori but nested PCR was able to detect H. pylori DNA in 40.8% (20/49) patients. Nested PCR gave a higher detection rate (40.8%, 20/49) than that of histology (36.7%, 18/49) and single-step PCR. When nested PCR results were compared with histology results there was no significant difference between the 2 methods. Our newly developed nested PCR assay is at least as sensitive as histology and may be useful for H. pylori detection in patients unfit for endoscopic examination.

Trap-Nesting Bees in Montane Grassland (Campo Rupestre) and Cerrado in Brazil: Collecting Generalist or Specialist Nesters.

PubMed

Araújo, P C S; Lourenço, A P; Raw, A

2016-10-01

Species richness and seasonal abundance of solitary bees were investigated in rocky, montane grassland (campo rupestre) (1180 m asl) and cerrado sensu stricto (680 m asl) in the Biribiri State Park, Diamantina, state of Minas Gerais, Brazil. Three hundred nineteen nest traps of bamboo canes and black cardboard tubes were monthly inspected at each site during 15 months. A total of eight species of bees built 97 nests. Four species were common to both sites. Tetrapedia aff. curvitarsis Friese and Tetrapedia aff. peckoltii Friese were the most abundant at campo rupestre and cerrado s.s., respectively, followed by Centris analis (Fabricius) in campo rupestre and Centris tarsata Smith in cerrado s.s. The nesting peaks occurred in May in campo rupestre and in February in cerrado s.s. Three cuckoo bees and one bee-fly were collected as natural enemies. The findings suggest that differences between the sites were related more to ecological factors (floral resources, natural nest sites) than to the altitudinal difference. The species richness was similar to that in other habitats with open vegetation. We demonstrate the need to use several types of trap-nest to increase the range of species sampled; some species used only one of the two types traps provided. We also comment on the limitations of trap-nests in cerrado vegetation. Most cerrado species of bees are very selective in their choice for a nesting site, but bees that use trap-nests are more generalists.

Pre- and post-experimental manipulation assessments confirm the increase in number of birds due to the addition of nest boxes.

PubMed

Cuatianquiz Lima, Cecilia; Macías Garcia, Constantino

2016-01-01

Secondary cavity nesting (SCN) birds breed in holes that they do not excavate themselves. This is possible where there are large trees whose size and age permit the digging of holes by primary excavators and only rarely happens in forest plantations, where we expected a deficit of both breeding holes and SCN species. We assessed whether the availability of tree cavities influenced the number of SCNs in two temperate forest types, and evaluated the change in number of SCNs after adding nest boxes. First, we counted all cavities within each of our 25-m radius sampling points in mature and young forest plots during 2009. We then added nest boxes at standardised locations during 2010 and 2011 and conducted fortnightly bird counts (January-October 2009-2011). In 2011 we added two extra plots of each forest type, where we also conducted bird counts. Prior to adding nest boxes, counts revealed more SCNs in mature than in young forest. Following the addition of nest boxes, the number of SCNs increased significantly in the points with nest boxes in both types of forest. Counts in 2011 confirmed the increase in number of birds due to the addition of nest boxes. Given the likely benefits associated with a richer bird community we propose that, as is routinely done in some countries, forest management programs preserve old tree stumps and add nest boxes to forest plantations in order to increase bird numbers and bird community diversity.

Conservation implications when the nest predators are known

USGS Publications Warehouse

Ribic, Christine; Thompson, Frank

2012-01-01

Conservation and management of passerines has largely focused on habitat manipulation or restoration because the natural communities on which these birds depend have been destroyed and fragmented. However, productivity is another important aspect of avian conservation, and nest predation can be a large source of nesting mortality for passerines. Recent studies using video surveillance to identify nest predators allow researchers to start evaluating what methods could be used to mitigate nest predation to help passerines of conservation concern. From recent studies, we identified latitudinal and habitat-related patterns in the importance of predator groups that depredate passerine nests. We then reviewed how knowledge of specific nest predators can benefit conservation of bird species of concern. Mammals were the dominant predator group in northern grasslands. Snakes were the dominant predator group in southern habitats. Fire ants were only a nest predator in southern latitudes. Differences in the importance of predator species or groups were likely the result of both their geographic patterns of distribution and habitat preferences. Some direct and indirect predator control measures developed for waterfowl management potentially could be used to benefit passerine productivity. We reviewed three examples-cowbirds, snakes in shrublands, and ground squirrels in grasslands-to illustrate how different predator control strategies may be needed in different situations. Mitigation of passerine nest predation will need to be based on knowledge of predator communities to be effective. This requires large samples of predation events with identified predators; video technology is essential for this task.

Identification of and Screening for Human Helicobacter cinaedi Infections and Carriers via Nested PCR

PubMed Central

Oyama, Kohta; Khan, Shahzada; Okamoto, Tatsuya; Fujii, Shigemoto; Ono, Katsuhiko; Matsunaga, Tetsuro; Yoshitake, Jun; Sawa, Tomohiro; Tomida, Junko; Kawamura, Yoshiaki

2012-01-01

Helicobacter cinaedi is the most frequently reported enterohepatic Helicobacter species isolated from humans. Earlier research suggested that certain patients with H. cinaedi infection may remain undiagnosed or incorrectly diagnosed because of difficulties in detecting the bacteria by conventional culture methods. Here, we report a nested PCR assay that rapidly detects the cytolethal distending toxin gene (cdt) of H. cinaedi with high specificity and sensitivity. Specificity of the assay was validated by using different species of Helicobacter and Campylobacter, as well as known H. cinaedi-positive and -negative samples. The sensitivity of detection for the cdt gene in the assay was 102 CFU/ml urine or 102 CFU/105 infected RAW 264.7 cells. In an H. cinaedi-infected mouse model, the cdt gene of H. cinaedi was effectively detected via the assay with urine (6/7), stool (2/3), and blood (2/6) samples. Importantly, it detected H. cinaedi in blood, urine, and stool samples from one patient with a suspected H. cinaedi infection and three patients with known infections. The assay was further used clinically to follow up two H. cinaedi-infected patients after antibiotic treatment. Stool samples from these two patients evaluated by nested PCR after antibiotic therapy showed clearance of bacterial DNA. Finally, analysis of stool specimens from healthy volunteers showed occasional positive reactions (4/30) to H. cinaedi DNA, which suggests intestinal colonization by H. cinaedi in healthy subjects. In conclusion, this nested PCR assay may be useful for the rapid diagnosis, antimicrobial treatment evaluation, and epidemiological study of H. cinaedi infection. PMID:23015666

Prevalence of coliforms, Salmonella, Listeria, and Campylobacter associated with eggs and the environment of conventional cage and free-range egg production.

PubMed

Jones, D R; Anderson, K E; Guard, J Y

2012-05-01

There is a desire by US consumers for eggs produced by hens in alternative production systems. As the retail shell-egg market offers these products to accommodate consumer demands, additional information is needed to ensure processing methodologies result in safe eggs from all egg sources. A study was conducted to determine if there were differences in the prevalence of coliforms, Salmonella, Listeria, and Campylobacter on and within eggs and in the environment of a sister flock of conventional cage and free-range laying hens. Microbial sampling occurred approximately every 6 wk between 20 and 79 wk of age. A random sampling of typical coliform colonies produced 371 viable isolates for biochemical identification. Twenty-nine genera or species of bacteria were identified. There was a significantly greater (P < 0.0001) prevalence of Campylobacter in the free-range nest box swabs compared with that in the free-range grass and conventional cage swab samples (number of positives: 8 nest box, 1 grass, 0 cage). Seven isolates of Listeria innocua were detected with no significant difference in prevalence between the treatments. Isolates were associated with eggshells (2 free-range floor, 1 cage) and the free-range environment (2 nest box, 2 grass). There were 21 Salmonella isolates detected between all sample locations, with no significant difference in the prevalence of Salmonella detection between the treatments. Additional studies are needed to fully understand the effect of alternative production methods on the prevalence of pathogens and coliforms associated with nest-run eggs and the production environment.

Sound absorption of a new oblique-section acoustic metamaterial with nested resonator

NASA Astrophysics Data System (ADS)

Gao, Nansha; Hou, Hong; Zhang, Yanni; Wu, Jiu Hui

2018-02-01

This study designs and investigates high-efficiency sound absorption of new oblique-section nested resonators. Impedance tube experiment results show that different combinations of oblique-section nest resonators have tunable low-frequency bandwidth characteristics. The sound absorption mechanism is due to air friction losses in the slotted region and the sample structure resonance. The acousto-electric analogy model demonstrates that the sound absorption peak and bandwidth can be modulated over an even wider frequency range by changing the geometric size and combinations of structures. The proposed structure can be easily fabricated and used in low-frequency sound absorption applications.

Can a Red Wood-Ant Nest Be Associated with Fault-Related CH4 Micro-Seepage? A Case Study from Continuous Short-Term In-Situ Sampling

PubMed Central

Grumpe, Arne; Becker, Adrian; Wöhler, Christian

2018-01-01

Simple Summary Methane (CH4) is common on Earth but its natural sources are not well-characterized. We investigated concentrations of CH4 and its stable carbon isotope (δ13C-CH4) within a red wood-ant (RWA; Formica polyctena) nest in the Neuwied Basin, a part of the East Eifel Volcanic Field (EEVF), and tested for associations between methane concentration and RWA activity patterns, earthquakes, and earth tides. Methane degassing was not synchronized with earth tides, nor was it influenced by a micro-earthquake or RWA activity. Elevated CH4 concentrations in nest gas appear to result from a combination of microbial activity and fault-related emissions. The latter could result from micro-seepage of methane derived from low-temperature gas-water-rock reactions that subsequently moves via fault networks through the RWA nest or from overlapping micro-seepage of magmatic CH4 from the Eifel plume. Given the abundance of RWA nests on the landscape, their role as sources of microbial CH4 and biological indicators for abiotically-derived CH4 should be included in estimations of methane emissions that are contributing to climatic change. Abstract We measured methane (CH4) and stable carbon isotope of methane (δ13C-CH4) concentrations in ambient air and within a red wood-ant (RWA; Formica polyctena) nest in the Neuwied Basin (Germany) using high-resolution in-situ sampling to detect microbial, thermogenic, and abiotic fault-related micro-seepage of CH4. Methane degassing from RWA nests was not synchronized with earth tides, nor was it influenced by micro-earthquake degassing or concomitantly measured RWA activity. Two δ13C-CH4 signatures were identified in nest gas: −69‰ and −37‰. The lower peak was attributed to microbial decomposition of organic matter within the RWA nest, in line with previous observations that RWA nests are hot-spots of microbial CH4. The higher peak has not been reported in previous studies. We attribute this peak to fault-related CH4 emissions moving via fault networks into the RWA nest, which could originate either from thermogenic or abiotic CH4 formation. Sources of these micro-seepages could be Devonian schists, iron-bearing “Klerf Schichten”, or overlapping micro-seepage of magmatic CH4 from the Eifel plume. Given the abundance of RWA nests on the landscape, their role as sources of microbial CH4 and biological indicators for abiotically-derived CH4 should be included in estimation of methane emissions that are contributing to climatic change. PMID:29597318

Influence of nesting shell size on brightness longevity and resistance to ultrasound-induced dissolution during enhanced B-mode contrast imaging.

PubMed

Wallace, N; Dicker, S; Lewin, P; Wrenn, S P

2014-12-01

This study aims to bridge the gap between transport mechanisms of an improved ultrasound contrast agent (UCA) and its resulting behavior in a clinical imaging study. Phospholipid-shelled microbubbles nested within the aqueous core of a polymer microcapsule are examined for their use and feasibility as an improved UCA. The nested formulation provides contrast comparable to traditional formulations, specifically an SF6 microbubble coated by a DSPC PEG-3000 monolayer, with the advantage that contrast persists at least nine times longer in a mock clinical, in vitro setting. The effectiveness of the sample was measured using a contrast ratio in units of decibels (dB) which compares the brightness of the nested microbubbles to a reference value of a phantom tissue mimic. During a 40min imaging study, six nesting formulations with average outer capsule diameters of 1.95, 2.53, 5.55, 9.95, 14.95, and 20.51μm reached final contrast ratio values of 0.25, 2.35, 3.68, 4.51, 5.93, and 8.00dB, respectively. The starting contrast ratio in each case was approximately 8dB and accounts for the brightness attributed to the nesting shell. As compared with empty microcapsules (no microbubbles nested within), enhancement of the initial contrast ratio increased systematically with decreasing microcapsule size. The time required to reach a steady state in the temporal contrast ratio profile also varied with microcapsule diameter and was found to be 420s for each of the four smallest shell diameters and 210s and 150s, respectively, for the largest two shell diameters. All nested formulations were longer-lived and gave higher final contrast ratios than a control sample comprising un-nested, but otherwise equivalent, microbubbles. Specifically, the contrast ratio of the un-nested microbubbles decreased to a negative value after 4min of continuous ultrasound exposure with complete disappearance of the microbubbles after 15min whereas all nested formulations maintained positive contrast ratio values for the duration of the 40min trial. The results are consistent with two distinct stages of gas transport: in the first stage, passive diffusion occurs under ambient conditions across the microbubble monolayer within the first few minutes after formulation until the aqueous interior of the microcapsule is saturated with gas; in the second stage ultrasound drives additional gas dissolution even further due to pressure modulation. It is important to understand the chemistry and transport mechanisms of this contrast agent under the influence of ultrasound to attain better perspicacity for enhanced applications in imaging. Results from this study will facilitate future preclinical studies and clinical applications of nested microbubbles for therapeutic and diagnostic imaging. Copyright © 2014 Elsevier B.V. All rights reserved.

Interactions of Multimodal Ligands with Proteins: Insights into Selectivity Using Molecular Dynamics Simulations.

PubMed

Parimal, Siddharth; Garde, Shekhar; Cramer, Steven M

2015-07-14

Fundamental understanding of protein-ligand interactions is important to the development of efficient bioseparations in multimodal chromatography. Here we employ molecular dynamics (MD) simulations to investigate the interactions of three different proteins--ubiquitin, cytochrome C, and α-chymotrypsinogen A, sampling a range of charge from +1e to +9e--with two multimodal chromatographic ligands containing similar chemical moieties--aromatic, carboxyl, and amide--in different structural arrangements. We use a spherical harmonic expansion to analyze ligand and individual moiety density profiles around the proteins. We find that the Capto MMC ligand, which contains an additional aliphatic group, displays stronger interactions than Nuvia CPrime ligand with all three proteins. Studying the ligand densities at the moiety level suggests that hydrophobic interactions play a major role in determining the locations of high ligand densities. Finally, the greater structural flexibility of the Capto MMC ligand compared to that of the Nuvia cPrime ligand allows for stronger structural complementarity and enables stronger hydrophobic interactions. These subtle and not-so-subtle differences in binding affinities and modalities for multimodal ligands can result in significantly different binding behavior towards proteins with important implications for bioprocessing.

Towards an ultra-thin medical endoscope: multimode fibre as a wide-field image transferring medium

NASA Astrophysics Data System (ADS)

Duriš, Miroslav; Bradu, Adrian; Podoleanu, Adrian; Hughes, Michael

2018-03-01

Multimode optical fibres are attractive for biomedical and industrial applications such as endoscopes because of the small cross section and imaging resolution they can provide in comparison to widely-used fibre bundles. However, the image is randomly scrambled by propagation through a multimode fibre. Even though the scrambling is unpredictable, it is deterministic, and therefore the scrambling can be reversed. To unscramble the image, we treat the multimode fibre as a linear, disordered scattering medium. To calibrate, we scan a focused beam of coherent light over thousands of different beam positions at the distal end and record complex fields at the proximal end of the fibre. This way, the inputoutput response of the system is determined, which then allows computational reconstruction of reflection-mode images. However, there remains the problem of illuminating the tissue via the fibre while avoiding back reflections from the proximal face. To avoid this drawback, we provide here the first preliminary confirmation that an image can be transferred through a 2x2 fibre coupler, with the sample at its distal port interrogated in reflection. Light is injected into one port for illumination and then collected from a second port for imaging.

Nested PCR for specific diagnosis of Taenia solium taeniasis.

PubMed

Mayta, Holger; Gilman, Robert H; Prendergast, Emily; Castillo, Janeth P; Tinoco, Yeny O; Garcia, Hector H; Gonzalez, Armando E; Sterling, Charles R

2008-01-01

Taeniasis due to Taenia solium is a disease with important public health consequences, since the larval stage is not exclusive to the animal intermediate, the pig, but also infects humans, causing neurocysticercosis. Early diagnosis and treatment of T. solium tapeworm carriers is important to prevent human cysticercosis. Current diagnosis based on microscopic observation of eggs lacks both sensitivity and specificity. In the present study, a nested-PCR assay targeting the Tso31 gene was developed for the specific diagnosis of taeniasis due to T. solium. Initial specificity and sensitivity testing was performed using stored known T. solium-positive and -negative samples. The assay was further analyzed under field conditions by conducting a case-control study of pretreatment stool samples collected from a population in an area of endemicity. Using the archived samples, the assay showed 97% (31/32) sensitivity and 100% (123/123) specificity. Under field conditions, the assay had 100% sensitivity and specificity using microscopy/enzyme-linked immunosorbent assay coproantigen testing as the gold standards. The Tso31 nested PCR described here might be a useful tool for the early diagnosis and prevention of taeniasis/cysticercosis.

Darwinian Model Building

NASA Astrophysics Data System (ADS)

Kester, Do; Bontekoe, Romke

2011-03-01

We present a way to generate heuristic mathematical models based on the Darwinian principles of variation and selection in a pool of individuals over many generations. Each individual has a genotype (the hereditary properties) and a phenotype (the expression of these properties in the environment). Variation is achieved by cross-over and mutation operations on the genotype which consists in the present case of a single chromosome. The genotypes `live' in the environment of the data. Nested Sampling is used to optimize the free parameters of the models given the data, thus giving rise to the phenotypes. Selection is based on the phenotypes. The evidences which naturally follow from the Nested Sampling Algorithm are used in a second level of Nested Sampling to find increasingly better models. The data in this paper originate from the Leiden Cytology and Pathology Laboratory (LCPL), which screens pap smears for cervical cancer. We have data for 1750 women who on average underwent 5 tests each. The data on individual women are treated as a small time series. We will try to estimate the next value of the prime cancer indicator from previous tests of the same woman.

Systemic multimodal approach to speech therapy treatment in autistic children.

PubMed

Tamas, Daniela; Marković, Slavica; Milankov, Vesela

2013-01-01

Conditions in which speech therapy treatment is applied in autistic children are often not in accordance with characteristics of opinions and learning of people with autism. A systemic multimodal approach means motivating autistic people to develop their language speech skill through the procedure which allows reliving of their personal experience according to the contents that are presented in the their natural social environment. This research was aimed at evaluating the efficiency of speech treatment based on the systemic multimodal approach to the work with autistic children. The study sample consisted of 34 children, aged from 8 to 16 years, diagnosed to have different autistic disorders, whose results showed a moderate and severe clinical picture of autism on the Childhood Autism Rating Scale. The applied instruments for the evaluation of ability were the Childhood Autism Rating Scale and Ganzberg II test. The study subjects were divided into two groups according to the type of treatment: children who were covered by the continuing treatment and systemic multimodal approach in the treatment, and children who were covered by classical speech treatment. It is shown that the systemic multimodal approach in teaching autistic children affects the stimulation of communication, socialization, self-service and work as well as that the progress achieved in these areas of functioning was retainable after long time, too. By applying the systemic multimodal approach when dealing with autistic children and by comparing their achievements on tests applied before, during and after the application of this mode, it has been concluded that certain improvement has been achieved in the functionality within the diagnosed category. The results point to a possible direction in the creation of new methods, plans and programs in dealing with autistic children based on empirical and interactive learning.

Avifauna associated with early growth vegetation on clearcuts in the Oregon coast ranges.

Treesearch

Michael L. Morrison; E. Charles Meslow

1983-01-01

This paper provides estimates of bird density, diversity, and evenness on 13 clearcut units of the Siuslaw National Forest in the Coast Ranges of Oregon, sampled during 1979,1980, and 1981. Total density of nesting birds ranged from 322 to 588 per 40.5 hectares (100 acres); there were 15 to 19 species nesting on each site.

The Empty Nest Syndrome: Ways to Enhance Quality of Life

ERIC Educational Resources Information Center

Chen, Dianbing; Yang, Xinxiao; Aagard, Steve Dale

2012-01-01

Empty nest syndrome occurs as a result of urbanization and loosened relationships among family members. It may threaten the life quality of older adults and stability of society as a whole. This survey was designed to investigate the situation and factors that influence the life quality of a sample of older adults in a western state. Thirty-five…

Optimal Design in Three-Level Block Randomized Designs with Two Levels of Nesting: An ANOVA Framework with Random Effects

ERIC Educational Resources Information Center

Konstantopoulos, Spyros

2013-01-01

Large-scale experiments that involve nested structures may assign treatment conditions either to subgroups such as classrooms or to individuals such as students within subgroups. Key aspects of the design of such experiments include knowledge of the variance structure in higher levels and the sample sizes necessary to reach sufficient power to…

[Iditification of five imported cases of Plasmodium ovale wallikeri infection in Zhejiang Province].

PubMed

Zhang, Ling-ling; Ruan, Wei; Chen, Hua-liang; Lu, Qiao-yi; Yao, Li-nong

2014-10-01

To identify and analyze Plasmodium ovale wallikeri in 5 imported malaria cases, who were detected positive by microscopy and negative by conventional PCR. Epidemiological information and blood samples were collected from the five patients. The detection was conducted by microscopy, Rapid Diagnostic Test (RDT) and nested PCR with Plasmodium genus-specific, species-specific and Plasmodium ovale wallikeri-specific primers. The amplified products were sequenced and Blast analysis was performed on line in NCBI. The five patients returned from Africa, and all had a history of malaria. They were microscopically positive for Plasmodium sp., and two cases showed Pan positive RDT result. All blood samples were negative for four Plasmodium spp. by conventional nested PCR, but positive by nested PCR with Plasmodium ovale wallikeri-specific primers. Blast analysis showed that the amplified sequences of the five cases had complete homology with P. ovale wallikeri clone RSH10 18S ribosomal RNA gene (Accession No. KF219561.1). The five cases which classified as positive by microscopy while negative by conventional PCR have been confirmed as Plasmodium ovale wallikeri infection by nested PCR with P. ovale wallikeri-specific primers.

Early diagnosis of typhoid fever by nested PCR for flagellin gene of Salmonella enterica serotype Typhi.

PubMed

Khan, S; Harish, B N; Menezes, G A; Acharya, N S; Parija, S C

2012-11-01

Typhoid fever caused by Salmonella Typhi continues to be a major health problem in spite of the use of antibiotics and the development of newer antibacterial drugs. Inability to make an early laboratory diagnosis and resort to empirical therapy, often lead to increased morbidity and mortality in cases of typhoid fever. This study was aimed to optimize a nested PCR for early diagnosis of typhoid fever and using it as a diagnostic tool in culture negative cases of suspected typhoid fever. Eighty patients with clinical diagnosis of typhoid fever and 40 controls were included in the study. The blood samples collected were subjected to culture, Widal and nested PCR targeting the flagellin gene of S. Typhi. The sensitivity of PCR on blood was found to be 100 per cent whereas the specificity was 76.9 per cent. The positive predictive value (PPV) of PCR was calculated to be 76.9 per cent with an accuracy of 86 per cent. None of the 40 control samples gave a positive PCR. Due to its high sensitivity and specificity nested PCR can be used as a useful tool to diagnose clinically suspected, culture negative cases of typhoid fever.

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

Wang, Yin; Wang, Wen; Wysocki, Gerard, E-mail: gwysocki@princeton.edu

In this Letter, we present a method of performing broadband mid-infrared spectroscopy with conventional, free-running, continuous wave Fabry-Perot quantum cascade lasers (FP-QCLs). The measurement method is based on multi-heterodyne down-conversion of optical signals. The sample transmission spectrum probed by one multi-mode FP-QCL is down-converted to the radio-frequency domain through an optical multi-heterodyne process using a second FP-QCL as the local oscillator. Both a broadband multi-mode spectral measurement as well as high-resolution (∼15 MHz) spectroscopy of molecular absorption are demonstrated and show great potential for development of high performance FP-laser-based spectrometers for chemical sensing.

Inferring Foraging Areas of Nesting Loggerhead Turtles Using Satellite Telemetry and Stable Isotopes

PubMed Central

Ceriani, Simona A.; Roth, James D.; Evans, Daniel R.; Weishampel, John F.; Ehrhart, Llewellyn M.

2012-01-01

In recent years, the use of intrinsic markers such as stable isotopes to link breeding and foraging grounds of migratory species has increased. Nevertheless, several assumptions still must be tested to interpret isotopic patterns found in the marine realm. We used a combination of satellite telemetry and stable isotope analysis to (i) identify key foraging grounds used by female loggerheads nesting in Florida and (ii) examine the relationship between stable isotope ratios and post-nesting migration destinations. We collected tissue samples for stable isotope analysis from 14 females equipped with satellite tags and an additional 57 untracked nesting females. Telemetry identified three post-nesting migratory pathways and associated non-breeding foraging grounds: (1) a seasonal continental shelf–constrained migratory pattern along the northeast U.S. coastline, (2) a non-breeding residency in southern foraging areas and (3) a residency in the waters adjacent to the breeding area. Isotopic variability in both δ13C and δ15N among individuals allowed identification of three distinct foraging aggregations. We used discriminant function analysis to examine how well δ13C and δ15N predict female post-nesting migration destination. The discriminant analysis classified correctly the foraging ground used for all but one individual and was used to predict putative feeding areas of untracked turtles. We provide the first documentation that the continental shelf of the Mid- and South Atlantic Bights are prime foraging areas for a large number (61%) of adult female loggerheads from the largest loggerhead nesting population in the western hemisphere and the second largest in the world. Our findings offer insights for future management efforts and suggest that this technique can be used to infer foraging strategies and residence areas in lieu of more expensive satellite telemetry, enabling sample sizes that are more representative at the population level. PMID:23028943

Reconstruction of calmodulin single-molecule FRET states, dye interactions, and CaMKII peptide binding by MultiNest and classic maximum entropy

NASA Astrophysics Data System (ADS)

DeVore, Matthew S.; Gull, Stephen F.; Johnson, Carey K.

2013-08-01

We analyzed single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.

Reconstruction of Calmodulin Single-Molecule FRET States, Dye-Interactions, and CaMKII Peptide Binding by MultiNest and Classic Maximum Entropy

PubMed Central

DeVore, Matthew S.; Gull, Stephen F.; Johnson, Carey K.

2013-01-01

We analyze single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data. PMID:24223465

Assessment of Contaminant Exposure and Effects on Ospreys Nesting along the Lower Duwamish River, Washington, 2006-07

USGS Publications Warehouse

Johnson, Branden L.; Henny, Charles J.; Kaiser, James L.; Davis, Jay W.; Schulz, Edmund P.

2009-01-01

We evaluated the effects of contaminants on osprey (Pandion haliaetus) nesting along the lower Duwamish River (LDR), Washington, and used the upper reach of the Willamette River (WR), Oregon, as a reference site. Osprey eggs and nestling blood (plasma) were collected at nests along the LDR (11 eggs, 7 plasmas) and WR (10 eggs, 6 plasmas) in 2006-07 and analyzed for contaminants. Additionally, hematology and serum chemistries were determined in the blood/plasma samples of nestlings (about 35-45 days old) and were used as potential indicators of stress induced by contaminant exposure. Detailed foraging information for ospreys nesting along the LDR was collected and evaluated to better understand contaminant profiles observed in the eggs and plasma. Additional residue data from 26 osprey eggs collected and analyzed in 2002-03 from nests along the LDR, Snohomish River Estuary (SRE) and Lake Washington (LW) in the Puget Sound (PS) region also were evaluated.

Relatedness predicts multiple measures of investment in cooperative nest construction in sociable weavers

PubMed Central

Leighton, Gavin M.; Echeverri, Sebastian; Heinrich, Dirk; Kolberg, Holger

2015-01-01

Although communal goods are often critical to society, they are simultaneously susceptible to exploitation and are evolutionarily stable only if mechanisms exist to curtail exploitation. Mechanisms such as punishment and kin selection have been offered as general explanations for how communal resources can be maintained. Evidence for these mechanisms comes largely from humans and social insects, leaving their generality in question. To assess how communal resources are maintained, we observed cooperative nest construction in sociable weavers (Philetairus socius). The communal nest of sociable weavers provides thermal benefits for all individuals but requires continual maintenance. We observed cooperative nest construction and also recorded basic morphological characteristics. We also collected blood samples, performed next-generation sequencing, and isolated 2358 variable single nucleotide polymorphisms (SNPs) to estimate relatedness. We find that relatedness predicts investment in cooperative nest construction, while no other morphological characters significantly explain cooperative output. We argue that indirect benefits are a critical fitness component for maintaining the cooperative behavior that maintains the communal good. PMID:26726282

Reconstruction of Calmodulin Single-Molecule FRET States, Dye-Interactions, and CaMKII Peptide Binding by MultiNest and Classic Maximum Entropy.

PubMed

Devore, Matthew S; Gull, Stephen F; Johnson, Carey K

2013-08-30

We analyze single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca 2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.

Balancing a U-Shaped Assembly Line by Applying Nested Partitions Method

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

Bhagwat, Nikhil V.

2005-01-01

In this study, we applied the Nested Partitions method to a U-line balancing problem and conducted experiments to evaluate the application. From the results, it is quite evident that the Nested Partitions method provided near optimal solutions (optimal in some cases). Besides, the execution time is quite short as compared to the Branch and Bound algorithm. However, for larger data sets, the algorithm took significantly longer times for execution. One of the reasons could be the way in which the random samples are generated. In the present study, a random sample is a solution in itself which requires assignment ofmore » tasks to various stations. The time taken to assign tasks to stations is directly proportional to the number of tasks. Thus, if the number of tasks increases, the time taken to generate random samples for the different regions also increases. The performance index for the Nested Partitions method in the present study was the number of stations in the random solutions (samples) generated. The total idle time for the samples can be used as another performance index. ULINO method is known to have used a combination of bounds to come up with good solutions. This approach of combining different performance indices can be used to evaluate the random samples and obtain even better solutions. Here, we used deterministic time values for the tasks. In industries where majority of tasks are performed manually, the stochastic version of the problem could be of vital importance. Experimenting with different objective functions (No. of stations was used in this study) could be of some significance to some industries where in the cost associated with creation of a new station is not the same. For such industries, the results obtained by using the present approach will not be of much value. Labor costs, task incompletion costs or a combination of those can be effectively used as alternate objective functions.« less

Tutorial: Asteroseismic Data Analysis with DIAMONDS

NASA Astrophysics Data System (ADS)

Corsaro, Enrico

Since the advent of the space-based photometric missions such as CoRoT and NASA's Kepler, asteroseismology has acquired a central role in our understanding about stellar physics. The Kepler spacecraft, especially, is still releasing excellent photometric observations that contain a large amount of information not yet investigated. For exploiting the full potential of these data, sophisticated and robust analysis tools are now essential, so that further constraining of stellar structure and evolutionary models can be obtained. In addition, extracting detailed asteroseismic properties for many stars can yield new insights on their correlations to fundamental stellar properties and dynamics. After a brief introduction to the Bayesian notion of probability, I describe the code Diamonds for Bayesian parameter estimation and model comparison by means of the nested sampling Monte Carlo (NSMC) algorithm. NSMC constitutes an efficient and powerful method, in replacement to standard Markov chain Monte Carlo, very suitable for high-dimensional and multimodal problems that are typical of detailed asteroseismic analyses, such as the fitting and mode identification of individual oscillation modes in stars (known as peak-bagging). Diamonds is able to provide robust results for statistical inferences involving tens of individual oscillation modes, while at the same time preserving a considerable computational efficiency for identifying the solution. In the tutorial, I will present the fitting of the stellar background signal and the peak-bagging analysis of the oscillation modes in a red-giant star, providing an example to use Bayesian evidence for assessing the peak significance of the fitted oscillation peaks.

THE HUNT FOR EXOMOONS WITH KEPLER (HEK). I. DESCRIPTION OF A NEW OBSERVATIONAL PROJECT

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

Kipping, D. M.; Bakos, G. A.; Buchhave, L.

2012-05-10

Two decades ago, empirical evidence concerning the existence and frequency of planets around stars, other than our own, was absent. Since that time, the detection of extrasolar planets from Jupiter-sized to, most recently, Earth-sized worlds has blossomed and we are finally able to shed light on the plurality of Earth-like, habitable planets in the cosmos. Extrasolar moons may also be frequently habitable worlds, but their detection or even systematic pursuit remains lacking in the current literature. Here, we present a description of the first systematic search for extrasolar moons as part of a new observational project called 'The Hunt formore » Exomoons with Kepler' (HEK). The HEK project distills the entire list of known transiting planet candidates found by Kepler (2326 at the time of writing) down to the most promising candidates for hosting a moon. Selected targets are fitted using a multimodal nested sampling algorithm coupled with a planet-with-moon light curve modeling routine. By comparing the Bayesian evidence of a planet-only model to that of a planet-with-moon, the detection process is handled in a Bayesian framework. In the case of null detections, upper limits derived from posteriors marginalized over the entire prior volume will be provided to inform the frequency of large moons around viable planetary hosts, {eta} leftmoon. After discussing our methodologies for target selection, modeling, fitting, and vetting, we provide two example analyses.« less

Effect of Methodological and Ecological Approaches on Heterogeneity of Nest-Site Selection of a Long-Lived Vulture

PubMed Central

Moreno-Opo, Rubén; Fernández-Olalla, Mariana; Margalida, Antoni; Arredondo, Ángel; Guil, Francisco

2012-01-01

The application of scientific-based conservation measures requires that sampling methodologies in studies modelling similar ecological aspects produce comparable results making easier their interpretation. We aimed to show how the choice of different methodological and ecological approaches can affect conclusions in nest-site selection studies along different Palearctic meta-populations of an indicator species. First, a multivariate analysis of the variables affecting nest-site selection in a breeding colony of cinereous vulture (Aegypius monachus) in central Spain was performed. Then, a meta-analysis was applied to establish how methodological and habitat-type factors determine differences and similarities in the results obtained by previous studies that have modelled the forest breeding habitat of the species. Our results revealed patterns in nesting-habitat modelling by the cinereous vulture throughout its whole range: steep and south-facing slopes, great cover of large trees and distance to human activities were generally selected. The ratio and situation of the studied plots (nests/random), the use of plots vs. polygons as sampling units and the number of years of data set determined the variability explained by the model. Moreover, a greater size of the breeding colony implied that ecological and geomorphological variables at landscape level were more influential. Additionally, human activities affected in greater proportion to colonies situated in Mediterranean forests. For the first time, a meta-analysis regarding the factors determining nest-site selection heterogeneity for a single species at broad scale was achieved. It is essential to homogenize and coordinate experimental design in modelling the selection of species' ecological requirements in order to avoid that differences in results among studies would be due to methodological heterogeneity. This would optimize best conservation and management practices for habitats and species in a global context. PMID:22413023

Contaminant exposure and reproductive success of Ospreys (Pandion haliaetus) nesting in Chesapeake Bay regions of concern

USGS Publications Warehouse

Rattner, B.A.; McGowan, P.C.; Golden, N.H.; Hatfield, J.S.; Toschik, P.C.; Lukei, R.F.; Hale, R.C.; Schmitz-Afonso, I.; Rice, C.P.

2004-01-01

The Chesapeake Bay osprey population has more than doubled in size since restrictions were placed on the production and use of DDT and other toxic organochlorine contaminants in the 1970s. Ospreys are now nesting in the most highly polluted portions of the Bay. In 2000 and 2001, contaminant exposure and reproduction were monitored in ospreys nesting in regions of concern, including Baltimore Harbor and the Patapsco River, the Anacostia and middle Potomac rivers, and the Elizabeth River, and a presumed reference site consisting of the South, West, and Rhode rivers. A 'sample egg' from each study nest was collected for contaminant analysis, and the fate of eggs remaining in each nest (n = 14-16/site) was monitored at 7- to 10-day intervals from egg incubation through fledging of young. Ospreys fledged young in regions of concern (observed success: 0.88 -1.53 fledglings/active nest), although productivity was marginal for sustaining local populations in Baltimore Harbor and the Patapsco River and in the Anacostia and middle Potomac rivers. Concentrations of p,p'DDE and many other organochlorine pesticides or metabolites, total PCBs, some arylhydrocarbon receptor-active PCB congeners and polybrominated diphenyl ether congeners, and perfluorooctanesulfonate were often greater in sample eggs from regions of concern compared to the reference site. Nonetheless, logistic regression analyses did not provide evidence linking marginal productivity to p,p' -DDE, total PCBs, or arylhydrocarbon receptor-active PCB congener exposure in regions of concern. In view of the moderate concentrations of total PCBs in eggs from the reference site, concerns related to new and emerging toxicants, and the absence of ecotoxicological data for terrestrial vertebrates in many Bay tributaries, a more thorough spatial evaluation of contaminant exposure in ospreys throughout the Chesapeake may be warranted.

A test of the nest sanitation hypothesis for the evolution of foreign egg rejection in an avian brood parasite rejecter host species

NASA Astrophysics Data System (ADS)

Luro, Alec B.; Hauber, Mark E.

2017-04-01

Hosts of avian brood parasites have evolved diverse defenses to avoid the costs associated with raising brood parasite nestlings. In egg ejection, the host recognizes and removes foreign eggs laid in its nest. Nest sanitation, a behavior similar in motor pattern to egg ejection, has been proposed repeatedly as a potential pre-adaptation to egg ejection. Here, we separately placed blue 3D-printed, brown-headed cowbird ( Molothrus ater) eggs known to elicit interindividual variation in ejection responses and semi-natural leaves into American robins' ( Turdus migratorius) nests to test proximate predictions that (1) rejecter hosts should sanitize debris from nests more frequently and consistently than accepter hosts and (2) hosts that sanitize their nests of debris prior to the presentation of a foreign egg will be more likely to eject the foreign egg. Egg ejection responses were highly repeatable within individuals yet variable between them, but were not influenced by prior exposure to debris, nor related to sanitation tendencies as a whole, because nearly all individuals sanitized their nests. Additionally, we collected published data for eight different host species to test for a potential positive correlation between sanitation and egg ejection. We found no significant correlation between nest sanitation and egg ejection rates; however, our comparative analysis was limited to a sample size of 8, and we advise that more data from additional species are necessary to properly address interspecific tests of the pre-adaptation hypothesis. In lack of support for the nest sanitation hypothesis, our study suggests that, within individuals, foreign egg ejection is distinct from nest sanitation tendencies, and sanitation and foreign egg ejection may not correlate across species.

A test of the nest sanitation hypothesis for the evolution of foreign egg rejection in an avian brood parasite rejecter host species.

PubMed

Luro, Alec B; Hauber, Mark E

2017-04-01

Hosts of avian brood parasites have evolved diverse defenses to avoid the costs associated with raising brood parasite nestlings. In egg ejection, the host recognizes and removes foreign eggs laid in its nest. Nest sanitation, a behavior similar in motor pattern to egg ejection, has been proposed repeatedly as a potential pre-adaptation to egg ejection. Here, we separately placed blue 3D-printed, brown-headed cowbird (Molothrus ater) eggs known to elicit interindividual variation in ejection responses and semi-natural leaves into American robins' (Turdus migratorius) nests to test proximate predictions that (1) rejecter hosts should sanitize debris from nests more frequently and consistently than accepter hosts and (2) hosts that sanitize their nests of debris prior to the presentation of a foreign egg will be more likely to eject the foreign egg. Egg ejection responses were highly repeatable within individuals yet variable between them, but were not influenced by prior exposure to debris, nor related to sanitation tendencies as a whole, because nearly all individuals sanitized their nests. Additionally, we collected published data for eight different host species to test for a potential positive correlation between sanitation and egg ejection. We found no significant correlation between nest sanitation and egg ejection rates; however, our comparative analysis was limited to a sample size of 8, and we advise that more data from additional species are necessary to properly address interspecific tests of the pre-adaptation hypothesis. In lack of support for the nest sanitation hypothesis, our study suggests that, within individuals, foreign egg ejection is distinct from nest sanitation tendencies, and sanitation and foreign egg ejection may not correlate across species.

Intermodal Attention Shifts in Multimodal Working Memory.

PubMed

Katus, Tobias; Grubert, Anna; Eimer, Martin

2017-04-01

Attention maintains task-relevant information in working memory (WM) in an active state. We investigated whether the attention-based maintenance of stimulus representations that were encoded through different modalities is flexibly controlled by top-down mechanisms that depend on behavioral goals. Distinct components of the ERP reflect the maintenance of tactile and visual information in WM. We concurrently measured tactile (tCDA) and visual contralateral delay activity (CDA) to track the attentional activation of tactile and visual information during multimodal WM. Participants simultaneously received tactile and visual sample stimuli on the left and right sides and memorized all stimuli on one task-relevant side. After 500 msec, an auditory retrocue indicated whether the sample set's tactile or visual content had to be compared with a subsequent test stimulus set. tCDA and CDA components that emerged simultaneously during the encoding phase were consistently reduced after retrocues that marked the corresponding (tactile or visual) modality as task-irrelevant. The absolute size of cue-dependent modulations was similar for the tCDA/CDA components and did not depend on the number of tactile/visual stimuli that were initially encoded into WM. Our results suggest that modality-specific maintenance processes in sensory brain regions are flexibly modulated by top-down influences that optimize multimodal WM representations for behavioral goals.

Design and validation of a diffuse reflectance and spectroscopic microendoscope with poly(dimethylsioxane)-based phantoms

PubMed Central

Greening, Gage J.; Powless, Amy J.; Hutcheson, Joshua A.; Prieto, Sandra P.; Majid, Aneeka A.; Muldoon, Timothy J.

2015-01-01

Many cases of epithelial cancer originate in basal layers of tissue and are initially undetected by conventional microendoscopy techniques. We present a bench-top, fiber-bundle microendoscope capable of providing high resolution images of surface cell morphology. Additionally, the microendoscope has the capability to interrogate deeper into material by using diffuse reflectance and broadband diffuse reflectance spectroscopy. The purpose of this multimodal technique was to overcome the limitation of microendoscopy techniques that are limited to only visualizing morphology at the tissue or cellular level. Using a custom fiber optic probe, high resolution surface images were acquired using topical proflavine to fluorescently stain non-keratinized epithelia. A 635 nm laser coupled to a 200 μm multimode fiber delivers light to the sample and the diffuse reflectance signal was captured by a 1 mm image guide fiber. Finally, a tungsten-halogen lamp coupled to a 200 μm multimode fiber delivers broadband light to the sample to acquire spectra at source-detector separations of 374, 729, and 1051 μm. To test the instrumentation, a high resolution proflavine-induced fluorescent image of resected healthy mouse colon was acquired. Additionally, five monolayer poly(dimethylsiloxane)-based optical phantoms with varying absorption and scattering properties were created to acquire diffuse reflectance profiles and broadband spectra. PMID:25983372

Design and validation of a diffuse reflectance and spectroscopic microendoscope with poly(dimethylsiloxane)-based phantoms

NASA Astrophysics Data System (ADS)

Greening, Gage J.; Powless, Amy J.; Hutcheson, Joshua A.; Prieto, Sandra P.; Majid, Aneeka A.; Muldoon, Timothy J.

2015-03-01

Many cases of epithelial cancer originate in basal layers of tissue and are initially undetected by conventional microendoscopy techniques. We present a bench-top, fiber-bundle microendoscope capable of providing high resolution images of surface cell morphology. Additionally, the microendoscope has the capability to interrogate deeper into material by using diffuse reflectance and broadband diffuse reflectance spectroscopy. The purpose of this multimodal technique was to overcome the limitation of microendoscopy techniques that are limited to only visualizing morphology at the tissue or cellular level. Using a custom fiber optic probe, high resolution surface images were acquired using topical proflavine to fluorescently stain non-keratinized epithelia. A 635 nm laser coupled to a 200 μm multimode fiber delivers light to the sample and the diffuse reflectance signal was captured by a 1 mm image guide fiber. Finally, a tungsten-halogen lamp coupled to a 200 μm multimode fiber delivers broadband light to the sample to acquire spectra at source-detector separations of 374, 729, and 1051 μm. To test the instrumentation, a high resolution proflavine-induced fluorescent image of resected healthy mouse colon was acquired. Additionally, five monolayer poly(dimethylsiloxane)-based optical phantoms with varying absorption and scattering properties were created to acquire diffuse reflectance profiles and broadband spectra.

Multimodal fiber-probe spectroscopy as a clinical tool for diagnosing and classifying biological tissues

NASA Astrophysics Data System (ADS)

Cicchi, Riccardo; Anand, Suresh; Fantechi, Riccardo; Giordano, Flavio; Gacci, Mauro; Conti, Valerio; Nesi, Gabriella; Buccoliero, Anna Maria; Carini, Marco; Guerrini, Renzo; Pavone, Francesco Saverio

2017-07-01

An optical fiber probe for multimodal spectroscopy was designed, developed and used for tissue diagnostics. The probe, based on a fiber bundle with optical fibers of various size and properties, allows performing spectroscopic measurements with different techniques, including fluorescence, Raman, and diffuse reflectance, using the same probe. Two visible laser diodes were used for fluorescence spectroscopy, a laser diode emitting in the NIR was used for Raman spectroscopy, and a fiber-coupled halogen lamp for diffuse reflectance. The developed probe was successfully employed for diagnostic purposes on various tissues, including brain and bladder. In particular, the device allowed discriminating healthy tissue from both tumor and dysplastic tissue as well as to perform tumor grading. The diagnostic capabilities of the method, determined using a cross-validation method with a leave-one-out approach, demonstrated high sensitivity and specificity for all the examined samples, as well as a good agreement with histopathological examination performed on the same samples. The obtained results demonstrated that the multimodal approach is crucial for improving diagnostic capabilities with respect to what can be obtained from individual techniques. The experimental setup presented here can improve diagnostic capabilities on a broad range of tissues and has the potential of being used clinically for guiding surgical resection in the near future.

In-situ Multimodal Imaging and Spectroscopy of Mg Electrodeposition at Electrode-Electrolyte Interfaces

NASA Astrophysics Data System (ADS)

Wu, Yimin A.; Yin, Zuwei; Farmand, Maryam; Yu, Young-Sang; Shapiro, David A.; Liao, Hong-Gang; Liang, Wen-I.; Chu, Ying-Hao; Zheng, Haimei

2017-02-01

We report the study of Mg cathodic electrochemical deposition on Ti and Au electrode using a multimodal approach by examining the sample area in-situ using liquid cell transmission electron microscopy (TEM), scanning transmission X-ray microscopy (STXM) and X-ray absorption spectroscopy (XAS). Magnesium Aluminum Chloride Complex was synthesized and utilized as electrolyte, where non-reversible features during in situ charging-discharging cycles were observed. During charging, a uniform Mg film was deposited on the electrode, which is consistent with the intrinsic non-dendritic nature of Mg deposition in Mg ion batteries. The Mg thin film was not dissolvable during the following discharge process. We found that such Mg thin film is hexacoordinated Mg compounds by in-situ STXM and XAS. This study provides insights on the non-reversibility issue and failure mechanism of Mg ion batteries. Also, our method provides a novel generic method to understand the in situ battery chemistry without any further sample processing, which can preserve the original nature of battery materials or electrodeposited materials. This multimodal in situ imaging and spectroscopy provides many opportunities to attack complex problems that span orders of magnitude in length and time scale, which can be applied to a broad range of the energy storage systems.

In-situ Multimodal Imaging and Spectroscopy of Mg Electrodeposition at Electrode-Electrolyte Interfaces

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

Wu, Yimin A.; Yin, Zuwei; Farmand, Maryam

We report the study of Mg cathodic electrochemical deposition on Ti and Au electrode using a multimodal approach by examining the sample area in-situ using liquid cell transmission electron microscopy (TEM), scanning transmission X-ray microscopy (STXM) and X-ray absorption spectroscopy (XAS). Magnesium Aluminum Chloride Complex was synthesized and utilized as electrolyte, where non-reversible features during in situ charging-discharging cycles were observed. During charging, a uniform Mg film was deposited on the electrode, which is consistent with the intrinsic non-dendritic nature of Mg deposition in Mg ion batteries. The Mg thin film was not dissolvable during the following discharge process. Wemore » found that such Mg thin film is hexacoordinated Mg compounds by in-situ STXM and XAS. This study provides insights on the non-reversibility issue and failure mechanism of Mg ion batteries. Also, our method provides a novel generic method to understand the in situ battery chemistry without any further sample processing, which can preserve the original nature of battery materials or electrodeposited materials. This multimodal in situ imaging and spectroscopy provides many opportunities to attack complex problems that span orders of magnitude in length and time scale, which can be applied to a broad range of the energy storage systems.« less

In-situ Multimodal Imaging and Spectroscopy of Mg Electrodeposition at Electrode-Electrolyte Interfaces

DOE PAGES

Wu, Yimin A.; Yin, Zuwei; Farmand, Maryam; ...

2017-02-10

We report the study of Mg cathodic electrochemical deposition on Ti and Au electrode using a multimodal approach by examining the sample area in-situ using liquid cell transmission electron microscopy (TEM), scanning transmission X-ray microscopy (STXM) and X-ray absorption spectroscopy (XAS). Magnesium Aluminum Chloride Complex was synthesized and utilized as electrolyte, where non-reversible features during in situ charging-discharging cycles were observed. During charging, a uniform Mg film was deposited on the electrode, which is consistent with the intrinsic non-dendritic nature of Mg deposition in Mg ion batteries. The Mg thin film was not dissolvable during the following discharge process. Wemore » found that such Mg thin film is hexacoordinated Mg compounds by in-situ STXM and XAS. This study provides insights on the non-reversibility issue and failure mechanism of Mg ion batteries. Also, our method provides a novel generic method to understand the in situ battery chemistry without any further sample processing, which can preserve the original nature of battery materials or electrodeposited materials. This multimodal in situ imaging and spectroscopy provides many opportunities to attack complex problems that span orders of magnitude in length and time scale, which can be applied to a broad range of the energy storage systems.« less

In-situ Multimodal Imaging and Spectroscopy of Mg Electrodeposition at Electrode-Electrolyte Interfaces.

PubMed

Wu, Yimin A; Yin, Zuwei; Farmand, Maryam; Yu, Young-Sang; Shapiro, David A; Liao, Hong-Gang; Liang, Wen-I; Chu, Ying-Hao; Zheng, Haimei

2017-02-10

We report the study of Mg cathodic electrochemical deposition on Ti and Au electrode using a multimodal approach by examining the sample area in-situ using liquid cell transmission electron microscopy (TEM), scanning transmission X-ray microscopy (STXM) and X-ray absorption spectroscopy (XAS). Magnesium Aluminum Chloride Complex was synthesized and utilized as electrolyte, where non-reversible features during in situ charging-discharging cycles were observed. During charging, a uniform Mg film was deposited on the electrode, which is consistent with the intrinsic non-dendritic nature of Mg deposition in Mg ion batteries. The Mg thin film was not dissolvable during the following discharge process. We found that such Mg thin film is hexacoordinated Mg compounds by in-situ STXM and XAS. This study provides insights on the non-reversibility issue and failure mechanism of Mg ion batteries. Also, our method provides a novel generic method to understand the in situ battery chemistry without any further sample processing, which can preserve the original nature of battery materials or electrodeposited materials. This multimodal in situ imaging and spectroscopy provides many opportunities to attack complex problems that span orders of magnitude in length and time scale, which can be applied to a broad range of the energy storage systems.

In-situ Multimodal Imaging and Spectroscopy of Mg Electrodeposition at Electrode-Electrolyte Interfaces

PubMed Central

Wu, Yimin A.; Yin, Zuwei; Farmand, Maryam; Yu, Young-Sang; Shapiro, David A.; Liao, Hong-Gang; Liang, Wen-I; Chu, Ying-Hao; Zheng, Haimei

2017-01-01

We report the study of Mg cathodic electrochemical deposition on Ti and Au electrode using a multimodal approach by examining the sample area in-situ using liquid cell transmission electron microscopy (TEM), scanning transmission X-ray microscopy (STXM) and X-ray absorption spectroscopy (XAS). Magnesium Aluminum Chloride Complex was synthesized and utilized as electrolyte, where non-reversible features during in situ charging-discharging cycles were observed. During charging, a uniform Mg film was deposited on the electrode, which is consistent with the intrinsic non-dendritic nature of Mg deposition in Mg ion batteries. The Mg thin film was not dissolvable during the following discharge process. We found that such Mg thin film is hexacoordinated Mg compounds by in-situ STXM and XAS. This study provides insights on the non-reversibility issue and failure mechanism of Mg ion batteries. Also, our method provides a novel generic method to understand the in situ battery chemistry without any further sample processing, which can preserve the original nature of battery materials or electrodeposited materials. This multimodal in situ imaging and spectroscopy provides many opportunities to attack complex problems that span orders of magnitude in length and time scale, which can be applied to a broad range of the energy storage systems. PMID:28186175

Pre- and post-experimental manipulation assessments confirm the increase in number of birds due to the addition of nest boxes

PubMed Central

Cuatianquiz Lima, Cecilia

2016-01-01

Secondary cavity nesting (SCN) birds breed in holes that they do not excavate themselves. This is possible where there are large trees whose size and age permit the digging of holes by primary excavators and only rarely happens in forest plantations, where we expected a deficit of both breeding holes and SCN species. We assessed whether the availability of tree cavities influenced the number of SCNs in two temperate forest types, and evaluated the change in number of SCNs after adding nest boxes. First, we counted all cavities within each of our 25-m radius sampling points in mature and young forest plots during 2009. We then added nest boxes at standardised locations during 2010 and 2011 and conducted fortnightly bird counts (January–October 2009–2011). In 2011 we added two extra plots of each forest type, where we also conducted bird counts. Prior to adding nest boxes, counts revealed more SCNs in mature than in young forest. Following the addition of nest boxes, the number of SCNs increased significantly in the points with nest boxes in both types of forest. Counts in 2011 confirmed the increase in number of birds due to the addition of nest boxes. Given the likely benefits associated with a richer bird community we propose that, as is routinely done in some countries, forest management programs preserve old tree stumps and add nest boxes to forest plantations in order to increase bird numbers and bird community diversity. PMID:26998410

Diagnosis of neonatal group B Streptococcus sepsis by nested-PCR of residual urine samples

PubMed Central

Cezarino, Bruno Nicolino; Yamamoto, Lidia; Del Negro, Gilda Maria Barbaro; Rocha, Daisy; Okay, Thelma Suely

2008-01-01

Group B streptococcus (GBS) remains the most common cause of early-onset sepsis in newborns. Laboratory gold-standard, broth culture methods are highly specific, but lack sensitivity. The aim of this study was to validate a nested-PCR and to determine whether residue volumes of urine samples obtained by non invasive, non sterile methods could be used to confirm neonatal GBS sepsis. The nested-PCR was performed with primers of the major GBS surface antigen. Unavailability of biological samples to perform life supporting exams, as well as others to elucidate the etiology of infections is a frequent problem concerning newborn patients. Nevertheless, we decided to include cases according to strict criteria: newborns had to present with signs and symptoms compatible with GBS infection; at least one of the following biological samples had to be sent for culture: blood, urine, or cerebrospinal fluid; availability of residue volumes of the samples sent for cultures, or of others collected on the day of hospitalization, prior to antibiotic therapy prescription, to be analyzed by PCR; favorable outcome after GBS empiric treatment. In only one newborn GBS infection was confirmed by cultures, while infection was only presumptive in the other three patients (they fulfilled inclusion criteria but were GBS-culture negative). From a total of 12 biological samples (5 blood, 3 CSF and 4 urine specimen), eight were tested by culture methods (2/8 were positive), and 8 were tested by PCR (7/8 were positive), and only 4 samples were simultaneously tested by both methods (1 positive by culture and 3 by PCR). In conclusion, although based on a restricted number of neonates and samples, our results suggest that the proposed nested-PCR might be used to diagnose GBS sepsis as it has successfully amplified the three types of biological samples analyzed (blood, urine and cerebrospinal fluid), and was more sensitive than culture methods as PCR in urine confirmed diagnosis in all four patients. Moreover, PCR has enabled us to use residue volumes of urine samples collected by non invasive, non sterile methods, what is technically adequate as GBS is not part of the normal urine flora, thus avoiding invasive procedures such as suprapubic bladder punction or transurethral catheterization. At the same time, the use of urine instead of blood samples could help preventing newborns blood spoliation. PMID:24031170

Food provisioning and parental status in songbirds: can occupancy models be used to estimate nesting performance?

PubMed

Corbani, Aude Catherine; Hachey, Marie-Hélène; Desrochers, André

2014-01-01

Indirect methods to estimate parental status, such as the observation of parental provisioning, have been problematic due to potential biases associated with imperfect detection. We developed a method to evaluate parental status based on a novel combination of parental provisioning observations and hierarchical modeling. In the summers of 2009 to 2011, we surveyed 393 sites, each on three to four consecutive days at Forêt Montmorency, Québec, Canada. We assessed parental status of 2331 adult songbirds based on parental food provisioning. To account for imperfect detection of parental status, we applied MacKenzie et al.'s (2002) two-state hierarchical model to obtain unbiased estimates of the proportion of sites with successfully nesting birds, and the proportion of adults with offspring. To obtain an independent evaluation of detection probability, we monitored 16 active nests in 2010 and conducted parental provisioning observations away from them. The probability of detecting food provisioning was 0.31 when using nest monitoring, a value within the 0.11 to 0.38 range that was estimated by two-state models. The proportion of adults or sites with broods approached 0.90 and varied depending on date during the sampling season and year, exemplifying the role of eastern boreal forests as highly productive nesting grounds for songbirds. This study offers a simple and effective sampling design for studying avian reproductive performance that could be implemented in national surveys such as breeding bird atlases.

Food Provisioning and Parental Status in Songbirds: Can Occupancy Models Be Used to Estimate Nesting Performance?

PubMed Central

Corbani, Aude Catherine; Hachey, Marie-Hélène; Desrochers, André

2014-01-01

Indirect methods to estimate parental status, such as the observation of parental provisioning, have been problematic due to potential biases associated with imperfect detection. We developed a method to evaluate parental status based on a novel combination of parental provisioning observations and hierarchical modeling. In the summers of 2009 to 2011, we surveyed 393 sites, each on three to four consecutive days at Forêt Montmorency, Québec, Canada. We assessed parental status of 2331 adult songbirds based on parental food provisioning. To account for imperfect detection of parental status, we applied MacKenzie et al.'s (2002) two-state hierarchical model to obtain unbiased estimates of the proportion of sites with successfully nesting birds, and the proportion of adults with offspring. To obtain an independent evaluation of detection probability, we monitored 16 active nests in 2010 and conducted parental provisioning observations away from them. The probability of detecting food provisioning was 0.31 when using nest monitoring, a value within the 0.11 to 0.38 range that was estimated by two-state models. The proportion of adults or sites with broods approached 0.90 and varied depending on date during the sampling season and year, exemplifying the role of eastern boreal forests as highly productive nesting grounds for songbirds. This study offers a simple and effective sampling design for studying avian reproductive performance that could be implemented in national surveys such as breeding bird atlases. PMID:24999969

Luminescence dating of anthropogenic features of the San Luis Valley, Colorado: from stone huts to stone walls

USGS Publications Warehouse

Mahan, Shannon; Donlan, Rebecca A.; Kardos, Barbara Maat

2015-01-01

The Snake Nest Wall site and the Crestone Stone Huts are in the northern San Luis Valley, Colorado, and provide a unique opportunity to date high-altitude archeological sites of unknown age and origin using optically stimulated luminescence (OSL). We sampled sediment underlying foundation stones of these structures to establish a chronological framework for each site's construction. OSL dating of the quartz grains directly under the Snake Nest Wall suggest that the stones and, therefore, the structure was most recently emplaced between 1855 and 1890 A.D. Dating of the sediment beneath the Crestone Stone Huts suggests the construction time of these huts is between 1860 and 1890 A.D. Analysis of the equivalent dose (DE) dispersion of the OSL samples at Snake Nest Wall and the Crestone Huts shows that the majority of sediments were fully bleached prior to deposition and the low scatter suggests that short-term or shallow alluvial processes were the dominant transport for sediments. In both cases, the OSL ages show that the construction was during very recent historical times, although it is likely that the Snake Nest Wall was rebuilt in the late 19th century. Further study is warranted at the Snake Nest Wall since it shows signs of greater antiquity and a continued presence of human use. The Crestone Huts are shown to be a product of railroad building during the boomtown days of Lucky and Crestone.

Genetic structure of Florida green turtle rookeries as indicated by mitochondrial DNA control region sequences

USGS Publications Warehouse

Shamblin, Brian M.; Bagley, Dean A.; Ehrhart, Llewellyn M.; Desjardin, Nicole A.; Martin, R. Erik; Hart, Kristen M.; Naro-Maciel, Eugenia; Rusenko, Kirt; Stiner, John C.; Sobel, Debra; Johnson, Chris; Wilmers, Thomas; Wright, Laura J.; Nairn, Campbell J.

2014-01-01

Green turtle (Chelonia mydas) nesting has increased dramatically in Florida over the past two decades, ranking the Florida nesting aggregation among the largest in the Greater Caribbean region. Individual beaches that comprise several hundred kilometers of Florida’s east coast and Keys support tens to thousands of nests annually. These beaches encompass natural to highly developed habitats, and the degree of demographic partitioning among rookeries was previously unresolved. We characterized the genetic structure of ten Florida rookeries from Cape Canaveral to the Dry Tortugas through analysis of 817 base pair mitochondrial DNA (mtDNA) control region sequences from 485 nesting turtles. Two common haplotypes, CM-A1.1 and CM-A3.1, accounted for 87 % of samples, and the haplotype frequencies were strongly partitioned by latitude along Florida’s Atlantic coast. Most genetic structure occurred between rookeries on either side of an apparent genetic break in the vicinity of the St. Lucie Inlet that separates Hutchinson Island and Jupiter Island, representing the finest scale at which mtDNA structure has been documented in marine turtle rookeries. Florida and Caribbean scale analyses of population structure support recognition of at least two management units: central eastern Florida and southern Florida. More thorough sampling and deeper sequencing are necessary to better characterize connectivity among Florida green turtle rookeries as well as between the Florida nesting aggregation and others in the Greater Caribbean region.

Clinical Usefulness of a One-Tube Nested Reverse Transcription Quantitative Polymerase Chain Reaction Assay for Evaluating Human Epidermal Growth Factor Receptor 2 mRNA Overexpression in Formalin-Fixed and Paraffin-Embedded Breast Cancer Tissue Samples.

PubMed

Wang, Hye-Young; Ahn, Sungwoo; Park, Sunyoung; Kim, SeungIl; Lee, Hyeyoung

2017-01-01

Currently, the two main methods used to analyze human epidermal growth factor receptor 2 (HER2) amplification or overexpression have a limited accuracy and high costs. These limitations can be overcome by the development of complementary quantitative methods. In this study, we analyzed HER2 mRNA expression in clinical formalin-fixed and paraffin-embedded (FFPE) samples using a one-tube nested reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay. We measured expression relative to 3 reference genes and compared the results to those obtained by conventional immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) assays with 226 FFPE breast cancer tissue samples. The one-tube nested RT-qPCR assay proved to be highly sensitive and specific based on comparisons with IHC (96.9 and 97.7%, respectively) and FISH (92.4 and 92.9%, respectively) obtained with the validation set. Comparisons with clinicopathological data revealed significant associations between HER2 overexpression and TNM stage (p < 0.01), histological type (p < 0.01), ER status (p < 0.001), PR status (p < 0.05), HER2 status (p < 0.001), and molecular subtypes (p < 0.001). Based on these findings, our one-tube nested RT-qPCR assay is a potentially useful and complementary screening tool for the detection of HER2 mRNA overexpression. © 2016 S. Karger AG, Basel.

Contribution of ants in modifying of soil acidity and particle size distribution

NASA Astrophysics Data System (ADS)

Morgun, Alexandra; Golichenkov, Maxim

2015-04-01

Being a natural body, formed by the influence of biota on the upper layers of the Earth's crust, the soil is the most striking example of biogenic-abiogenic interactions in the biosphere. Invertebrates (especially ants that build soil nests) are important agents that change soil properties in well developed terrestrial ecosystems. Impact of soil microorganisms on soil properties is particularly described in numerous literature and concerns mainly chemical properties and general indicators of soil biological activity. Influence of ants (as representatives of the soil mesofauna) mostly appears as mechanical movement of soil particles and aggregates, and chemical effects caused by concentration of organic matter within the ant's nest. The aim of this research was to evaluate the effect of ants on physical and chemical soil attributes such as particle size distribution and soil acidity. The samples were taken from aerial parts of Lasius niger nests, selected on different elements of the relief (summit position, slope, terrace and floodplain) in the Arkhangelsk region (north of the European part of Russia) and compared with the specimens of the upper horizons of the reference soils. Particle size distribution was determined by laser diffraction method using laser diffraction particle size analyzer «Analysette 22 comfort» (FRITSCH, Germany). The acidity (pH) was determined by potentiometry in water suspension. Particle size distribution of the samples from the nests is more variable as compared to the control samples. For example, the content of 5-10 μm fraction ranges from 9% to 12% in reference soils, while in the anthill samples the variation is from 8% to 15%. Similarly, for 50-250 μm fraction - it ranges from 15% to 18% in reference soils, whereas in anthills - from 6% to 29%. The results of particle size analysis showed that the reference sample on the terrace has silty loam texture and nests soil L. niger are medium loam. The reference soil on the slope is characterized as medium loam, and ant's nest material has silty loam texture. The control samples of soil and ants nests on the summit position are similar and have medium loam texture. Generally we outline that the particle size distribution of anthill samples shows more variability. We assume that ants operate with small soil aggregates, in which fine fractions may link together coarser particles. pH measurements show that the reference soils have a strongly acidic reaction on the summit position (pH 4.6), slightly acidic on the slope (pH 5.5) and neutral on the terrace and on the floodplain (pH 7.2). While the material of the anthills tends to be slightly alkalinized on the summit (pH 4.8) and alkalinized on the slope (pH 7.2), but acidified to neutral on the floodplain and terrace (pH 6.4 and 5.7). Therefore, the ants form specific physico-chemical conditions that are different from the surrounding (native) soil, significantly increasing the complexity of soil cover structure. This is a clear example of ecosystem engineering functions of ants in nature. Increased complexity of soil pattern is the result of variations in pH and particle size distribution. Both cause the preconditions for the formation of new environmental niches and enhance biodiversity in natural ecosystems.

Detection of Wuchereria bancrofti DNA in paired serum and urine samples using polymerase chain reaction-based systems.

PubMed

Ximenes, Camila; Brandão, Eduardo; Oliveira, Paula; Rocha, Abraham; Rego, Tamisa; Medeiros, Rafael; Aguiar-Santos, Ana; Ferraz, João; Reis, Christian; Araujo, Paulo; Carvalho, Luiz; Melo, Fabio L

2014-12-01

The Global Program for the Elimination of Lymphatic Filariasis (GPELF) aims to eliminate this disease by the year 2020. However, the development of more specific and sensitive tests is important for the success of the GPELF. The present study aimed to standardise polymerase chain reaction (PCR)-based systems for the diagnosis of filariasis in serum and urine. Twenty paired biological urine and serum samples from individuals already known to be positive for Wuchereria bancrofti were collected during the day. Conventional PCR and semi-nested PCR assays were optimised. The detection limit of the technique for purified W. bancrofti DNA extracted from adult worms was 10 fg for the internal systems (WbF/Wb2) and 0.1 fg by using semi-nested PCR. The specificity of the primers was confirmed experimentally by amplification of 1 ng of purified genomic DNA from other species of parasites. Evaluation of the paired urine and serum samples by the semi-nested PCR technique indicated only two of the 20 tested individuals were positive, whereas the simple internal PCR system (WbF/Wb2), which has highly promising performance, revealed that all the patients were positive using both samples. This study successfully demonstrated the possibility of using the PCR technique on urine for the diagnosis of W. bancrofti infection.

Serological and molecular diagnosis of Toxoplasma gondii in patients with schizophrenia.

PubMed

Ebrahimzadeh, Adel; Shahraki, Mehdi Khoshsima; Mohammadi, Azad

2018-06-01

Schizophrenia is a persistent neuropsychiatric syndrome of uncertain source. Toxoplasmosis is the most prevalent parasitic protozoan infecting one-third of the worldwide human population. Infectious agents such as toxoplasma are the probable cause of schizophrenia. This study was aimed to evaluate the association between schizophrenia and toxoplasmosis using SAG1 and B1 Target gene. During February to December 2016, 92 patients with schizophrenia are imported in our study. All cases were assessed by serological (IgG and IgM antibodies) and molecular examinations. ELISA was performed by Commercial kits according to manufactures procedure. DNA was extracted and nested PCR was done using two pairs of primers. From 92 patients, 59 (64.13%) cases were positive for toxoplasmosis by serological examinations (14 samples positive for IgM and IgG, 40 samples positive for only IgG and 5 samples Positive for only IgM) and 58 (63.04%) were positive by Nested PCR technique. Based on the nested PCR method, 68.47 and 47.82% of samples were positive by B1 and SAG1 genes, respectively. Our results showed the importance of use both serological and molecular diagnostic methods for accurate recognition of T . gondii in patients with schizophrenia. Moreover our results indicated that B1 gene is more sensitive than SAG1 gene.

Drought-caused delay in nesting of Sonoran Desert birds and its facilitation of parasite- and predator-mediated variation in reproductive success

USGS Publications Warehouse

McCreedy, Chris; van Riper, Charles

2015-01-01

As our understanding of climate change has increased, so has our awareness of the impacts of these changes on biotic systems. Climate models are nearly unanimous in their predictions for increased drought frequency in southwestern North America, and delays in nest initiation due to drought may influence nesting success and productivity for many Sonoran Desert bird species. In southeastern California and western Arizona in 2004–2009, we found negative correlations for 13 of 13 species between nest initiation date and rainfall accumulation during the preceding 4-month winter rainy season. Nesting was delayed more than 3 weeks for some species during extreme droughts in 2006 and 2007. During 2004–2009, we found a significant negative effect of nest initiation date on nest survival probability (β̂ = −0.031 ± 0.005 SE, P < 0.001) for the four species of greatest sample size. To investigate the role of nesting delay in nesting success and productivity, in 2010 we conducted a manipulative experiment with Black-tailed Gnatcatchers (Polioptila melanura; BTGN) and Verdins (Auriparus flaviceps; VERD). Following a wet winter, we delayed clutch initiation dates for treatment pairs to match first-egg dates that we observed during droughts in 2006 and 2007. Nest initiation date had a significant negative effect on nest survival of both species (BTGN: β̂ = −1.18 ± 0.27 SE, P < 0.001; VERD: β̂ = −2.33 ± 0.51 SE, P = 0.003). Treatment pairs were unable to overcome the lost period of high productivity in March and early April, and had lower productivity than control pairs over the entire breeding season. As nest predation and Brown-headed Cowbird (Molothrus ater) parasitism were the most common causes of nest failure, we conclude that the impacts of climate change–caused drought on annual reproductive output in the Sonoran Desert will be further compounded by parasitism and predation for Black-tailed Gnatcatchers and by predation for Verdins.

A Surrogate-based Adaptive Sampling Approach for History Matching and Uncertainty Quantification

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

Li, Weixuan; Zhang, Dongxiao; Lin, Guang

A critical procedure in reservoir simulations is history matching (or data assimilation in a broader sense), which calibrates model parameters such that the simulation results are consistent with field measurements, and hence improves the credibility of the predictions given by the simulations. Often there exist non-unique combinations of parameter values that all yield the simulation results matching the measurements. For such ill-posed history matching problems, Bayesian theorem provides a theoretical foundation to represent different solutions and to quantify the uncertainty with the posterior PDF. Lacking an analytical solution in most situations, the posterior PDF may be characterized with a samplemore » of realizations, each representing a possible scenario. A novel sampling algorithm is presented here for the Bayesian solutions to history matching problems. We aim to deal with two commonly encountered issues: 1) as a result of the nonlinear input-output relationship in a reservoir model, the posterior distribution could be in a complex form, such as multimodal, which violates the Gaussian assumption required by most of the commonly used data assimilation approaches; 2) a typical sampling method requires intensive model evaluations and hence may cause unaffordable computational cost. In the developed algorithm, we use a Gaussian mixture model as the proposal distribution in the sampling process, which is simple but also flexible to approximate non-Gaussian distributions and is particularly efficient when the posterior is multimodal. Also, a Gaussian process is utilized as a surrogate model to speed up the sampling process. Furthermore, an iterative scheme of adaptive surrogate refinement and re-sampling ensures sampling accuracy while keeping the computational cost at a minimum level. The developed approach is demonstrated with an illustrative example and shows its capability in handling the above-mentioned issues. Multimodal posterior of the history matching problem is captured and are used to give a reliable production prediction with uncertainty quantification. The new algorithm reveals a great improvement in terms of computational efficiency comparing previously studied approaches for the sample problem.« less

Inter-assemblage facilitation: the functional diversity of cavity-producing beetles drives the size diversity of cavity-nesting bees.

PubMed

Sydenham, Markus A K; Häusler, Lise D; Moe, Stein R; Eldegard, Katrine

2016-01-01

Inter-specific interactions are important drivers and maintainers of biodiversity. Compared to trophic and competitive interactions, the role of non-trophic facilitation among species has received less attention. Cavity-nesting bees nest in old beetle borings in dead wood, with restricted diameters corresponding to the body size of the bee species. The aim of this study was to test the hypothesis that the functional diversity of cavity-producing wood boring beetles - in terms of cavity diameters - drives the size diversity of cavity-nesting bees. The invertebrate communities were sampled in 30 sites, located in forested landscapes along an elevational gradient. We regressed the species richness and abundance of cavity nesting bees against the species richness and abundance of wood boring beetles, non-wood boring beetles and elevation. The proportion of cavity nesting bees in bee species assemblage was regressed against the species richness and abundance of wood boring beetles. We also tested the relationships between the size diversity of cavity nesting bees and wood boring beetles. The species richness and abundance of cavity nesting bees increased with the species richness and abundance of wood boring beetles. No such relationship was found for non-wood boring beetles. The abundance of wood boring beetles was also related to an increased proportion of cavity nesting bee individuals. Moreover, the size diversity of cavity-nesting bees increased with the functional diversity of wood boring beetles. Specifically, the mean and dispersion of bee body sizes increased with the functional dispersion of large wood boring beetles. The positive relationships between cavity producing bees and cavity nesting bees suggest that non-trophic facilitative interactions between species assemblages play important roles in organizing bee species assemblages. Considering a community-wide approach may therefore be required if we are to successfully understand and conserve wild bee species assemblages in forested landscapes.

The performance of multimodal hyperspectral spectroscopy in the detection of precancerous cervical lesions

NASA Astrophysics Data System (ADS)

Trahmono; Lusiana, N.; Indarti, J.

2017-08-01

The aim of this study was to compare the performance of multimodal hyperspectral spectroscopy (MHS), which combines fluorescence and reflectance spectroscopy, with that of conventional laboratory-based screening tests, such as the Papanicolaou (Pap) smear test and human papilloma virus (HPV) DNA test, for detecting precancerous lesions of the cervix. The study utilized a cross-sectional design, and the kappa test was used in the analytical assessment. MHS scans were obtained from a sample of 70 consecutive patients, followed by sample collection for Pap and HPV DNA analysis and colposcopy referral, if indicated. Of the 70 patients evaluated, the results of cervical spectroscopy were normal in 38 (54.3%) patients, and they were abnormal in 32 (45.7%) patients. Based on the cytology results, 45 (64.3%) samples were normal, and 25 (35.7%) samples were abnormal. According to the results of the HPV DNA test, 47 (67.14%) samples were normal, and 17 (24.28%) samples were abnormal. Based on the results of the kappa test, the agreement between MHS and cytology was 0.793 (p < 0.001). The agreement between MHS and the HPV DNA test was 0.195 (p = 0.086), and the agreement between MHS and colposcopy was 0.479 (p < 0.001).

The Intersection of Multimodality and Critical Perspective: Multimodality as Subversion

ERIC Educational Resources Information Center

Huang, Shin-ying

2015-01-01

This study explores the relevance of multimodality to critical media literacy. It is based on the understanding that communication is intrinsically multimodal and multimodal communication is inherently social and ideological. By analysing two English-language learners' multimodal ensembles, the study reports on how multimodality contributes to a…

Comparison between single PCR and nested PCR in detection of human papilloma viruses in paraffin-embedded OSCC and fresh oral mucosa.

PubMed

Jalouli, Miranda; Jalouli, Jamshid; Ibrahim, Salah O; Hirsch, Jan-Michaél; Sand, Lars

2015-01-01

Infection with human papilloma virus (HPV) has been implicated as one of the risk factors for the development of oropharyngeal cancer. Many different HPV tests exist, and information regarding their specific technical, analytical, and clinical properties is increasing. This study aimed to compare the level of detection of HPV using two reliable polymerase chain reaction (PCR) methods, nested PCR (NPCR) and single PCR (SPCR), in archival paraffin-embedded oral squamous cell carcinoma (OSCC) samples and fresh oral mucosa specimens. The presence of HPV genome in two groups of tissue samples was analyzed: (i) 57 paraffin-embedded OSCC samples from Sudan and (ii) eight healthy fresh oral mucosal samples from Swedish volunteers. The specimens were tested by SPCR with primer pair MY9/MY11 and NPCR using GP5+/GP6+ primer sets. Eighteen (32%) out of the 57 paraffin-embedded OSCC samples, and five (62%) out of the eight fresh clinically healthy samples were found to be HPV-positive with NPCR. With SPCR, four (7%) out of the paraffin-embedded OSCC samples were HPV-positive. A statistically significant difference between HPV-positive and -negative samples was found when comparing NPCR and SPCR in OSCC and fresh oral mucosa (p<0.0001). The comparative test between SPCR and NPCR showed 100% sensitivity and 69% specificity for OSCC. The use of the GP5+/GP6+ nested PCR increased the positivity rate, efficiency rate and sensitivity of HPV detection in oral samples significantly and should be considered as the method of choice. Copyright © 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Mode switching in volcanic seismicity: El Hierro 2011-2013

NASA Astrophysics Data System (ADS)

Roberts, Nick S.; Bell, Andrew F.; Main, Ian G.

2016-05-01

The Gutenberg-Richter b value is commonly used in volcanic eruption forecasting to infer material or mechanical properties from earthquake distributions. Such studies typically analyze discrete time windows or phases, but the choice of such windows is subjective and can introduce significant bias. Here we minimize this sample bias by iteratively sampling catalogs with randomly chosen windows and then stack the resulting probability density functions for the estimated b>˜ value to determine a net probability density function. We examine data from the El Hierro seismic catalog during a period of unrest in 2011-2013 and demonstrate clear multimodal behavior. Individual modes are relatively stable in time, but the most probable b>˜ value intermittently switches between modes, one of which is similar to that of tectonic seismicity. Multimodality is primarily associated with intermittent activation and cessation of activity in different parts of the volcanic system rather than with respect to any systematic inferred underlying process.

Multiplexed electronically programmable multimode ionization detector for chromatography

DOEpatents

Wise, M.B.; Buchanan, M.V.

1988-05-19

Method and apparatus for detecting and differentiating organic compounds based on their electron affinity. An electron capture detector cell (ECD) is operated in a plurality of multiplexed electronically programmable operating modes to alter the detector response during a single sampling cycle to acquire multiple simultaneous chromatograms corresponding to each of the different operating modes. The cell is held at a constant subatmospheric pressure while the electron collection bias voltage applied to the cell is modulated electronically to allow acquisition of multiple chromatograms for a single sample elution from a chromatograph representing three distinctly different response modes. A system is provided which automatically controls the programmed application of bias pulses at different intervals and/or amplitudes to switch the detector from an ionization mode to the electron capture mode and various degrees therebetween to provide an improved means of tuning an ECD for multimode detection and improved specificity. 6 figs.

Multiplexed electronically programmable multimode ionization detector for chromatography

DOEpatents

Wise, Marcus B.; Buchanan, Michelle V.

1989-01-01

Method and apparatus for detecting and differentiating organic compounds based on their electron affinity. An electron capture detector cell (ECD) is operated in a plurality of multiplexed electroncially programmable operating modes to alter the detector response during a single sampling cycle to acquire multiple simultaneous chromatograms corresponding to each of the different operating modes. The cell is held at a constant subatmospheric pressure while the electron collection bias voltage applied to the cell is modulated electronically to allow acquisition of multiple chromatograms for a single sample elution from a chromatograph representing three distinctly different response modes. A system is provided which automatically controls the programmed application of bias pulses at different intervals and/or amplitudes to switch the detector from an ionization mode to the electron capture mode and various degrees therebetween to provide an improved means of tuning an ECD for multimode detection and improved specificity.

Temnothorax crasecundus sp. n. – a cryptic Eurocaucasian ant species (Hymenoptera, Formicidae) discovered by Nest Centroid Clustering

PubMed Central

Seifert, Bernhard; Csösz, Sandor

2015-01-01

Abstract The paper integrates two independent studies of numeric morphology-based alpha-taxonomy of the cryptic ant species Temnothorax crassispinus (Karavajev, 1926) and Temnothorax crasecundus sp. n. conducted by different investigators, using different equipment, considering different character combinations and evaluating different samples. Samples investigated included 603 individual workers from 203 nests – thereof 104 nest samples measured by Seifert and 99 by Csösz. The material originated from Europe, Asia Minor and Caucasia. There was a very strong interspecific overlap in any of the 29 shape characters recorded and subjective expert determination failed in many cases. Primary classification hypotheses were formed by the exploratory data analysis Nest Centroid (NC) clustering and corrected to final species hypotheses by an iterative linear discriminant analysis algorithm. The evaluation of Seifert’s and Csösz’s data sets arrived at fully congruent conclusions. NC-Ward and NC-K-means clustering disagreed from the final species hypothesis in only 1.9 and 1.9% of the samples in Seifert’s data set and by 1.1 and 2.1% in Csösz’s data set which is a strong argument for heterospecificity. The type series of Temnothorax crassispinus and Temnothorax crasecundus sp. n. were allocated to different clusters with p = 0.9851 and p = 0.9912 respectively. The type series of the junior synonym Temnothorax slavonicus (Seifert, 1995) was allocated to the Temnothorax crassispinus cluster with p = 0.9927. Temnothorax crasecundus sp. n. and Temnothorax crassispinus are parapatric species with a long contact zone stretching from the Peloponnisos peninsula across Bulgaria northeast to the southern Ukraine. There is no indication for occurrence of interspecifically mixed nests or intraspecific polymorphism. However, a significant reduction of interspecific morphological distance at sites with syntopic occurrence of both species indicates local hybridization. The results are discussed within the context of the Pragmatic Species Concept of Seifert (2014). The taxonomic description and a differential diagnosis of Temnothorax crasecundus sp. n. are given. PMID:25685016

The multi-mode polarization modulation spectrometer: part 1: simultaneous detection of absorption, turbidity, and optical activity.

PubMed

Arvinte, Tudor; Bui, Tam T T; Dahab, Ali A; Demeule, Barthélemy; Drake, Alex F; Elhag, Dhia; King, Peter

2004-09-01

Circular dichroism (CD) is an important spectroscopic technique for monitoring chirality and biological macromolecule conformation. However, during a CD measurement, absorbance, light scattering/turbidity, and fluorescence can also be detected. The simultaneous measurement of these different spectral features for a single sample is the basis of a multi-mode optical spectrometer. This allows time-efficient gathering of complementary information and provides a scheme to ensure that CD measurements are reliable. Aspects of circular polarization differential light scattering, pH, and temperature variation of a protein (antibody) solution are described. A procedure to help ensure that CD measurements are reliable is described.

Behavior change, acceptance, and coping flexibility in highly distressed patients with rheumatic diseases: feasibility of a cognitive-behavioral therapy in multimodal rehabilitation.

PubMed

Vriezekolk, Johanna E; Geenen, Rinie; van den Ende, Cornelia H M; Slot, Helma; van Lankveld, Wim G J M; van Helmond, Toon

2012-05-01

To describe the development and feasibility of the integration of a cognitive-behavioral therapy (CBT) within a multimodal rehabilitation program for highly distressed patients with rheumatic diseases. Development included the detailed specification of the theoretical and empirical-based underpinnings of the CBT and the comprehensive description of its design and content. Feasibility was assessed by percentage of eligible patients, attrition and attendance rates, and patient satisfaction. The developed CBT component seeks to decrease psychological distress and improve activities and participation across multiple life domains by accomplishing behavior change, acceptance, and coping flexibility. Motivational interviewing was applied to endorse patients' own reasons to change. Forty percent (35/87) of the eligible patients were admitted to the program. Attendance rate (>95%) was high. Patient satisfaction ranged from 6.8 to 8.0 (10-point scale). Integrating CBT within a multimodal rehabilitation program is feasible. An acceptable proportion of the intended patient sample is eligible and patient's attendance and satisfaction is high. Patients with impaired physical and psychosocial functioning despite adequate medical treatment pose a great challenge. Their treatment outcome may be improved by screening and selecting highly distressed patients and offering them a CBT embedded in multimodal rehabilitation program. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Nearest clusters based partial least squares discriminant analysis for the classification of spectral data.

PubMed

Song, Weiran; Wang, Hui; Maguire, Paul; Nibouche, Omar

2018-06-07

Partial Least Squares Discriminant Analysis (PLS-DA) is one of the most effective multivariate analysis methods for spectral data analysis, which extracts latent variables and uses them to predict responses. In particular, it is an effective method for handling high-dimensional and collinear spectral data. However, PLS-DA does not explicitly address data multimodality, i.e., within-class multimodal distribution of data. In this paper, we present a novel method termed nearest clusters based PLS-DA (NCPLS-DA) for addressing the multimodality and nonlinearity issues explicitly and improving the performance of PLS-DA on spectral data classification. The new method applies hierarchical clustering to divide samples into clusters and calculates the corresponding centre of every cluster. For a given query point, only clusters whose centres are nearest to such a query point are used for PLS-DA. Such a method can provide a simple and effective tool for separating multimodal and nonlinear classes into clusters which are locally linear and unimodal. Experimental results on 17 datasets, including 12 UCI and 5 spectral datasets, show that NCPLS-DA can outperform 4 baseline methods, namely, PLS-DA, kernel PLS-DA, local PLS-DA and k-NN, achieving the highest classification accuracy most of the time. Copyright © 2018 Elsevier B.V. All rights reserved.

Integration of Multi-Modal Biomedical Data to Predict Cancer Grade and Patient Survival.

PubMed

Phan, John H; Hoffman, Ryan; Kothari, Sonal; Wu, Po-Yen; Wang, May D

2016-02-01

The Big Data era in Biomedical research has resulted in large-cohort data repositories such as The Cancer Genome Atlas (TCGA). These repositories routinely contain hundreds of matched patient samples for genomic, proteomic, imaging, and clinical data modalities, enabling holistic and multi-modal integrative analysis of human disease. Using TCGA renal and ovarian cancer data, we conducted a novel investigation of multi-modal data integration by combining histopathological image and RNA-seq data. We compared the performances of two integrative prediction methods: majority vote and stacked generalization. Results indicate that integration of multiple data modalities improves prediction of cancer grade and outcome. Specifically, stacked generalization, a method that integrates multiple data modalities to produce a single prediction result, outperforms both single-data-modality prediction and majority vote. Moreover, stacked generalization reveals the contribution of each data modality (and specific features within each data modality) to the final prediction result and may provide biological insights to explain prediction performance.

Area and Family Effects on the Psychopathology of the Millennium Cohort Study Children and Their Older Siblings

ERIC Educational Resources Information Center

Flouri, Eirini; Tzavidis, Nikos; Kallis, Constantinos

2010-01-01

Background: To model and compare contextual (area and family) effects on the psychopathology of children nested in families nested in areas. Method: Data from the first two sweeps of the UK's Millennium Cohort Study were used. The final study sample was 9,630 children clustered in 6,052 families clustered in 1,681 Lower-layer Super Output Areas.…

Detection of Pneumocystis jirovecii dihydropteroate synthase polymorphisms in patients with Pneumocystis pneumonia.

PubMed

Costa, M C; Gaspar, J; Mansinho, K; Esteves, F; Antunes, F; Matos, O

2005-01-01

In the present study, in order to improve the detection of Pneumocystis jirovecii dihydropteroate synthase (DHPS) mutations in pulmonary specimens of HIV-infected patients with P. jirovecii pneumonia, we evaluated a microfiltration procedure for the removal of human cell contamination and a nested-PCR method, for amplification in specimens with low parasite load. In the studied population, PCR amplification of the DHPS gene was more successful in unfiltered than in filtered specimens, with both touchdown-PCR and nested-PCR procedures (p<0.05 and p<0.001, respectively), but the amount of host DNA in the samples analysed seems to be inversely related with the successful PCR parasite detection. Amplification of P. jirovecii DHPS gene with nested-PCR was achieved in 77.5% of the specimens studied, demonstrating that this is a useful method for the identification of mutations in pulmonary specimens, including samples with low parasite loads, and will facilitate the evaluation of the relationship between the P. jirovecii DHPS polymorphisms and clinical resistance to sulfa drugs.

Evidence of simian retrovirus type D by polymerase chain reaction.

PubMed

Hwa, Christian Z R; Tsai, Sheung Pun; Yee, JoAnn L; Van Rompay, Koen K; Roberts, Jeffrey A

2017-06-01

Over the past few years, there have been reports of finding Simian retrovirus type D (SRV) in macaque colonies where some animals were characterized as antibody positive but virus negative raising questions about how SRV was transmitted or whether there is a variant strain detected by antibody but not polymerase chain reaction (PCR) in current use. We developed a three-round nested PCR assay using degenerate primers targeting the pol gene to detect for SRV serotypes 1-5 and applied this newly validated PCR assay to test macaque DNA samples collected in China from 2010 to 2015. Using the nested PCR assay validated in this study, we found 0.15% of the samples archived on FTA ® cards were positive. The source of SRV infection identified within domestic colonies might have originated from imported macaques. The multiplex nested PCR assay developed here may supplement the current assays for SRV. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Darwinian Model Building

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

Kester, Do; Bontekoe, Romke

2011-03-14

We present a way to generate heuristic mathematical models based on the Darwinian principles of variation and selection in a pool of individuals over many generations. Each individual has a genotype (the hereditary properties) and a phenotype (the expression of these properties in the environment). Variation is achieved by cross-over and mutation operations on the genotype which consists in the present case of a single chromosome. The genotypes 'live' in the environment of the data. Nested Sampling is used to optimize the free parameters of the models given the data, thus giving rise to the phenotypes. Selection is based onmore » the phenotypes.The evidences which naturally follow from the Nested Sampling Algorithm are used in a second level of Nested Sampling to find increasingly better models.The data in this paper originate from the Leiden Cytology and Pathology Laboratory (LCPL), which screens pap smears for cervical cancer. We have data for 1750 women who on average underwent 5 tests each. The data on individual women are treated as a small time series. We will try to estimate the next value of the prime cancer indicator from previous tests of the same woman.« less

Food habits of the southwestern willow flycatcher during the nesting season

USGS Publications Warehouse

Drost, Charles A.; Paxton, Eben H.; Sogge, Mark K.; Whitfield, Mary J.

2003-01-01

The food habits and prey base of the endangered Southwestern Willow Flycatcher (Empidonax traillii extimus) are not well known. We analyzed prey remains in 59 fecal samples from an intensively-studied population of this flycatcher at the Kern River Preserve in southern California. These samples were collected during the nesting season in 1996 and 1997 from adults caught in mist nets, and from nestlings temporarily removed from the nest for banding. A total of 379 prey individuals were identified in the samples. Dominant prey taxa, both in total numbers and in percent occurrence, were true bugs (Hemiptera), flies (Diptera), and beetles (Coleoptera). Leafhoppers (Homoptera: Cicadellidae), spiders (Araneae), bees and wasps (Hymenoptera), and dragonflies and damselflies (Odonata) were also common items. Diet composition was significantly different between years, due to a large difference in the numbers of spiders between 1996 and 1997. There was also a significant difference between the diet of young and adults, with the diet of young birds having significantly higher numbers of odonates and beetles. There was a trend toward diet differences between males and females, but this was not significant at the P = 0.05 level.

Characterisation of microbial communities in Chinese liquor fermentation starters Daqu using nested PCR-DGGE.

PubMed

Zhang, Liqiang; Wu, Chongde; Ding, Xiaofei; Zheng, Jia; Zhou, Rongqing

2014-12-01

In this study, characterises of the microbial community structures of three typical Chinese liquor Daqu, as well as different kinds of light flavour Daqu were investigated using nested PCR-denaturing gradient gel electrophoresis (DGGE). The results showed that microbial diversity was considerably different, and the microfloral compositions were highly variable among various Daqu. Lactic acid bacteria, which accounted for 30.95 % of all identified bacteria, were dominant in all Daqu samples, whereas Bacillus species were also predominant in the Luzhou (14.8 %) and Langjiu Daqu (18.2 %). Citrobacter and Burkholderia were first identified in light flavour Daqu. Aspergillus was the dominant moulds, and the non-Saccharomyces yeast species, Saccharomycopsis fibuligera, Wallemia sebi, Wallemia muriae, and Pichia subpelliculosa, were the dominant yeasts. Rasamsonia, Galactomyces, Geotrichum and Wallemia were first identified using nested PCR-DGGE. Cluster analysis indicated that the microbial community structures of different Daqu samples exhibited some differences. These may be ascribed to the different peak production temperatures, raw material constituents and microhabitats around the liquor enterprises. The current study provides insights into the microbial community structures of three typical Daqu samples, and may facilitate the development of starter cultures for manufacturing Chinese liquor.

Contextualising the Last Survivors: Population Structure of Marine Turtles in the Dominican Republic.

PubMed

Carreras, Carlos; Godley, Brendan J; León, Yolanda M; Hawkes, Lucy A; Revuelta, Ohiana; Raga, Juan A; Tomás, Jesús

2013-01-01

Nesting by three species of marine turtles persists in the Dominican Republic, despite historic threats and long-term population decline. We conducted a genetic survey of marine turtles in the Dominican Republic in order to link them with other rookeries around the Caribbean. We sequenced a 740bp fragment of the control region of the mitochondrial DNA of 92 samples from three marine turtle species [hawksbill (n = 48), green (n = 2) and leatherback (n = 42)], and incorporated published data from other nesting populations and foraging grounds. The leatherback turtle (Dermochelys coriacea) in the Dominican Republic appeared to be isolated from Awala-Yalimapo, Cayenne, Trinidad and St. Croix but connected with other Caribbean populations. Two distinct nesting populations of hawksbill turtles (Eremochelys imbricata) were detected in the Dominican Republic and exhibited interesting patterns of connectivity with other nesting sites and juvenile and adult male foraging aggregations. The green sea turtle (Chelonia mydas) has almost been extirpated from the Dominican Republic and limited inference could be made from our samples. Finally, results were compared with Lagrangian drifting buoys and published Lagrangian virtual particles that travelled through the Dominican Republic and Caribbean waters. Conservation implications of sink-source effects or genetic isolation derived from these complex inter-connections are discussed for each species and population.

Contextualising the Last Survivors: Population Structure of Marine Turtles in the Dominican Republic

PubMed Central

Carreras, Carlos; Godley, Brendan J.; León, Yolanda M.; Hawkes, Lucy A.; Revuelta, Ohiana; Raga, Juan A.; Tomás, Jesús

2013-01-01

Nesting by three species of marine turtles persists in the Dominican Republic, despite historic threats and long-term population decline. We conducted a genetic survey of marine turtles in the Dominican Republic in order to link them with other rookeries around the Caribbean. We sequenced a 740bp fragment of the control region of the mitochondrial DNA of 92 samples from three marine turtle species [hawksbill (n = 48), green (n = 2) and leatherback (n = 42)], and incorporated published data from other nesting populations and foraging grounds. The leatherback turtle (Dermochelys coriacea) in the Dominican Republic appeared to be isolated from Awala-Yalimapo, Cayenne, Trinidad and St. Croix but connected with other Caribbean populations. Two distinct nesting populations of hawksbill turtles (Eremochelys imbricata) were detected in the Dominican Republic and exhibited interesting patterns of connectivity with other nesting sites and juvenile and adult male foraging aggregations. The green sea turtle (Chelonia mydas) has almost been extirpated from the Dominican Republic and limited inference could be made from our samples. Finally, results were compared with Lagrangian drifting buoys and published Lagrangian virtual particles that travelled through the Dominican Republic and Caribbean waters. Conservation implications of sink-source effects or genetic isolation derived from these complex inter-connections are discussed for each species and population. PMID:23840394

Temporal flexibility of reproduction in temperate-breeding dabbling ducks

USGS Publications Warehouse

Krapu, Gary L.

2000-01-01

I compared nesting intervals during three consecutive years in five species of temperate-nesting dabbling ducks (Mallard [Anas platyrhynchos], Northern Pintail [Anas acuta], Northern Shoveler [Anas clypeata], Blue-winged Teal [Anas discors], Gadwall [Anas strepera]) and assessed whether differences existed in timing of refractoriness. Most nesting by females of all five species ended by the summer solstice. Nesting ended earliest for Northern Shovelers and Northern Pintails and latest for Gadwalls. Some Mallards, Blue-winged Teal, and Gadwalls continued to nest into mid- and late summer, whereas Northern Shovelers and Northern pintails did not. Mallards, Blue-winged Teal, and Gadwalls accounted for 99% (81 of 82) of flightless broods resulting from nests initiated during mid- or late summer in North Dakota and 98% (58 of 59) of flightless juveniles shot on or after 1 October by a random sample of duck hunters from across the United States. Early cessation of breeding by Northern Shovelers may have evolved in response to the species' limited flexibility in diet. Photorefractory mechanisms that limit most breeding to spring presumably evolved in response to severe constraints on reproductive success when nesting continued through summer(e.g. mortality of late-hatched young and molting females due to low temperatures). Interspecific differences in photosensitivity may account for variation in timing of cessation of nesting in late spring, but controlled experiments are needed to assess the possible role of non-photic influences. My results suggest that the refractory mechanisms controlling length of the breeding in temperate-nesting dabbling ducks are more varied and complex than previously thought, with non-photic influences (e.g. water conditions, food availability, food quality) having a larger role than indicated by earlier research.

Mixed-stock analysis reveals the migrations of juvenile hawksbill turtles (Eretmochelys imbricata) in the Caribbean Sea.

PubMed

Bowen, B W; Grant, W S; Hillis-Starr, Z; Shaver, D J; Bjorndal, K A; Bolten, A B; Bass, A L

2007-01-01

Hawksbill turtles (Eretmochelys imbricata) migrate between nesting beaches and feeding habitats that are often associated with tropical reefs, but it is uncertain which nesting colonies supply which feeding habitats. To address this gap in hawksbill biology, we compile previously published and new mitochondrial DNA (mtDNA) haplotype data for 10 nesting colonies (N = 347) in the western Atlantic and compare these profiles to four feeding populations and four previously published feeding samples (N = 626). Nesting colonies differ significantly in mtDNA haplotype frequencies (Phi(ST) = 0.588, P < 0.001), corroborating earlier conclusions of nesting site fidelity and setting the stage for mixed-stock analysis. Feeding aggregations show lower but significant structure (Phi(ST) = 0.089, P < 0.001), indicating that foraging populations are not homogenous across the Caribbean Sea. Bayesian mixed-stock estimates of the origins of juveniles in foraging areas show a highly significant, but shallow, correlation with nesting population size (r = 0.378, P = 0.004), supporting the premise that larger rookeries contribute more juveniles to feeding areas. A significant correlation between the estimated contribution and geographical distance from nesting areas (r = -0.394, P = 0.003) demonstrates the influence of proximity on recruitment to feeding areas. The influence of oceanic currents is illustrated by pelagic stage juveniles stranded in Texas, which are assigned primarily (93%) to the upstream rookery in Yucatan. One juvenile had a haplotype previously identified only in the eastern Atlantic, invoking rare trans-oceanic migrations. The mixed-stock analysis demonstrates that harvests in feeding habitats will impact nesting colonies throughout the region, with the greatest detriment to nearby nesting populations.

Relationships of environmental contaminants to reproductive success in red-breasted mergansers (Mergus serrator) from Lake Michigan

USGS Publications Warehouse

Heinz, G.H.; Haseltine, S.D.; Reichel, W.L.; Hensler, G.L.

1983-01-01

In 1977 and 1978, we studied red-breasted mergansers Mergus serrator nesting on islands in northwestern Lake Michigan to determine whether environmental contaminants were having effects on reproduction. Seventeen contaminants were measured in randomly chosen eggs from 206 nests under study. Using a variety of statistical approaches, we looked for effects of individual contaminants and combinations of contaminants on reproductive measurements such as nest desertion, failure of eggs to hatch, death of newly hatched ducklings, percentage hatching success, number of ducklings leaving the nest and eggshell thickness. We also looked for relationships between the levels of some contaminants in blood samples of 39 incubating females and reproductive success. A small degree of eggshell thinning was attributed to DDE and a few other statistical tests were significant, but no contaminant or combination of contaminants we measured seemed to have a pronounced effect on the aspects of reproduction we followed.

Multi-Generational Kinship, Multiple Mating, and Flexible Modes of Parental Care in a Breeding Population of the Veery (Catharus fuscescens), a Trans-Hemispheric Migratory Songbird

PubMed Central

Kalavacharla, Venugopal

2016-01-01

We discovered variable modes of parental care in a breeding population of color-banded Veeries (Catharus fuscescens), a Nearctic-Neotropical migratory songbird, long thought to be socially monogamous, and performed a multi-locus DNA microsatellite analysis to estimate parentage and kinship in a sample of 37 adults and 21 offspring. We detected multiple mating in both sexes, and four modes of parental care that varied in frequency within and between years including multiple male feeders at some nests, and males attending multiple nests in the same season, each with a different female. Unlike other polygynandrous systems, genetic evidence indicates that multi-generational patterns of kinship occur among adult Veeries at our study site, and this was corroborated by the capture of an adult male in 2013 that had been banded as a nestling in 2011 at a nest attended by multiple male feeders. All genotyped adults (n = 37) were related to at least one other bird in the sample at the cousin level or greater (r ≥ 0.125), and 81% were related to at least one other bird at the half-sibling level or greater (r ≥ 0.25, range 0.25–0.60). Although our sample size is small, it appears that the kin structure is maintained by natal philopatry in both sexes, and that Veeries avoid mating with close genetic kin. At nests where all adult feeders were genotyped (n = 9), the male(s) were unrelated to the female (mean r = -0.11 ± 0.15), whereas genetic data suggest close kinship (r = 0.254) between two male co-feeders at the nests of two females in 2011, and among three of four females that were mated to the same polygynous male in 2012. To our knowledge, this is the first evidence of polygynandry occurring among multiple generations of close genetic kin on the breeding ground of a Nearctic-Neotropical migratory songbird. PMID:27331399

Natural cavities used by wood ducks in north-central Minnesota

USGS Publications Warehouse

Gilmer, D.S.; Ball, I.J.; Cowardin, L.M.; Mathisen, J.

1978-01-01

Radio telemetry was used to locate 31 wood duck (Aix sponsa) nest cavity sites in 16 forest stands. Stands were of 2 types: (1) mature (mean = 107 years) northern hardwoods (10 nest sites), and (2) mature (mean = 68 years) quaking aspen (Populus tremuloides) (21 nest sites). Aspen was the most important cavity-producing tree used by wood ducks and accounted for 57 percent of 28 cavities inspected. In stands used by wood ducks, the average density of suitable cavities was about 4 per hectare. Trees containing nests were closer to water areas (P < 0.05) and the nearest forest canopy openings (P < 0.01) than was a random sample of trees from the same stands. A significant (P < 0.005) relationship existed between the orientation of the cavity entrance and the nearest canopy opening. Potential wood duck cavities usually were clustered within a stand rather than randomly distributed. Selection of trees by woodpeckers for nest hole construction probably influenced the availability of cavities used by wood ducks. A plan for managing forests to benefit wood ducks and other wildlife dependent on old-growth timber is discussed.

Compilation of 1990 annual reports of the Navy ELF communications system ecological monitoring program. Volume 2: Tabs C thru F

NASA Astrophysics Data System (ADS)

Zapotosky, J. E.

1991-08-01

This portion of the report includes monitoring of and data for arthropoda and earthworms; pollinating insects; and small mammals and nesting birds. During the 1990 growing season the ELF antenna was operated more frequently than in prior years. This provides 2 years of intermittent ELF exposure for the biological systems to react to the radiation, one year of very limited exposure and greater exposure in 1990. Arthropod and earthworm sampling was conducted at intervals of two weeks from early May to late October. High voltage transmission lines and magnetic fields have been shown to affect honeybee reproduction, survival, orientation, and nest structure. ELF EM fields could have similar effects on native megachild bees. Changes in cell length, number of cells per nest, number of leaver per cell, orientation of nest entrances, and time to collect a round leaf pierce to cap a cell were monitored. We have not detected significant changes that could be attributed to ELF EM fields. Small mammal and nesting bird biological studies in the western Upper Peninsula of Michigan for the year 1990 are reported.

Lyme disease with facial nerve palsy: rapid diagnosis using a nested polymerase chain reaction-restriction fragment length polymorphism analysis.

PubMed

Hashimoto, Y; Takahashi, H; Kishiyama, K; Sato, Y; Nakao, M; Miyamoto, K; Iizuka, H

1998-02-01

A 64-year-old woman with Lyme disease and manifesting facial nerve palsy had been bitten by a tick on the left frontal scalp 4 weeks previously. Erythema migrans appeared on the left forehead, accompanied by left facial paralysis. Nested polymerase chain reaction-restriction fragment length polymorphism analysis (nested PCR-RFLP) was performed on DNA extracted from a skin biopsy of the erythema on the left forehead. Borrelia flagellin gene DNA was detected and its RFLP pattern indicated that the organism was B. garinii, Five weeks later, B. garinii was isolated by conventional culture from the erythematous skin lesion, but not from the cerebrospinal fluid. After treatment with ceftriaxone intravenously for 10 days and oral administration of minocycline for 7 days, both the erythema and facial nerve palsy improved significantly. Nested PCR and culture taken after the lesion subsided, using skin samples obtained from a site adjacent to the original biopsy, were both negative. We suggest that nested PCR-RFLP analysis might be useful for the rapid diagnosis of Lyme disease and for evaluating therapy.

Multimodal lung cancer screening using the ITALUNG biomarker panel and low dose computed tomography. Results of the ITALUNG biomarker study.

PubMed

Carozzi, Francesca Maria; Bisanzi, Simonetta; Carrozzi, Laura; Falaschi, Fabio; Lopes Pegna, Andrea; Mascalchi, Mario; Picozzi, Giulia; Peluso, Marco; Sani, Cristina; Greco, Luana; Ocello, Cristina; Paci, Eugenio

2017-07-01

Asymptomatic high-risk subjects, randomized in the intervention arm of the ITALUNG trial (1,406 screened for lung cancer), were enrolled for the ITALUNG biomarker study (n = 1,356), in which samples of blood and sputum were analyzed for plasma DNA quantification (cut off 5 ng/ml), loss of heterozygosity and microsatellite instability. The ITALUNG biomarker panel (IBP) was considered positive if at least one of the two biomarkers included in the panel was positive. Subjects with and without lung cancer diagnosis at the end of the screening cycle with LDCT (n = 517) were evaluated. Out of 18 baseline screen detected lung cancer cases, 17 were IBP positive (94%). Repeat screen-detected lung cancer cases were 18 and 12 of them positive at baseline IBP test (66%). Interval cancer cases (2-years) and biomarker tests after a suspect Non Calcific Nodule follow-up were investigated. The single test versus multimodal screening measures of accuracy were compared in a simulation within the screened ITALUNG intervention arm, considering screen-detected and interval cancer cases. Sensitivity was 90% at baseline screening. Specificity was 71 and 61% for LDCT and IBP as baseline single test, and improved at 89% with multimodal, combined screening. The positive predictive value was 4.3% for LDCT at baseline and 10.6% for multimodal screening. Multimodal screening could improve the screening efficiency at baseline and strategies for future implementation are discussed. If IBP was used as primary screening test, the LDCT burden might decrease of about 60%. © 2017 UICC.

A Molecular Approach to Nested RT-PCR Using a New Set of Primers for the Detection of the Human Immunodeficiency Virus Protease Gene.

PubMed

Zarei, Mohammad; Ravanshad, Mehrdad; Bagban, Ashraf; Fallahi, Shahab

2016-07-01

The human immunodeficiency virus (HIV-1) is the etiologic agent of AIDS. The disease can be transmitted via blood in the window period prior to the development of antibodies to the disease. Thus, an appropriate method for the detection of HIV-1 during this window period is very important. This descriptive study proposes a sensitive, efficient, inexpensive, and easy method to detect HIV-1. In this study 25 serum samples of patients under treatment and also 10 positive and 10 negative control samples were studied. Twenty-five blood samples were obtained from HIV-1-infected individuals who were receiving treatment at the acquired immune deficiency syndrome (AIDS) research center of Imam Khomeini hospital in Tehran. The identification of HIV-1-positive samples was done by using reverse transcription to produce copy deoxyribonucleic acid (cDNA) and then optimizing the nested polymerase chain reaction (PCR) method. Two pairs of primers were then designed specifically for the protease gene fragment of the nested real time-PCR (RT-PCR) samples. Electrophoresis was used to examine the PCR products. The results were analyzed using statistical tests, including Fisher's exact test, and SPSS17 software. The 325 bp band of the protease gene was observed in all the positive control samples and in none of the negative control samples. The proposed method correctly identified HIV-1 in 23 of the 25 samples. These results suggest that, in comparison with viral cultures, antibody detection by enzyme linked immunosorbent assay (ELISAs), and conventional PCR methods, the proposed method has high sensitivity and specificity for the detection of HIV-1.

Using variance components to estimate power in a hierarchically nested sampling design improving monitoring of larval Devils Hole pupfish

USGS Publications Warehouse

Dzul, Maria C.; Dixon, Philip M.; Quist, Michael C.; Dinsomore, Stephen J.; Bower, Michael R.; Wilson, Kevin P.; Gaines, D. Bailey

2013-01-01

We used variance components to assess allocation of sampling effort in a hierarchically nested sampling design for ongoing monitoring of early life history stages of the federally endangered Devils Hole pupfish (DHP) (Cyprinodon diabolis). Sampling design for larval DHP included surveys (5 days each spring 2007–2009), events, and plots. Each survey was comprised of three counting events, where DHP larvae on nine plots were counted plot by plot. Statistical analysis of larval abundance included three components: (1) evaluation of power from various sample size combinations, (2) comparison of power in fixed and random plot designs, and (3) assessment of yearly differences in the power of the survey. Results indicated that increasing the sample size at the lowest level of sampling represented the most realistic option to increase the survey's power, fixed plot designs had greater power than random plot designs, and the power of the larval survey varied by year. This study provides an example of how monitoring efforts may benefit from coupling variance components estimation with power analysis to assess sampling design.

A Preliminary Analysis of the Linguistic Complexity of Numeracy Skills Test Items for Pre Service Teachers

ERIC Educational Resources Information Center

O'Keeffe, Lisa

2016-01-01

Language is frequently discussed as barrier to mathematics word problems. Hence this paper presents the initial findings of a linguistic analysis of numeracy skills test sample items. The theoretical perspective of multi-modal text analysis underpinned this study, in which data was extracted from the ten sample numeracy test items released by the…

Foraging ecology of least terns and piping plovers nesting on Central Platte River sandpits and sandbars

USGS Publications Warehouse

Sherfy, Mark H.; Anteau, Michael J.; Shaffer, Terry L.; Sovada, Marsha A.; Stucker, Jennifer H.

2012-01-01

Federally listed least terns (Sternula antillarum) and piping plovers (Charadrius melodus) nest on riverine sandbars on many major midcontinent river systems. On the Central Platte River, availability of sandbar habitat is limited, and both species nest on excavated sandpits in the river's floodplain. However, the extent to which sandpit-nesting birds use riverine habitats for foraging is unknown. We evaluated use of foraging habitats by least terns and piping plovers by collecting data on movements, behavior, foraging habitat, and productivity. We radiomarked 16 piping plovers and 23 least terns in 2009-2010 and monitored their movements using a network of fixed telemetry dataloggers. Piping plovers were detected primarily by the datalogger located in their nesting sandpit, whereas least terns were more frequently detected on dataloggers outside of the nesting sandpit. Telemetry data and behavioral observations showed that least terns tended to concentrate at the Kearney Canal Diversion Gates, where forage fish were apparently readily available. Fish sampling data suggested that forage fish were more abundant in riverine than in sandpit habitats, and behavioral observations showed that least terns foraged more frequently in riverine than in sandpit habitats. Piping plovers tended to forage in wet substrates along sandpit shorelines, but also used dry substrates and sandpit interior habitats. The greater mobility of least terns makes a wider range of potential foraging habitats available during brood rearing, making them able to exploit concentrations of fish outside the nesting colony. Thus, our data suggest that different spatial scales should be considered in managing nesting and foraging habitat complexes for piping plovers and least terns.

Better cancer biomarker discovery through better study design.

PubMed

Rundle, Andrew; Ahsan, Habibul; Vineis, Paolo

2012-12-01

High-throughput laboratory technologies coupled with sophisticated bioinformatics algorithms have tremendous potential for discovering novel biomarkers, or profiles of biomarkers, that could serve as predictors of disease risk, response to treatment or prognosis. We discuss methodological issues in wedding high-throughput approaches for biomarker discovery with the case-control study designs typically used in biomarker discovery studies, especially focusing on nested case-control designs. We review principles for nested case-control study design in relation to biomarker discovery studies and describe how the efficiency of biomarker discovery can be effected by study design choices. We develop a simulated prostate cancer cohort data set and a series of biomarker discovery case-control studies nested within the cohort to illustrate how study design choices can influence biomarker discovery process. Common elements of nested case-control design, incidence density sampling and matching of controls to cases are not typically factored correctly into biomarker discovery analyses, inducing bias in the discovery process. We illustrate how incidence density sampling and matching of controls to cases reduce the apparent specificity of truly valid biomarkers 'discovered' in a nested case-control study. We also propose and demonstrate a new case-control matching protocol, we call 'antimatching', that improves the efficiency of biomarker discovery studies. For a valid, but as yet undiscovered, biomarker(s) disjunctions between correctly designed epidemiologic studies and the practice of biomarker discovery reduce the likelihood that true biomarker(s) will be discovered and increases the false-positive discovery rate. © 2012 The Authors. European Journal of Clinical Investigation © 2012 Stichting European Society for Clinical Investigation Journal Foundation.

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

USGS Publications Warehouse

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

2007-01-01

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

Prevalence and molecular characterization of Giardia duodenalis in dogs in Aydin, Turkey.

PubMed

Gultekin, Mehmet; Ural, Kerem; Aysul, Nuran; Ayan, Adnan; Balikci, Canberk; Akyildiz, Gurkan

2017-06-01

The purpose of the present study was to investigate the prevalence and molecular characterization of Giardia duodenalis among dogs in Aydin, Turkey. A total of 473 faecal samples from dogs were collected. The overall prevalence of G. duodenalis was 18.8%. Higher infection rates were observed in dogs younger than three months old, from shelters, and with diarrhoea. Faecal samples of 89 dogs, diagnosed Giardia-positive by microscopy, were found positive by nested PCR. The β-giardin nested PCR assay revealed assemblage B in all samples (100%), whereas 38 of the samples were mixed with assemblage A (42%). Sequence analysis of isolates indicated sub-genotypes A3 and B4 which have been previously detected in human isolates from Turkey. The results of the present study indicated the relatively high prevalence of giardiasis and the presence of the zoonotic sub-genotypes suggesting the important role of dogs as potential reservoirs of human infections.

Multimodal Interfaces: Literature Review of Ecological Interface Design, Multimodal Perception and Attention, and Intelligent Adaptive Multimodal Interfaces

DTIC Science & Technology

2010-05-01

Multimodal Interfaces Literature Review of Ecological Interface Design , Multimodal Perception and Attention, and Intelligent... Design , Multimodal Perception and Attention, and Intelligent Adaptive Multimodal Interfaces Wayne Giang, Sathya Santhakumaran, Ehsan Masnavi, Doug...Advanced Interface Design Laboratory, E2-1303N 200 University Avenue West Waterloo, Ontario Canada N2L 3G1 Contract Project Manager: Dr. Catherine

A novel loop-mediated isothermal amplification-based test for detecting Neospora caninum DNA.

PubMed

Ramos, Andrea Estefanía; Muñoz, Marina; Cortés-Vecino, Jesús Alfredo; Barato, Paola; Patarroyo, Manuel Alfonso

2017-11-29

Neospora caninum is a cyst-forming, coccidian parasite which is known to cause neurological disorders in dogs and abortion and neonatal mortality in cows and other livestock. This study reports the development of a loop-mediated isothermal amplification (LAMP) assay based on the Neospora caninum Nc-5 gene and compares its efficacy for detecting DNA to that of a semi-nested PCR test. Six primers were designed based on the Nc-5 repeat region of N. caninum. Specific LAMP primers led to successful amplification of N. caninum DNA at 63 °C in 30 min. The LAMP assay was highly specific (i.e. it did not reveal cross-reactivity with other parasite species) and had a low N. caninum plasmid DNA limit of detection (1 fg), which is ten times higher than that for the semi-nested PCR. LAMP applicability was evaluated using a set of naturally-infected samples (59 from canine faeces and five from bovine abortions). Thirty-nine percent (25/64) of the naturally-infected samples were positive for N. caninum DNA by LAMP and 36% (23/64) by semi-nested PCR. However, the LAMP assay is much faster to perform than semi-nested PCR and provides results in 30 min. The optimized reaction conditions described in this study resulted in a sensitive, specific and rapid technique for detecting N. caninum DNA. Considering the advantages of LAMP for detecting N. caninum DNA, further assays aimed at testing its usefulness on a wider range of field samples are recommended.

Physiological ecology of overwintering in the hatchling painted turtle: multiple-scale variation in response to environmental stress.

PubMed

Costanzo, Jon P; Dinkelacker, Stephen A; Iverson, John B; Lee, Richard E

2004-01-01

We integrated field and laboratory studies in an investigation of water balance, energy use, and mechanisms of cold-hardiness in hatchling painted turtles (Chrysemys picta) indigenous to west-central Nebraska (Chrysemys picta bellii) and northern Indiana (Chrysemys picta marginata) during the winters of 1999-2000 and 2000-2001. We examined 184 nests, 80 of which provided the hatchlings (n=580) and/or samples of soil used in laboratory analyses. Whereas winter 1999-2000 was relatively dry and mild, the following winter was wet and cold; serendipitously, the contrast illuminated a marked plasticity in physiological response to environmental stress. Physiological and cold-hardiness responses of turtles also varied between study locales, largely owing to differences in precipitation and edaphics and the lower prevailing and minimum nest temperatures (to -13.2 degrees C) encountered by Nebraska turtles. In Nebraska, winter mortality occurred within 12.5% (1999-2000) and 42.3% (2000-2001) of the sampled nests; no turtles died in the Indiana nests. Laboratory studies of the mechanisms of cold-hardiness used by hatchling C. picta showed that resistance to inoculative freezing and capacity for freeze tolerance increased as winter approached. However, the level of inoculation resistance strongly depended on the physical characteristics of nest soil, as well as its moisture content, which varied seasonally. Risk of inoculative freezing (and mortality) was greatest in midwinter when nest temperatures were lowest and soil moisture and activity of constituent organic ice nuclei were highest. Water balance in overwintering hatchlings was closely linked to dynamics of precipitation and soil moisture, whereas energy use and the size of the energy reserve available to hatchlings in spring depended on the winter thermal regime. Acute chilling resulted in hyperglycemia and hyperlactemia, which persisted throughout winter; this response may be cryoprotective. Some physiological characteristics and cold-hardiness attributes varied between years, between study sites, among nests at the same site, and among siblings sharing nests. Such variation may reflect adaptive phenotypic plasticity, maternal or paternal influence on an individual's response to environmental challenge, or a combination of these factors. Some evidence suggests that life-history traits, such as clutch size and body size, have been shaped by constraints imposed by the harsh winter environment.

Challenging loop-mediated isothermal amplification (LAMP) technique for molecular detection of Toxoplasma gondii.

PubMed

Fallahi, Shirzad; Mazar, Zahra Arab; Ghasemian, Mehrdad; Haghighi, Ali

2015-05-01

To compare analytical sensitivity and specificity of a newly described DNA amplification technique, LAMP and nested PCR assay targeting the RE and B1 genes for the detection of Toxoplasma gondii (T. gondii) DNA. The analytical sensitivity of LAMP and nested-PCR was obtained against10-fold serial dilutions of T. gondii DNA ranging from 1 ng to 0.01 fg. DNA samples of other parasites and human chromosomal DNA were used to determine the specificity of molecular assays. After testing LAMP and nested-PCR in duplicate, the detection limit of RE-LAMP, B1-LAMP, RE-nested PCR and B1-nested PCR assays was one fg, 100 fg, 1 pg and 10 pg of T. gondii DNA respectively. All the LAMP assays and nested PCRs were 100% specific. The RE-LAMP assay revealed the most sensitivity for the detection of T. gondii DNA. The obtained results demonstrate that the LAMP technique has a greater sensitivity for detection of T. gondii. Furthermore, these findings indicate that primers based on the RE are more suitable than those based on the B1 gene. However, the B1-LAMP assay has potential as a diagnostic tool for detection of T. gondii. Copyright © 2015 Hainan Medical College. Production and hosting by Elsevier B.V. All rights reserved.

Sporadic nesting reveals long distance colonisation in the philopatric loggerhead sea turtle (Caretta caretta).

PubMed

Carreras, Carlos; Pascual, Marta; Tomás, Jesús; Marco, Adolfo; Hochscheid, Sandra; Castillo, Juan José; Gozalbes, Patricia; Parga, Mariluz; Piovano, Susanna; Cardona, Luis

2018-01-23

The colonisation of new suitable habitats is crucial for species survival at evolutionary scale under changing environmental conditions. However, colonisation potential may be limited by philopatry that facilitates exploiting successful habitats across generations. We examine the mechanisms of long distance dispersal of the philopatric loggerhead sea turtle (Caretta caretta) by analysing 40 sporadic nesting events in the western Mediterranean. The analysis of a fragment of the mitochondrial DNA and 7 microsatellites of 121 samples from 18 of these nesting events revealed that these nests were colonising events associated with juveniles from distant populations feeding in nearby foraging grounds. Considering the temperature-dependent sex determination of the species, we simulated the effect of the incubation temperature and propagule pressure on a potential colonisation scenario. Our results indicated that colonisation will succeed if warm temperature conditions, already existing in some of the beaches in the area, extend to the whole western Mediterranean. We hypothesize that the sporadic nesting events in developmental foraging grounds may be a mechanism to overcome philopatry limitations thus increasing the dispersal capabilities of the species and the adaptability to changing environments. Sporadic nesting in the western Mediterranean can be viewed as potential new populations in a scenario of rising temperatures.

Raman-in-SEM, a multimodal and multiscale analytical tool: performance for materials and expertise.

PubMed

Wille, Guillaume; Bourrat, Xavier; Maubec, Nicolas; Lahfid, Abdeltif

2014-12-01

The availability of Raman spectroscopy in a powerful analytical scanning electron microscope (SEM) allows morphological, elemental, chemical, physical and electronic analysis without moving the sample between instruments. This paper documents the metrological performance of the SEMSCA commercial Raman interface operated in a low vacuum SEM. It provides multiscale and multimodal analyses as Raman/EDS, Raman/cathodoluminescence or Raman/STEM (STEM: scanning transmission electron microscopy) as well as Raman spectroscopy on nanomaterials. Since Raman spectroscopy in a SEM can be influenced by several SEM-related phenomena, this paper firstly presents a comparison of this new tool with a conventional micro-Raman spectrometer. Then, some possible artefacts are documented, which are due to the impact of electron beam-induced contamination or cathodoluminescence contribution to the Raman spectra, especially with geological samples. These effects are easily overcome by changing or adapting the Raman spectrometer and the SEM settings and methodology. The deletion of the adverse effect of cathodoluminescence is solved by using a SEM beam shutter during Raman acquisition. In contrast, this interface provides the ability to record the cathodoluminescence (CL) spectrum of a phase. In a second part, this study highlights the interest and efficiency of the coupling in characterizing micrometric phases at the same point. This multimodal approach is illustrated with various issues encountered in geosciences. Copyright © 2014 Elsevier Ltd. All rights reserved.

Prevalence of mip virulence gene and PCR-base sequence typing of Legionella pneumophila from cooling water systems of two cities in Iran.

PubMed

Ahmadrajabi, Roya; Shakibaie, Mohammad Reza; Iranmanesh, Zahra; Mollaei, Hamid Reza; Sobhanipoor, Mohammad Hossein

2016-07-03

Legionella pneumophila is the primary respiratory pathogen and mostly transmitted to human through water cooling systems and cause mild to severe pneumonia with high mortality rate especially in elderly both in hospitals and community. However, current Legionella risk assessments may be compromised by uncertainties in Legionella detection methods. Here, we investigated the presence of L. pneumophila mip gene in water samples collected from different hospitals cooling towers, nursing homes and building/hotels water coolants from two geographical locations of Iran (Kerman and Bam cities) during summer season of 2015 by both nested and real-time PCR methods. Analysis of the 128 water samples for presence of the mip gene by nested-PCR revealed, 18 (23%) positive cases in Kerman and 7(14%) in Bam. However, when samples were tested by real-time PCR, we identified 4 more new cases of L. pneumophila in the hospitals as well as nursing homes water systems that were missed by nested-PCR. The highest rate of contamination was detected in water obtained from hospitals cooling towers in both the cities (p≤0.05). Dendrogram analysis and clonal relationship by PCR-base sequence typing (SBT) of the L. pneumophila genomic DNAs in Kerman water samples showed close clonal similarities among the isolates, in contrast, isolates identified from Bam city demonstrated two fingerprint patterns. The clones from hospital water samples were more related to the L. pneumophila serogroup- 1.

Prevalence of mip virulence gene and PCR-base sequence typing of Legionella pneumophila from cooling water systems of two cities in Iran

PubMed Central

Ahmadrajabi, Roya; Shakibaie, Mohammad Reza; Iranmanesh, Zahra; Mollaei, Hamid Reza; Sobhanipoor, Mohammad Hossein

2016-01-01

ABSTRACT Legionella pneumophila is the primary respiratory pathogen and mostly transmitted to human through water cooling systems and cause mild to severe pneumonia with high mortality rate especially in elderly both in hospitals and community. However, current Legionella risk assessments may be compromised by uncertainties in Legionella detection methods. Here, we investigated the presence of L. pneumophila mip gene in water samples collected from different hospitals cooling towers, nursing homes and building/hotels water coolants from two geographical locations of Iran (Kerman and Bam cities) during summer season of 2015 by both nested and real-time PCR methods. Analysis of the 128 water samples for presence of the mip gene by nested-PCR revealed, 18 (23%) positive cases in Kerman and 7(14%) in Bam. However, when samples were tested by real-time PCR, we identified 4 more new cases of L. pneumophila in the hospitals as well as nursing homes water systems that were missed by nested-PCR. The highest rate of contamination was detected in water obtained from hospitals cooling towers in both the cities (p≤0.05). Dendrogram analysis and clonal relationship by PCR-base sequence typing (SBT) of the L. pneumophila genomic DNAs in Kerman water samples showed close clonal similarities among the isolates, in contrast, isolates identified from Bam city demonstrated two fingerprint patterns. The clones from hospital water samples were more related to the L. pneumophila serogroup- 1. PMID:27028760

Multimodal Perception and Multicriterion Control of Nested Systems. 1; Coordination of Postural Control and Vehicular Control

NASA Technical Reports Server (NTRS)

Riccio, Gary E.; McDonald, P. Vernon

1998-01-01

The purpose of this report is to identify the essential characteristics of goal-directed whole-body motion. The report is organized into three major sections (Sections 2, 3, and 4). Section 2 reviews general themes from ecological psychology and control-systems engineering that are relevant to the perception and control of whole-body motion. These themes provide an organizational framework for analyzing the complex and interrelated phenomena that are the defining characteristics of whole-body motion. Section 3 of this report applies the organization framework from the first section to the problem of perception and control of aircraft motion. This is a familiar problem in control-systems engineering and ecological psychology. Section 4 examines an essential but generally neglected aspect of vehicular control: coordination of postural control and vehicular control. To facilitate presentation of this new idea, postural control and its coordination with vehicular control are analyzed in terms of conceptual categories that are familiar in the analysis of vehicular control.

Development of a reverse transcription polymerase chain reaction method for yellow fever virus detection.

PubMed

Méndez, María C; Domingo, Cristina; Tenorio, Antonio; Pardo, Lissethe C; Rey, Gloria J; Méndez, Jairo A

2013-09-01

Yellow fever is considered a re-emerging disease and is endemic in tropical regions of Africa and South America. At present, there are no standardized or commercialized kits available for yellow fever virus detection. Therefore, diagnosis must be made by time-consuming routine techniques, and sometimes, the virus or its proteins are not detected. Furthermore, co-circulation with other flaviviruses, including dengue virus, increases the difficulty of diagnosis. To develop a specific reverse transcriptase-polymerase chain reaction (RT-PCR) and nested PCR-based assay to improve the detection and diagnosis of yellow fever virus using both serum and fresh tissue samples. RT-PCR primers were designed to amplify a short fragment of all yellow fever virus genotypes reported. A second set of primers was used in a nested PCR to increase sensitivity. Thirty-three clinical samples were tested with the standardized reaction. The expected amplicon was obtained in 25 out of 33 samples analyzed using this approach, and 2 more samples tested positive after a subsequent nested PCR approach. This improved technique not only ensures the specific detection of a wide range of yellow fever virus genotypes but also may increase the sensitivity of detection by introducing a second round of amplification, allowing a rapid differential diagnosis between dengue and yellow fever infection, which is required for effective surveillance and opportune epidemiologic measures.

Comparison of Microscopy, Nested-PCR, and Real-Time-PCR Assays Using High-Throughput Screening of Pooled Samples for Diagnosis of Malaria in Asymptomatic Carriers from Areas of Endemicity in Myanmar

PubMed Central

Wang, Bo; Han, Soe-Soe; Cho, Cho; Han, Jin-Hee; Cheng, Yang; Lee, Seong-Kyun; Galappaththy, Gawrie N. L; Thimasarn, Krongthong; Soe, Myat Thu; Oo, Htet Wai; Kyaw, Myat Phone

2014-01-01

Asymptomatic infection is an important obstacle for controlling disease in countries where malaria is endemic. Because asymptomatic carriers do not seek treatment for their infections, they can have high levels of gametocytes and constitute a reservoir available for new infection. We employed a sample pooling/PCR-based molecular detection strategy for screening malaria infection in residents from areas of Myanmar where malaria is endemic. Blood samples (n = 1,552) were collected from residents in three areas of malaria endemicity (Kayin State, Bago, and Tanintharyi regions) of Myanmar. Two nested PCR and real-time PCR assays showed that asymptomatic infection was detected in about 1.0% to 9.4% of residents from the surveyed areas. The sensitivities of the two nested PCR and real-time PCR techniques were higher than that of microscopy examination (sensitivity, 100% versus 26.4%; kappa values, 0.2 to 0.5). Among the three regions, parasite-positive samples were highly detected in subjects from the Bago and Tanintharyi regions. Active surveillance of residents from regions of intense malaria transmission would reduce the risk of morbidity and mitigate transmission to the population in these areas of endemicity. Our data demonstrate that PCR-based molecular techniques are more efficient than microscopy for nationwide surveillance of malaria in countries where malaria is endemic. PMID:24648557

A novel and highly sensitive real-time nested RT-PCR assay in a single closed tube for detection of enterovirus.

PubMed

Shen, Xin-Xin; Qiu, Fang-Zhou; Zhao, Huai-Long; Yang, Meng-Jie; Hong, Liu; Xu, Song-Tao; Zhou, Shuai-Feng; Li, Gui-Xia; Feng, Zhi-Shan; Ma, Xue-Jun

2018-03-01

The sensitivity of qRT-PCR assay is not adequate for the detection of the samples with lower viral load, particularly in the cerebrospinal fluid (CSF) of patients. Here, we present the development of a highly sensitive real-time nested RT-PCR (RTN RT-PCR) assay in a single closed tube for detection of human enterovirus (HEV). The clinical performance of both RTN RT-PCR and qRT-PCR was also tested and compared using 140 CSF and fecal specimens. The sensitivities of RTN RT-PCR assay for EV71, Coxsackievirus A (CVA)16, CVA6 and CVA10 achieved 10 -8 dilution with a corresponding Ct value of 38.20, 36.45, 36.75, and 36.45, respectively, which is equal to traditional two-step nested RT-PCR assay and approximately 2-10-fold lower than that of qRT-PCR assay. The specificity of RTN RT-PCR assay was extensively analyzed insilico and subsequently verified using the reference isolates and clinical samples. Sixteen qRT-PCR-negative samples were detected by RTN RT-PCR and a variety of enterovirus serotypes was identified by sequencing of inner PCR products. We conclude RTN RT-PCR is more sensitive than qRT-PCR for the detection of HEV in clinical samples. Copyright © 2017 Elsevier Inc. All rights reserved.

Differentiating Entamoeba histolytica, Entamoeba dispar and Entamoeba moshkovskii using nested polymerase chain reaction (PCR) in rural communities in Malaysia

PubMed Central

2012-01-01

Background In this study, a total of 426 human faecal samples were examined for the presence of Entamoeba histolytica, Entamoeba dispar, Entamoeba moshkovskii infection via a combination of microscopic examination and nested polymerase chain reaction (PCR) targeting 16S ribosomal RNA of Entamoeba species. Methods Faecal sample were collected from 426 participants in five rural villages in Peninsular Malaysia. The faecal samples were processed by direct wet smear and formalin ethyl acetate concentration technique followed by iodine staining and examined via microscopy for the presence of Entamoeba species and other intestinal parasites. Microscopically positive samples for Entamoeba species cysts were further characterized using a Nested Polymerase Chain Reaction (Nested-PCR) targeting 16S-like ribosomal RNA gene. The data entry and analysis was carried out using the SPSS software (Statistical Package for the Social Sciences) program for Windows version 17 (SPSS, Chicago, IL, USA). Results Based on single faecal examination, overall prevalence of Entamoeba infection was 17.6% (75/426). Females (19.1%) were more commonly infected compared to males (15.9%). Comparison by age groups showed that adults (23.9%) had higher infection rates than children (15.3%). The PCR results showed that 52 out of 75 microscopy positive samples successfully generated species-specific amplicons. The infection with E. histolytica (75.0%; 39/52) was the most common, followed by E. dispar (30.8%; 18/52) and E. moshkovskii (5.8%; 3/52). Of these, 33 (63.5%) were shown to contain only E. histolytica, 10 (19.2%) contained E. dispar and 3 (5.8%) contained only E. moshkovskii. Mixed infection with E. histolytica and E. dispar was found in 6 (11.5%) samples. Conclusions The present study essentially emphasized the benefit of molecular techniques in discriminating the pathogenic Entamoeba species from the non-pathogenic for accurate diagnosis and better management of amoebiasis. The presence of E. moshkovskii is of great public health concern as it was the first time it has been reported in Malaysia. PMID:22947430

Spline methods for approximating quantile functions and generating random samples

NASA Technical Reports Server (NTRS)

Schiess, J. R.; Matthews, C. G.

1985-01-01

Two cubic spline formulations are presented for representing the quantile function (inverse cumulative distribution function) of a random sample of data. Both B-spline and rational spline approximations are compared with analytic representations of the quantile function. It is also shown how these representations can be used to generate random samples for use in simulation studies. Comparisons are made on samples generated from known distributions and a sample of experimental data. The spline representations are more accurate for multimodal and skewed samples and to require much less time to generate samples than the analytic representation.

Efficacy of the detection of Legionella in hot and cold water samples by culture and PCR. I. Standardization of methods.

PubMed

Wójcik-Fatla, Angelina; Stojek, Nimfa Maria; Dutkiewicz, Jacek

2012-01-01

The aim of the present study was: - to compare methods for concentration and isolation of Legionella DNA from water; - to examine the efficacy of various modifications of PCR test (PCR, semi-nested PCR, and real-time PCR) for the detection of known numbers of Legionella pneumophila in water samples artificially contaminated with the strain of this bacterium and in randomly selected samples of environmental water, in parallel with examination by culture. It was found that filtration is much more effective than centrifugation for the concentration of DNA in water samples, and that the Qiamp DNA Mini-Kit is the most efficient for isolation of Legionella DNA from water. The semi-nested PCR and real-time PCR proved to be the most sensitive methods for detection of Legionella DNA in water samples. Both PCR modifications showed a high correlation with recovery of Legionella by culture (p<0.01), while no correlation occurred between the results of one-stage PCR and culture (p>0.1).

Occurrence of Giardia intestinalis and Cryptosporidium sp. in wastewater samples from São Paulo State, Brazil, and Lima, Peru.

PubMed

Ulloa-Stanojlović, Francisco Miroslav; Aguiar, Bruna; Jara, Luis M; Sato, Maria Inês Zanoli; Guerrero, Juana Arzola; Hachich, Elayse; Matté, Glavur Rogério; Dropa, Milena; Matté, Maria Helena; de Araújo, Ronalda Silva

2016-11-01

The objectives of the study were to detect and genotype Cryptosporidium spp. and Giardia intestinalis in wastewater samples obtained from five cities with high transit of people in the State of São Paulo, Brazil, and at the entrance of a Wastewater Treatment Plant (WWTP) in Lima, Peru. Samples were collected and concentrated by centrifugation. The genomic DNA was extracted for molecular characterization by nested PCR for Cryptosporidium and double nested PCR for Giardia, followed by sequencing and phylogenetic analysis. G. intestinalis was found in 63.6 % of the samples, and the human assemblages A and B were identified. Cryptosporidium sp. was found in 36.4 % of the samples, and the species were corresponding to Cryptosporidium hominis, Cryptosporidium cuniculus, and Cryptosporidium muris. Results revealed the presence of human pathogenic Cryptosporidium species and G. intestinalis human pathogenic assemblages. Molecular tools highlight the importance to map the genetic diversity of these parasites, as well as to detect their epidemiological circulation pathway in the environment.

Inertial cavitation threshold of nested microbubbles.

PubMed

Wallace, N; Dicker, S; Lewin, Peter; Wrenn, S P

2015-04-01

Cavitation of ultrasound contrast agents (UCAs) promotes both beneficial and detrimental bioeffects in vivo (Radhakrishnan et al., 2013) [1]. The ability to determine the inertial cavitation threshold of UCA microbubbles has potential application in contrast imaging, development of therapeutic agents, and evaluation of localized effects on the body (Ammi et al., 2006) [2]. This study evaluates a novel UCA and its inertial cavitation behavior as determined by a home built cavitation detection system. Two 2.25 MHz transducers are placed at a 90° angle to one another where one transducer is driven by a high voltage pulser and the other transducer receives the signal from the oscillating microbubble. The sample chamber is placed in the overlap of the focal region of the two transducers where the microbubbles are exposed to a pulser signal consisting of 600 pulse trains per experiment at a pulse repetition frequency of 5 Hz where each train has four pulses of four cycles. The formulation being analyzed is comprised of an SF6 microbubble coated by a DSPC PEG-3000 monolayer nested within a poly-lactic acid (PLA) spherical shell. The effect of varying shell diameters and microbubble concentration on cavitation threshold profile for peak negative pressures ranging from 50 kPa to 2 MPa are presented and discussed in this paper. The nesting shell decreases inertial cavitation events from 97.96% for an un-nested microbubble to 19.09% for the same microbubbles nested within a 2.53 μm shell. As shell diameter decreases, the percentage of inertially cavitating microbubbles also decreases. For nesting formulations with average outer capsule diameters of 20.52, 14.95, 9.95, 5.55, 2.53, and 1.95 μm, the percentage of sample destroyed at 1 MPa was 51.02, 38.94, 33.25, 25.27, 19.09, and 5.37% respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular detection of Toxoplasma gondii in water samples from Scotland and a comparison between the 529bp real-time PCR and ITS1 nested PCR.

PubMed

Wells, Beth; Shaw, Hannah; Innocent, Giles; Guido, Stefano; Hotchkiss, Emily; Parigi, Maria; Opsteegh, Marieke; Green, James; Gillespie, Simon; Innes, Elisabeth A; Katzer, Frank

2015-12-15

Waterborne transmission of Toxoplasma gondii is a potential public health risk and there are currently no agreed optimised methods for the recovery, processing and detection of T. gondii oocysts in water samples. In this study modified methods of T. gondii oocyst recovery and DNA extraction were applied to 1427 samples collected from 147 public water supplies throughout Scotland. T. gondii DNA was detected, using real time PCR (qPCR) targeting the 529bp repeat element, in 8.79% of interpretable samples (124 out of 1411 samples). The samples which were positive for T. gondii DNA originated from a third of the sampled water sources. The samples which were positive by qPCR and some of the negative samples were reanalysed using ITS1 nested PCR (nPCR) and results compared. The 529bp qPCR was the more sensitive technique and a full analysis of assay performance, by Bayesian analysis using a Markov Chain Monte Carlo method, was completed which demonstrated the efficacy of this method for the detection of T. gondii in water samples. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

PIRLS 2011 User Guide for the International Database. Supplement 4: PIRLS 2011 Sampling Stratification Information

ERIC Educational Resources Information Center

Foy, Pierre, Ed.; Drucker, Kathleen T., Ed.

2013-01-01

This supplement contains documentation on the explicit and implicit stratification variables included in the PIRLS 2011 data files. The explicit strata are smaller sampling frames, created from the national sampling frames, from which national samples of schools were drawn. The implicit strata are nested within the explicit strata, and were used…

TIMSS 2011 User Guide for the International Database. Supplement 4: TIMSS 2011 Sampling Stratification Information

ERIC Educational Resources Information Center

Foy, Pierre, Ed.; Arora, Alka, Ed.; Stanco, Gabrielle M., Ed.

2013-01-01

This supplement contains documentation on the explicit and implicit stratification variables included in the TIMSS 2011 data files. The explicit strata are smaller sampling frames, created from the national sampling frames, from which national samples of schools were drawn. The implicit strata are nested within the explicit strata, and were used…

Molecular detection of a novel paramyxovirus in fruit bats from Indonesia

PubMed Central

2012-01-01

Background Fruit bats are known to harbor zoonotic paramyxoviruses including Nipah, Hendra, and Menangle viruses. The aim of this study was to detect the presence of paramyxovirus RNA in fruit bats from Indonesia. Methods RNA samples were obtained from the spleens of 110 fruit bats collected from four locations in Indonesia. All samples were screened by semi-nested broad spectrum reverse transcription PCR targeting the paramyxovirus polymerase (L) genes. Results Semi-nested reverse transcription PCR detected five previously unidentified paramyxoviruses from six fruit bats. Phylogenetic analysis showed that these virus sequences were related to henipavirus or rubulavirus. Conclusions This study indicates the presence of novel paramyxoviruses among fruit bat populations in Indonesia. PMID:23082748

On estimation of linear transformation models with nested case–control sampling

PubMed Central

Liu, Mengling

2011-01-01

Nested case–control (NCC) sampling is widely used in large epidemiological cohort studies for its cost effectiveness, but its data analysis primarily relies on the Cox proportional hazards model. In this paper, we consider a family of linear transformation models for analyzing NCC data and propose an inverse selection probability weighted estimating equation method for inference. Consistency and asymptotic normality of our estimators for regression coefficients are established. We show that the asymptotic variance has a closed analytic form and can be easily estimated. Numerical studies are conducted to support the theory and an application to the Wilms’ Tumor Study is also given to illustrate the methodology. PMID:21912975

Fiber-coupled three-micron pulsed laser source for CFRP laser treatment

NASA Astrophysics Data System (ADS)

Nyga, Sebastian; Blass, David; Katzy, Veronika; Westphalen, Thomas; Jungbluth, Bernd; Hoffmann, Hans-Dieter

2018-02-01

We present a laser source providing up to 18 W and 1.5 mJ at a wavelength of 3 μm. The output is generated by frequency conversion of randomly polarized multimode radiation at 1064 nm of an Nd:YAG laser in a two-stage conversion setup. The frequency converter comprises an optical parametric oscillator and a subsequent optical parametric amplifier using PPLN as nonlinear medium in both stages. To implement fiber-based beam delivery for materials processing, we coupled the output at 3 μm to a multimode ZrF4-fiber. This source was then used to remove epoxy resin from the surface of CFRP samples.

Tapered enlarged ends in multimode optical fibers.

PubMed

Brenci, M; Falciai, R; Scheggi, A M

1982-01-15

Radiation characteristics of multimode fibers with enlarged tapers were investigated on a number of samples obtained by varying the fiber drawing speed with a given law corresponding to a prefixed taper profile. The characterization of the fibers was made by near- and far-field intensity pattern measurements as well as by measuring the losses introduced by the taper. With a suitable choice of parameters the taper constitutes a reasonable low-loss component useful, for example, for either efficient coupling to large-spot high-power density sources or connecting fibers of different sizes. Conversely at the exit of the fiber the taper can be used for beam shaping which is of interest for mechanical or surgical applications.

Soil hydric characteristics and environmental ice nuclei influence supercooling capacity of hatchling painted turtles Chrysemys picta.

PubMed

Costanzo, J P; Litzgus, J D; Iverson, J B; Lee, R E

1998-11-01

Hatchling painted turtles (Chrysemys picta) hibernate in their shallow natal nests where temperatures occasionally fall below -10 C during cold winters. Because the thermal limit of freeze tolerance in this species is approximately -4 C, hatchlings rely on supercooling to survive exposure to extreme cold. We investigated the influence of environmental ice nuclei on susceptibility to inoculative freezing in hatchling C. picta indigenous to the Sandhills of west-central Nebraska. In the absence of external ice nuclei, hatchlings cooled to -14.6 1.9 C (mean s.e.m.; N=5) before spontaneously freezing. Supercooling capacity varied markedly among turtles cooled in physical contact with sandy soil collected from nesting locales or samples of the native soil to which water-binding agents (clay or peat) had been added, despite the fact that all substrata contained the same amount of moisture (7.5 % moisture, w/w). The temperature of crystallization (Tc) of turtles exposed to frozen native soil was -1.6 0.4 C (N=5), whereas turtles exposed to frozen soil/clay and soil/peat mixtures supercooled extensively (mean Tc values approximately -13 C). Hatchlings cooled in contact with drier (less than or equal to 4 % moisture) native soil also supercooled extensively. Thus, inoculative freezing is promoted by exposure to sandy soils containing abundant moisture and little clay or organic matter. Soil collected at turtle nesting locales in mid and late winter contained variable amounts of moisture (4-15 % w/w) and organic matter (1-3 % w/w). In addition to ice, the soil at turtle nesting locales may harbor inorganic and organic ice nuclei that may also seed the freezing of hatchlings. Bulk samples of native soil, which were autoclaved to destroy any organic nuclei, nucleated aqueous solutions at approximately -7 C (Tc range -6.1 to -8.2 C). Non-autoclaved samples contained water-extractable, presumably organic, ice nuclei (Tc range -4.4 to -5.3 C). Ice nuclei of both classes varied in potency among turtle nesting locales. Interaction with ice nuclei in the winter microenvironment determines whether hatchling C. picta remain supercooled or freeze and may ultimately account for differential mortality in nests at a given locale and for variation in winter survival rates among populations.

Predation of artificial ground nests on white-tailed prairie dog colonies

USGS Publications Warehouse

Baker, B.W.; Stanley, T.R.; Sedgwick, J.A.

1999-01-01

Prairie dog (Cynomys spp.) colonies are unique to prairie and shrub-steppe landscapes. However, widespread eradication, habitat loss, and sylvatic plague (Yersinia pestis) have reduced their numbers by 98% since historical times. Birds associated with prairie dogs also are declining. Potential nest predators, such as coyotes (Canis latrans), swift foxes (Vulpes velox), and badgers (Taxidea taxus), may be attracted to colonies where a high concentration of prairie dogs serve as available prey. Increased abundance of small mammals, including prairie dogs, also may increase the risk of predation for birds nesting on colonies. Finally, because grazing by prairie dogs may decrease vegetation height and canopy cover, bird nests may be easier for predators to locate. In this study, we placed 1,444 artificial ground nests on and off 74 white-tailed prairie dog (C. leucurus) colonies to test the hypothesis that nest predation rates are higher on colonies than at nearby off sites (i.e., uncolonized habitat). We sampled colonies from 27 May to 16 July 1997 at the following 3 complexes: Coyote Basin, Utah and Colorado; Moxa Arch, Wyoming; and Shirley Basin, Wyoming. Differences in daily predation rates between colonies and paired off sites averaged 1.0% (P = 0.060). When converted to a typical 14-day incubation period, predation rates averaged 14% higher on colonies (57.7 ?? 2.7%; ?? ?? SE) than at off sites (50.4 ?? 3.1%). Comparisons of habitat variables on colonies to off sites showed percent canopy cover of vegetation was similar (P = 0.114), percent bare ground was higher on colonies (P 0.288). Although we found the risk of nest predation was higher on white-tailed prairie dog colonies than at off sites, fitness of birds nesting on colonies might depend on other factors that influence foraging success, reproductive success, or nestling survival.

Association of empty nest with depressive symptom in a Chinese elderly population: A cross-sectional study.

PubMed

Zhai, Yujia; Yi, Huaiming; Shen, Wei; Xiao, Yuanyuan; Fan, Haixiao; He, Fan; Li, Fudong; Wang, Xinyi; Shang, Xiaopeng; Lin, Junfen

2015-11-15

Empty nest has been becoming the main family pattern among old people, and influencing the traditional family providing for the aged in China. This study aimed to investigate the association of empty nest with depressive symptom in a Chinese elderly population. Our study was based on the baseline investigation of Zhejiang Major Public Health Surveillance which was conducted in 2014. The final analyzed sample consisted of 9215 participants aged no less than 60 years. Subjects completed a questionnaire including demographic characteristics, living arrangements, behavioral risk factors, health status, subjective assessments, and Patient Health Questionnaire-9 scale. More than half of the participants were empty nest elders (57.4%). The overall prevalence of depressive symptom was 10.3%, while it was higher in empty nest group than in non-empty nest group (11.6% vs. 8.6%, P<0.001). A positive association was found between empty nest and depressive symptom, the OR (95%CI) was 1.223(1.045, 1.431). After stratified by gender/age/education level/employment status, this association was just prominent in participants of male, 70 years old and above, primary school education, and retirees. No matter living with spouse or living alone, empty nesters were more likely to have depressive symptoms than non-empty nesters. Cross-sectional study could not make a causation conclusion. The social supports of participants were not been investigated in detail. Empty nest elders, especially those who are male, 70 years old and above, primary school education, and retired, are more vulnerable to depressive symptom. Copyright © 2015 Elsevier B.V. All rights reserved.

[Reproductive activity of Chelonia mydas (Testudines: Cheloniidae) in Isla de Aves, Venezuela (2001-2008)].

PubMed

Vera, Vicente; Buitrago, Joaquín

2012-06-01

The second major nesting-site for green turtles in the Caribbean is Isla de Aves, an island protected as a wildlife refuge since 1972, located at 650km Northeast from La Guaira, Venezuela. In this island, the nesting population monitoring started in 1972 and in a more continuous way after 1978, when a Scientific-Naval Station was established and scientific observations started. Since historical data show that female captures had severely affected population levels in this island before 1978, this study aim to describe recent reproductive activities. For this, during the nesting seasons of 2001-2002 and 2005-2008, nesting females were measured and tagged using metal flipper tags. A total of 458 nights were sampled observing 5 154 female emergences, with a maximum of 53 in a single night. Non-observed emergences were calculated fitting the temporal distribution of observed emergences to a normal curve. Total emergences estimated varied from X=637.1+/-106.6 in 2001 to X =2 853+/-42.5 in 2008 (ANOVA F(6.5df)=60.37, p<0.0001). Internesting interval in the same season was estimated in X=10.71+/-1.32 days. Clutch frequency in a nesting season was calculated as X=1.71+/-1.6 times per female and season. Estimated number of nesting females per year varied from X=373+/-12.5 females in 2001 to X=l 669+/-56.1 females in 2008 (ANOVA F 55.6df)=89.42, p<0.0001); with a positive and significant trend (r=0.842, p=0.036). Results show that nesting females numbers are increasing. We suggest that the protection of the nesting area for more than 30 years, has contributed with this population increase.

Crucial nesting habitat for gunnison sage-grouse: A spatially explicit hierarchical approach

USGS Publications Warehouse

Aldridge, Cameron L.; Saher, D.J.; Childers, T.M.; Stahlnecker, K.E.; Bowen, Z.H.

2012-01-01

Gunnison sage-grouse (Centrocercus minimus) is a species of special concern and is currently considered a candidate species under Endangered Species Act. Careful management is therefore required to ensure that suitable habitat is maintained, particularly because much of the species' current distribution is faced with exurban development pressures. We assessed hierarchical nest site selection patterns of Gunnison sage-grouse inhabiting the western portion of the Gunnison Basin, Colorado, USA, at multiple spatial scales, using logistic regression-based resource selection functions. Models were selected using Akaike Information Criterion corrected for small sample sizes (AIC c) and predictive surfaces were generated using model averaged relative probabilities. Landscape-scale factors that had the most influence on nest site selection included the proportion of sagebrush cover >5%, mean productivity, and density of 2 wheel-drive roads. The landscape-scale predictive surface captured 97% of known Gunnison sage-grouse nests within the top 5 of 10 prediction bins, implicating 57% of the basin as crucial nesting habitat. Crucial habitat identified by the landscape model was used to define the extent for patch-scale modeling efforts. Patch-scale variables that had the greatest influence on nest site selection were the proportion of big sagebrush cover >10%, distance to residential development, distance to high volume paved roads, and mean productivity. This model accurately predicted independent nest locations. The unique hierarchical structure of our models more accurately captures the nested nature of habitat selection, and allowed for increased discrimination within larger landscapes of suitable habitat. We extrapolated the landscape-scale model to the entire Gunnison Basin because of conservation concerns for this species. We believe this predictive surface is a valuable tool which can be incorporated into land use and conservation planning as well the assessment of future land-use scenarios. ?? 2011 The Wildlife Society.

Nest poaching in Neotropical parrots

USGS Publications Warehouse

Wright, T.F.; Toft, C.A.; Enkerlin-Hoeflich, E.; Gonzalez-Elizondo, J.; Albornoz, M.; Rodriguez-Ferraro, A.; Rojas-Suarez, F.; Sanz, V.; Trujillo, A.; Beissinger, S.R.; Berovides A., V.; Galvez A., X.; Brice, A.T.; Joyner, K.; Eberhard, J.; Gilardi, J.; Koenig, S.E.; Stoleson, S.; Martuscelli, P.; Meyers, J.M.; Renton, K.; Rodriguez, A.M.; Sosa-Asanza, A.C.; Vilella, F.J.; Wiley, J.W.

2001-01-01

Although the poaching of nestlings for the pet trade is thought to contribute to the decline of many species of parrots, its effects have been poorly demonstrated. We calculated rates of mortality due to nest poaching in 23 studies of Neotropical parrots, representing 4024 nesting attempts in 21 species and 14 countries. We also examined how poaching rates vary with geographic region, presence of active protection programs, conservation status and economic value of a species, and passage of the U.S. Wild Bird Conservation Act. The average poaching rate across all studies was 30% of all nests observed. Thirteen studies reported poaching rates of >20%, and four reported rates of >70%. Only six studies documented no nest poaching. Of these, four were conducted on islands in the Caribbean region, which had significantly lower poaching rates than the mainland Neotropics. The other two studies that showed no poaching were conducted on the two species with the lowest economic value in our sample (U.S. retail price). In four studies that allowed direct comparison between poaching at sites with active nest protection versus that at unprotected sites, poaching rates were significantly lower at protected sites, suggesting that active protection efforts can be effective in reducing nest poaching. In those studies conducted both before and after the passage of the U.S. Wild Bird Conservation Act, poaching rates were found to be significantly lower following its enactment than in the period before. This result supports the hypothesis that the legal and illegal parrot trades are positively related, rather than inversely related as has been suggested by avicultural interests. Overall, our study indicates that poaching of parrot nestlings for economic gain is a widespread and biologically significant source of nest mortality in Neotropical parrots.

Rapid identification of HPV 16 and 18 by multiplex nested PCR-immunochromatographic test.

PubMed

Kuo, Yung-Bin; Li, Yi-Shuan; Chan, Err-Cheng

2015-02-01

Human papillomavirus (HPV) types 16 and 18 are known to be high-risk viruses that cause cervical cancer. An HPV rapid testing kit that could help physicians to make early and more informed decisions regarding patient care is needed urgently but not yet available. This study aimed to develop a multiplex nested polymerase chain reaction-immunochromatographic test (PCR-ICT) for the rapid identification of HPV 16 and 18. A multiplex nested PCR was constructed to amplify the HPV 16 and 18 genotype-specific L1 gene fragments and followed by ICT which coated with antibodies to identify rapidly the different PCR products. The type-specific gene regions of high-risk HPV 16 and 18 could be amplified successfully by multiplex nested PCR at molecular sizes of approximately 99 and 101bp, respectively. The capture antibodies raised specifically against the moleculars labeled on the PCR products could be detected simultaneously both HPV 16 and 18 in one strip. Under optimal conditions, this PCR-ICT assay had the capability to detect HPV in a sample with as low as 100 copies of HPV viral DNA. The PCR-ICT system has the advantage of direct and simultaneous detection of two high-risk HPV 16 and 18 DNA targets in one sample, which suggested a significant potential of this assay for clinical application. Copyright © 2014. Published by Elsevier B.V.

Egg laying sequence influences egg mercury concentrations and egg size in three bird species: Implications for contaminant monitoring programs

USGS Publications Warehouse

Ackerman, Joshua T.; Eagles-Smith, Collin A.; Herzog, Mark P.; Yee, Julie L.; Hartman, C. Alex

2016-01-01

Bird eggs are commonly used in contaminant monitoring programs and toxicological risk assessments, but intra-clutch variation and sampling methodology could influence interpretability. We examined the influence of egg laying sequence on egg mercury concentrations and burdens in American avocets, black-necked stilts, and Forster's terns. The average decline in mercury concentrations between the first and last egg laid was 33% for stilts, 22% for terns, and 11% for avocets, and most of this decline occurred between the first and second eggs laid (24% for stilts, 18% for terns, and 9% for avocets). Trends in egg size with egg laying order were inconsistent among species and overall differences in egg volume, mass, length, and width were <3%. We summarized the literature and, among 17 species studied, mercury concentrations generally declined by 16% between the first and second eggs laid. Despite the strong effect of egg laying sequence, most of the variance in egg mercury concentrations still occurred among clutches (75%-91%) rather than within clutches (9%-25%). Using simulations, we determined that to accurately estimate a population's mean egg mercury concentration using only a single random egg from a subset of nests, it would require sampling >60 nests to represent a large population (10% accuracy) or ≥14 nests to represent a small colony that contained <100 nests (20% accuracy).

Detection of Herpesvirus anguillae (AngHV-1) in European eel Anguilla anguilla (L.) originating from northern Poland-assessment of suitability of selected diagnostic methods.

PubMed

Nguyen, Tuan Thuc; Jin, Yeonhwa; Kiełpińska, Jolanta; Bergmann, Sven M; Lenk, Matthias; Panicz, Remigiusz

2017-11-01

The Community Action Plan requests EU member states to implement measures that ensure the recovery of the severely depleted European eel stocks. One of the main threats is posed by Anguillid herpesvirus 1 (AngHV-1) leading to increased mortality in both wild and farmed eels. Following recommendations of the OIE to minimize the risk of obtaining false-negative results, the main aim of the study was to optimize diagnostic methods for AngHV-1 detection using conventional PCR, nested PCR and in situ hybridization assay. While 53.3% of the individual organ samples were tested positive for AngHV-1 by PCR, the additional virus analysis via nested PCR revealed that the actual prevalence was 93.3%. In the cell cultivation passages, a cytopathic effect was hardly found in the first two rounds. In the third passage onto cell cultures, a lytic CPE was detected. The identification and confirmation of the viruses obtained from cell cultures as well as directly from the organ tissues were proceeded by PCR, nested PCR and sequencing of the PCR products. While no positive signal was detectable in the first round by PCR using samples from the third cell culture passages, the nested PCR provided weak but visible positive signals. © 2017 John Wiley & Sons Ltd.

MMX-I: A data-processing software for multi-modal X-ray imaging and tomography

NASA Astrophysics Data System (ADS)

Bergamaschi, A.; Medjoubi, K.; Messaoudi, C.; Marco, S.; Somogyi, A.

2017-06-01

Scanning hard X-ray imaging allows simultaneous acquisition of multimodal information, including X-ray fluorescence, absorption, phase and dark-field contrasts, providing structural and chemical details of the samples. Combining these scanning techniques with the infrastructure developed for fast data acquisition at Synchrotron Soleil permits to perform multimodal imaging and tomography during routine user experiments at the Nanoscopium beamline. A main challenge of such imaging techniques is the online processing and analysis of the generated very large volume (several hundreds of Giga Bytes) multimodal data-sets. This is especially important for the wide user community foreseen at the user oriented Nanoscopium beamline (e.g. from the fields of Biology, Life Sciences, Geology, Geobiology), having no experience in such data-handling. MMX-I is a new multi-platform open-source freeware for the processing and reconstruction of scanning multi-technique X-ray imaging and tomographic datasets. The MMX-I project aims to offer, both expert users and beginners, the possibility of processing and analysing raw data, either on-site or off-site. Therefore we have developed a multi-platform (Mac, Windows and Linux 64bit) data processing tool, which is easy to install, comprehensive, intuitive, extendable and user-friendly. MMX-I is now routinely used by the Nanoscopium user community and has demonstrated its performance in treating big data.

Construction of a multimodal CT-video chest model

NASA Astrophysics Data System (ADS)

Byrnes, Patrick D.; Higgins, William E.

2014-03-01

Bronchoscopy enables a number of minimally invasive chest procedures for diseases such as lung cancer and asthma. For example, using the bronchoscope's continuous video stream as a guide, a physician can navigate through the lung airways to examine general airway health, collect tissue samples, or administer a disease treatment. In addition, physicians can now use new image-guided intervention (IGI) systems, which draw upon both three-dimensional (3D) multi-detector computed tomography (MDCT) chest scans and bronchoscopic video, to assist with bronchoscope navigation. Unfortunately, little use is made of the acquired video stream, a potentially invaluable source of information. In addition, little effort has been made to link the bronchoscopic video stream to the detailed anatomical information given by a patient's 3D MDCT chest scan. We propose a method for constructing a multimodal CT-video model of the chest. After automatically computing a patient's 3D MDCT-based airway-tree model, the method next parses the available video data to generate a positional linkage between a sparse set of key video frames and airway path locations. Next, a fusion/mapping of the video's color mucosal information and MDCT-based endoluminal surfaces is performed. This results in the final multimodal CT-video chest model. The data structure constituting the model provides a history of those airway locations visited during bronchoscopy. It also provides for quick visual access to relevant sections of the airway wall by condensing large portions of endoscopic video into representative frames containing important structural and textural information. When examined with a set of interactive visualization tools, the resulting fused data structure provides a rich multimodal data source. We demonstrate the potential of the multimodal model with both phantom and human data.

A randomized phase II feasibility trial of a multimodal intervention for the management of cachexia in lung and pancreatic cancer.

PubMed

Solheim, Tora S; Laird, Barry J A; Balstad, Trude Rakel; Stene, Guro B; Bye, Asta; Johns, Neil; Pettersen, Caroline H; Fallon, Marie; Fayers, Peter; Fearon, Kenneth; Kaasa, Stein

2017-10-01

Cancer cachexia is a syndrome of weight loss (including muscle and fat), anorexia, and decreased physical function. It has been suggested that the optimal treatment for cachexia should be a multimodal intervention. The primary aim of this study was to examine the feasibility and safety of a multimodal intervention (n-3 polyunsaturated fatty acid nutritional supplements, exercise, and anti-inflammatory medication: celecoxib) for cancer cachexia in patients with incurable lung or pancreatic cancer, undergoing chemotherapy. Patients receiving two cycles of standard chemotherapy were randomized to either the multimodal cachexia intervention or standard care. Primary outcome measures were feasibility assessed by recruitment, attrition, and compliance with intervention (>50% of components in >50% of patients). Key secondary outcomes were change in weight, muscle mass, physical activity, safety, and survival. Three hundred and ninety-nine were screened resulting in 46 patients recruited (11.5%). Twenty five patients were randomized to the treatment and 21 as controls. Forty-one completed the study (attrition rate 11%). Compliance to the individual components of the intervention was 76% for celecoxib, 60% for exercise, and 48% for nutritional supplements. As expected from the sample size, there was no statistically significant effect on physical activity or muscle mass. There were no intervention-related Serious Adverse Events and survival was similar between the groups. A multimodal cachexia intervention is feasible and safe in patients with incurable lung or pancreatic cancer; however, compliance to nutritional supplements was suboptimal. A phase III study is now underway to assess fully the effect of the intervention. © 2017 The Authors. Journal of Cachexia, Sarcopenia and Muscle published by John Wiley & Sons Ltd on behalf of the Society on Sarcopenia, Cachexia and Wasting Disorders.

Mercury in blood and eggs of the sea turtle Lepidochelys olivacea from a nesting colony in Oaxaca, Mexico.

PubMed

Páez-Osuna, F; Calderón-Campuzano, M F; Soto-Jiménez, M F; Ruelas-Inzunza, J

2011-06-01

Mercury concentrations were assessed in the sea turtle Lepidochelys olivacea from a nesting colony of Oaxaca, Mexico; 25 female turtles were sampled, a total of 250 eggs were collected during the season 2005-2006. Higher concentrations were found in yolk fraction, while in blood and albumen mean levels were below of 0.0010μg g(-1) dry wt. On the basis of one nesting season, the maternal transfer of Hg via eggs-laying was estimated in 2.0±1.1%. According to international norms, the health of this population and its habitats is acceptable for Hg and corresponds to baseline levels of a nearly pristine environment. Copyright © 2011 Elsevier Ltd. All rights reserved.

Constant-pressure nested sampling with atomistic dynamics

NASA Astrophysics Data System (ADS)

Baldock, Robert J. N.; Bernstein, Noam; Salerno, K. Michael; Pártay, Lívia B.; Csányi, Gábor

2017-10-01

The nested sampling algorithm has been shown to be a general method for calculating the pressure-temperature-composition phase diagrams of materials. While the previous implementation used single-particle Monte Carlo moves, these are inefficient for condensed systems with general interactions where single-particle moves cannot be evaluated faster than the energy of the whole system. Here we enhance the method by using all-particle moves: either Galilean Monte Carlo or the total enthalpy Hamiltonian Monte Carlo algorithm, introduced in this paper. We show that these algorithms enable the determination of phase transition temperatures with equivalent accuracy to the previous method at 1 /N of the cost for an N -particle system with general interactions, or at equal cost when single-particle moves can be done in 1 /N of the cost of a full N -particle energy evaluation. We demonstrate this speed-up for the freezing and condensation transitions of the Lennard-Jones system and show the utility of the algorithms by calculating the order-disorder phase transition of a binary Lennard-Jones model alloy, the eutectic of copper-gold, the density anomaly of water, and the condensation and solidification of bead-spring polymers. The nested sampling method with all three algorithms is implemented in the pymatnest software.

Breeding sex ratios in adult leatherback turtles (Dermochelys coriacea) may compensate for female-biased hatchling sex ratios.

PubMed

Stewart, Kelly R; Dutton, Peter H

2014-01-01

For vertebrates with temperature-dependent sex determination, primary (or hatchling) sex ratios are often skewed, an issue of particular relevance to concerns over effects of climate change on populations. However, the ratio of breeding males to females, or the operational sex ratio (OSR), is important to understand because it has consequences for population demographics and determines the capacity of a species to persist. The OSR also affects mating behaviors and mate choice, depending on the more abundant sex. For sea turtles, hatchling and juvenile sex ratios are generally female-biased, and with warming nesting beach temperatures, there is concern that populations may become feminized. Our purpose was to evaluate the breeding sex ratio for leatherback turtles at a nesting beach in St. Croix, USVI. In 2010, we sampled nesting females and later sampled their hatchlings as they emerged from nests. Total genomic DNA was extracted and all individuals were genotyped using 6 polymorphic microsatellite markers. We genotyped 662 hatchlings from 58 females, matching 55 females conclusively to their nests. Of the 55, 42 females mated with one male each, 9 mated with 2 males each and 4 mated with at least 3 males each, for a multiple paternity rate of 23.6%. Using GERUD1.0, we reconstructed parental genotypes, identifying 47 different males and 46 females for an estimated breeding sex ratio of 1.02 males for every female. Thus we demonstrate that there are as many actively breeding males as females in this population. Concerns about female-biased adult sex ratios may be premature, and mate choice or competition may play more of a role in sea turtle reproduction than previously thought. We recommend monitoring breeding sex ratios in the future to allow the integration of this demographic parameter in population models.

Wintering area DDE source to migratory white-faced ibis revealed by satellite telemetry and prey sampling.

PubMed

Yates, Michael A; Fuller, Mark R; Henny, Charles J; Seegar, William S; Garcia, Jaqueline

2010-01-01

Locations of contaminant exposure for nesting migratory species are difficult to fully understand because of possible additional sources encountered during migration or on the wintering grounds. A portion of the migratory white-faced ibis (Plegadis chihi) nesting at Carson Lake, Nevada continues to be exposed to dichloro-diphenyldichloro-ethylene (DDE) with no change, which is unusual, observed in egg concentrations between 1985 and 2000. About 45-63% of the earliest nesting segment shows reduced reproductive success correlated with elevated egg concentrations of >4 microg/g wet weight (ww). Local prey (primarily earthworms) near nests contained little DDE so we tracked the migration and wintering movements of 20 adult males during 2000-2004 to determine the possible source. At various wintering sites, we found a correlation (r (2) = 0.518, P = 0.0125, N = 11) between DDE in earthworm composites and DDE in blood plasma of white-faced ibis wintering there, although the plasma was collected on their breeding grounds soon after arrival. The main source of DDE was wintering areas in the Mexicali Valley of Baja California Norte, Mexico, and probably the adjacent Imperial Valley, California, USA. This unusual continuing DDE problem for white-faced ibis is associated with: the long-term persistence in soil of DDE; the earthworms' ability to bioconcentrate DDE from soil; the proclivity of white-faced ibis to feed on earthworms in agricultural fields; the species's extreme sensitivity to DDE in their eggs; and perhaps its life history strategy of being a "capital breeder". We suggest surveying and sampling white-faced ibis eggs at nesting colonies, especially at Carson Lake, to monitor the continuing influence of DDE.

Development of a highly sensitive real-time nested RT-PCR assay in a single closed tube for detection of enterovirus 71 in hand, foot, and mouth disease.

PubMed

Niu, Peihua; Qi, Shunxiang; Yu, Benzhang; Zhang, Chen; Wang, Ji; Li, Qi; Ma, Xuejun

2016-11-01

Enterovirus 71 (EV71) is one of the major causative agents of outbreaks of hand, foot, and mouth disease (HFMD). A commercial TaqMan probe-based real-time PCR assay has been widely used for the differential detection of EV71 despite its relatively high cost and failure to detect samples with a low viral load (Ct value > 35). In this study, a highly sensitive real-time nested RT-PCR (RTN RT-PCR) assay in a single closed tube for detection of EV71 in HFMD was developed. The sensitivity and specificity of this assay were evaluated using a reference EV71 stock and a panel of controls consisting of coxsackievirus A16 (CVA16) and common respiratory viruses, respectively. The clinical performance of this assay was evaluated and compared with those of a commercial TaqMan probe-based real-time PCR (qRT-PCR) assay and a traditional two-step nested RT-PCR assay. The limit of detection for the RTN RT-PCR assay was 0.01 TCID50/ml, with a Ct value of 38.3, which was the same as that of the traditional two-step nested RT-PCR assay and approximately tenfold lower than that of the qRT-PCR assay. When testing the reference strain EV71, this assay showed favorable detection reproducibility and no obvious cross-reactivity. The testing results of 100 clinical throat swabs from HFMD-suspected patients revealed that 41 samples were positive for EV71 by both RTN RT-PCR and traditional two-step nested RT-PCR assays, whereas only 29 were EV71 positive by qRT-PCR assay.

Nested PCR detection of malaria directly using blood filter paper samples from epidemiological surveys.

PubMed

Li, Peipei; Zhao, Zhenjun; Wang, Ying; Xing, Hua; Parker, Daniel M; Yang, Zhaoqing; Baum, Elizabeth; Li, Wenli; Sattabongkot, Jetsumon; Sirichaisinthop, Jeeraphat; Li, Shuying; Yan, Guiyun; Cui, Liwang; Fan, Qi

2014-05-08

Nested PCR is considered a sensitive and specific method for detecting malaria parasites and is especially useful in epidemiological surveys. However, the preparation of DNA templates for PCR is often time-consuming and costly. A simplified PCR method was developed to directly use a small blood filter paper square (2 × 2 mm) as the DNA template after treatment with saponin. This filter paper-based nested PCR method (FP-PCR) was compared to microscopy and standard nested PCR with DNA extracted by using a Qiagen DNA mini kit from filter paper blood spots of 204 febrile cases. The FP-PCR technique was further applied to evaluate malaria infections in 1,708 participants from cross-sectional epidemiological surveys conducted in Myanmar and Thailand. The FP-PCR method had a detection limit of ~0.2 parasites/μL blood, estimated using cultured Plasmodium falciparum parasites. With 204 field samples, the sensitivity of the FP-PCR method was comparable to that of the standard nested PCR method, which was significantly higher than that of microscopy. Application of the FP-PCR method in large cross-sectional studies conducted in Myanmar and Thailand detected 1.9% (12/638) and 6.2% (66/1,070) asymptomatic Plasmodium infections, respectively, as compared to the detection rates of 1.3% (8/638) and 0.04% (4/1,070) by microscopy. This FP-PCR method was much more sensitive than microscopy in detecting Plasmodium infections. It drastically increased the detection sensitivity of asymptomatic infections in cross-sectional surveys conducted in Thailand and Myanmar, suggesting that this FP-PCR method has a potential for future applications in malaria epidemiology studies.

Wintering area DDE source to migratory white-faced ibis revealed by satellite telemetry and prey sampling

USGS Publications Warehouse

Yates, M.A.; Fuller, M.R.; Henny, C.J.; Seegar, W.S.; Garcia, Jorge H.

2010-01-01

Locations of contaminant exposure for nesting migratory species are difficult to fully understand because of possible additional sources encountered during migration or on the wintering grounds. A portion of the migratory white-faced ibis (Plegadis chihi) nesting at Carson Lake, Nevada continues to be exposed to dichloro-diphenyldichloro-ethylene (DDE) with no change, which is unusual, observed in egg concentrations between 1985 and 2000. About 45-63% of the earliest nesting segment shows reduced reproductive success correlated with elevated egg concentrations of >4 ??g/g wet weight (ww). Local prey (primarily earthworms) near nests contained little DDE so we tracked the migration and wintering movements of 20 adult males during 2000-2004 to determine the possible source. At various wintering sites, we found a correlation (r 2 = 0.518, P = 0.0125, N = 11) between DDE in earthworm composites and DDE in blood plasma of white-faced ibis wintering there, although the plasma was collected on their breeding grounds soon after arrival. The main source of DDE was wintering areas in the Mexicali Valley of Baja California Norte, Mexico, and probably the adjacent Imperial Valley, California, USA. This unusual continuing DDE problem for white-faced ibis is associated with: the long-term persistence in soil of DDE; the earthworms' ability to bioconcentrate DDE from soil; the proclivity of white-faced ibis to feed on earthworms in agricultural fields; the species's extreme sensitivity to DDE in their eggs; and perhaps its life history strategy of being a "capital breeder". We suggest surveying and sampling white-faced ibis eggs at nesting colonies, especially at Carson Lake, to monitor the continuing influence of DDE. ?? 2009 Springer Science+Business Media, LLC.

The efficacy of a nested PCR in detecting cytochrome c oxidase subunit 1 gene of Sarcoptes scabiei var. Hominis for diagnosing scabies.

PubMed

Hahm, J E; Kim, C W; Kim, S S

2018-04-06

A widespread scabies infestation, associated to long-term residence in nursing homes, is becoming a serious issue in developed countries. Mineral oil examination is regarded as the gold standard in diagnosing scabies, but the sensitivity of this method is generally low-approximately 50%. Molecular tests may contribute to enhance the sensitivity of current tests for laboratory diagnosis of human scabies. In this study, we developed new primers for a nested PCR for the cytochrome c oxidase subunit 1 (cox1) gene of Sarcoptes scabiei var. hominis to increase the sensitivity of a previously developed conventional PCR. Clinically suspected scabies patients underwent dermoscopy-guided skin scraping with microscopic examination. The diagnosis was positive for scabies when mites or eggs were found under the microscope, and patients were then designated as 'microscopy-positive'. Patients in the 'microscopy-negative' group presented with negative microscopic results. Skin scrapings were collected from both groups for PCR. Of the total 63 samples, 28 were microscopy-positive and 35 were negative with no differences in sex and age between the two groups. All microscopically proven scabies cases were positive with the cox1 nested PCR. Among microscopy-negative ones, S. scabiei DNA was detected in 9 samples. If sensitivity of the cox1 nested PCR is considered 100% (95% CI, 90.51-100), then sensitivity of microscopy is 75.68% (95% CI, 58.80-88.23; P = 0.004). Nested PCR can be successfully used as an alternative method for diagnosing suspected scabies patient. Therefore, infection control measures and treatments can be initiated before significant transmission occurs, minimizing the risk of outbreaks. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Chemosterilization of the sea lamprey (Petromyzon marinus)

USGS Publications Warehouse

Hanson, Lee H.; Manion, Patrick J.

1978-01-01

The chemical, P,P-bis(1-aziridinyl)-N-methylphosphinothioic amide (bisazir), was found in laboratory studies to be an effective sterilant for both sexes of adult sea lampreys (Petromyzon marinus) when given intraperitoneally at a dosage of 100 mg per kilogram of body weight. A total of 300 normal spawning-run sea lampreys and 300 injected with bisazir were released into the Big Garlic River, Marquette County, Michigan, (a small stream divided into five sections by natural barriers), to determine the effect of bisazir on the nesting and spawning behavior of the adults and on the production of larvae. The lampreys constructed and spawned in 95 nests. Sterile adults showed no abnormal nest building or spawning behavior. Sterile males competed effectively with normal males for females. Egg samples taken from nests indicated that eggs in nests where sterile males spawned with sterile or normal females did not hatch, although some embryonic development occurred. Extensive surveys with electric shockers produced no larvae in stream sections where sterile males spawned, but yielded numerous larvae in sections where normal males spawned with normal females. These findings suggest that the release of sterile males may be an effective tool in an integrated approach to control of sea lampreys in the Great Lakes.

Nest predation and circulating corticosterone levels within and among species

USGS Publications Warehouse

Fontaine, Joseph J.; Arriero, Elena; Schwabl, Hubert; Martin, Thomas E.

2011-01-01

Variation in the risk of predation to offspring can influence the expression of reproductive strategies both within and among species. Appropriate expression of reproductive strategies in environments that differ in predation risk can have clear advantages for fitness. Although adult-predation risk appears to influence glucocorticosteroid levels, leading to changes in behavioral and life-history strategies, the influence of offspring-predation risk on adult glucocorticosteroid levels remains unclear. We compared total baseline corticosterone concentrations in Gray-headed Juncos (Junco hyemalis dorsalis) nesting on plots with and without experimentally reduced risk of nest predation. Despite differences in risk between treatments, we failed to find differences in total baseline corticosterone concentrations. When we examined corticosterone concentrations across a suite of sympatric species, however, higher risk of nest predation correlated with higher total baseline corticosterone levels. As found previously, total baseline corticosterone was negatively correlated with body condition and positively correlated with date of sampling. However, we also found that corticosterone levels increased seasonally, independent of stage of breeding. Nest predation can alter the expression of birds' reproductive strategies, but our findings suggest that total baseline corticosterone is not the physiological mechanism regulating these responses.

Nest predation and circulating corticosterone levels within and among species

USGS Publications Warehouse

Fontaine, J.J.; Arriero, E.; Schwabl, H.; Martin, T.E.

2011-01-01

Variation in the risk of predation to offspring can influence the expression of reproductive strategies both within and among species. Appropriate expression of reproductive strategies in environments that differ in predation risk can have clear advantages for fitness. Although adult-predation risk appears to influence glucocorticosteroid levels, leading to changes in behavioral and life-history strategies, the influence of offspring-predation risk on adult glucocorticosteroid levels remains unclear. We compared total baseline corticosterone concentrations in Gray-headed Juncos (Junco hyemalis dorsalis) nesting on plots with and without experimentally reduced risk of nest predation. Despite differences in risk between treatments, we failed to find differences in total baseline corticosterone concentrations. When we examined corticosterone concentrations across a suite of sympatric species, however, higher risk of nest predation correlated with higher total baseline corticosterone levels. As found previously, total baseline corticosterone was negatively correlated with body condition and positively correlated with date of sampling. However, we also found that corticosterone levels increased seasonally, independent of stage of breeding. Nest predation can alter the expression of birds' reproductive strategies, but our findings suggest that total baseline corticosterone is not the physiological mechanism regulating these responses. ?? The Cooper Ornithological Society 2011.

Anti-parasite treatment, but not mercury burdens, influence nesting propensity dependent on arrival time or body condition in a marine bird.

PubMed

Provencher, J F; Forbes, M R; Mallory, M L; Wilson, S; Gilchrist, H G

2017-01-01

Arctic wildlife can be exposed to high mercury (Hg) levels, and are also naturally exposed to gastrointestinal parasites that can reduce condition and negatively affect reproductive output and/or survival in similar ways. Importantly, both Hg and parasites are increasing in wildlife in some Arctic regions. We studied the northern common eider duck (Somateria mollissima) to explore how Hg in association with both natural levels and experimentally reduced parasitic infections, affect reproduction and survival. Female eiders were measured, banded, and blood sampled to determine blood Hg burdens, prior to breeding. Propensity to nest, clutch size, nest survival, nest attendance, and return rates were assessed in relation to both Hg burden and parasite treatment. Neither reproduction nor return rates of females varied with Hg concentrations, but females arriving late to the colony, or in low body condition, showed increased nesting propensity when given the anti-parasite treatment as compared to placebo treatment. Our results suggest that parasites can play a critical role in decisions to invest in avian breeding annually, particularly among individuals with a late onset to breeding, and in poor condition. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Compilation of 1990 annual reports of the Navy ELF Communications System Ecological-Monitoring Program. Volume 2. Tabs C thru F. Annual report, Jan-Dec 90

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

Zapotosky, J.E.

1991-08-01

This portion of the report includes monitoring of and data for arthropoda and earthworms; pollinating insects; and small mammals and nesting birds. During the 1990 growing season the ELF antenna was operated more frequently than in prior years. This provides 2 years of intermittent ELF exposure for the biological systems to react to the radiation, one year of very limited exposure and greater exposure in 1990. Arthropod and earthworm sampling was conducted at intervals of two weeks from early May to late October. High voltage transmission lines and magnetic fields have been shown to affect honeybee reproduction, survival, orientation, andmore » nest structure. ELF EM fields could have similar effects on native megachild bees. Changes in cell length, number of cells per nest, number of leaver per cell, orientation of nest entrances, and time to collect a round leaf pierce to cap a cell were monitored. We have not detected significant changes that could be attributed to ELF EM fields. Small mammal and nesting bird biological studies in the western Upper Peninsula of Michigan for the year 1990 are reported.« less

Biomarker discovery study design for type 1 diabetes in The Environmental Determinants of Diabetes in the Young (TEDDY) study.

PubMed

Lee, Hye-Seung; Burkhardt, Brant R; McLeod, Wendy; Smith, Susan; Eberhard, Chris; Lynch, Kristian; Hadley, David; Rewers, Marian; Simell, Olli; She, Jin-Xiong; Hagopian, Bill; Lernmark, Ake; Akolkar, Beena; Ziegler, Anette G; Krischer, Jeffrey P

2014-07-01

The Environmental Determinants of Diabetes in the Young planned biomarker discovery studies on longitudinal samples for persistent confirmed islet cell autoantibodies and type 1 diabetes using dietary biomarkers, metabolomics, microbiome/viral metagenomics and gene expression. This article describes the details of planning The Environmental Determinants of Diabetes in the Young biomarker discovery studies using a nested case-control design that was chosen as an alternative to the full cohort analysis. In the frame of a nested case-control design, it guides the choice of matching factors, selection of controls, preparation of external quality control samples and reduction of batch effects along with proper sample allocation. Our design is to reduce potential bias and retain study power while reducing the costs by limiting the numbers of samples requiring laboratory analyses. It also covers two primary end points (the occurrence of diabetes-related autoantibodies and the diagnosis of type 1 diabetes). The resulting list of case-control matched samples for each laboratory was augmented with external quality control samples. Copyright © 2013 John Wiley & Sons, Ltd.

Distribution of Hepatitis C virus (HCV) genotypes in seropositive patients in the state of Alagoas, Brazil

PubMed Central

Gonzaga, Rosa Maria S.; Rodart, Itatiana F.; Reis, Mitermayer Galvão; Ramalho Neto, Cícero Eduardo; Silva, Denise Wanderlei

2008-01-01

We determined the frequency of hepatitis C virus (HCV) genotypes in anti-HCV seropositive patients in the state of Alagoas, Brazil, by means of nested-reverse transcription-polymerase chain reaction (RT-nested-PCR) followed by restriction fragment length polymorphism (RFLP) of amplified fragments of the 5´NCR. The nested-PCR with genotype-specific primers from the core region was carried out when detection was not possible by the first approach. Detectable HCV-RNA was present in 115 (74.7%) of 154 serum samples. Genotype 1 was the most frequent (77.4%), against 20.9% of genotype 3 and 0.8% of genotype 2. Subtype 1b was predominant (65.2%), followed by subtypes 1a (8.7%), and 3a (6.1%). Coinfection (1a/3a) was detected in 0.8% of the samples. Indeed, there was no significant differences in the prevalence of genotype 1 compared to what has been obtained from anti-HCV seropositive patients from other locations in Brazil. Here we report for the first time the genotype 2 in the state of Alagoas. PMID:24031281

Inferences about nested subsets structure when not all species are detected

USGS Publications Warehouse

Cam, E.; Nichols, J.D.; Hines, J.E.; Sauer, J.R.

2000-01-01

Comparisons of species composition among ecological communities of different size have often provided evidence that the species in communities with lower species richness form nested subsets of the species in larger communities. In the vast majority of studies, the question of nested subsets has been addressed using information on presence-absence, where a '0' is interpreted as the absence of a given species from a given location. Most of the methodological discussion in earlier studies investigating nestedness concerns the approach to generation of model-based matrices. However, it is most likely that in many situations investigators cannot detect all the species present in the location sampled. The possibility that zeros in incidence matrices reflect nondetection rather than absence of species has not been considered in studies addressing nested subsets, even though the position of zeros in these matrices forms the basis of earlier inference methods. These sampling artifacts are likely to lead to erroneous conclusions about both variation over space in species richness and the degree of similarity of the various locations. Here we propose an approach to investigation of nestedness, based on statistical inference methods explicitly incorporating species detection probability, that take into account the probabilistic nature of the sampling process. We use presence-absence data collected under Pollock?s robust capture-recapture design, and resort to an estimator of species richness originally developed for closed populations to assess the proportion of species shared by different locations. We develop testable predictions corresponding to the null hypothesis of a nonnested pattern, and an alternative hypothesis of perfect nestedness. We also present an index for assessing the degree of nestedness of a system of ecological communities. We illustrate our approach using avian data from the North American Breeding Bird Survey collected in Florida Keys.

Evaluation of four molecular methods to detect Leishmania infection in dogs.

PubMed

Albuquerque, Andreia; Campino, Lenea; Cardoso, Luís; Cortes, Sofia

2017-03-13

Canine leishmaniasis, a zoonotic disease caused by Leishmania infantum vectored by phlebotomine sand flies, is considered a relevant veterinary and public health problem in various countries, namely in the Mediterranean basin and Brazil, where dogs are considered the main reservoir hosts. Not only diseased dogs but also those subclinically infected play a relevant role in the transmission of L. infantum to vectors; therefore, early diagnosis is essential, under both a clinical and an epidemiological perspective. Molecular tools can be a more accurate and sensitive approach for diagnosis, with a wide range of protocols currently in use. The aim of the present report was to compare four PCR based protocols for the diagnosis of canine Leishmania infection in a cohort of dogs from the Douro region, Portugal. A total of 229 bone marrow samples were collected from dogs living in the Douro region, an endemic region for leishmaniasis. Four PCR protocols were evaluated for Leishmania DNA detection in canine samples, three single (ITS1-PCR, MC-PCR and Uni21/Lmj4-PCR) and one nested (nested SSU rRNA-PCR). Two of the protocols were based on nuclear targets and the other two on kinetoplastid targets. The higher overall percentage of infected dogs was detected with the nested SSU rRNA-PCR (37.6%), which also was able to detect Leishmania DNA in a higher number of samples from apparently healthy dogs (25.3%). The ITS1-PCR presented the lowest level of Leishmania detection. Nested SSU rRNA-PCR is an appropriate method to detect Leishmania infection in dogs. Accurate and early diagnosis in clinically suspect as well as apparently healthy dogs is essential, in order to treat and protect animals and public health and contribute to the control and awareness of the disease.

Detection of Leishmania DNA in saliva among patients with HIV/AIDS in Trang Province, southern Thailand.

PubMed

Pandey, Netranapha; Siripattanapipong, Suradej; Leelayoova, Saovanee; Manomat, Jipada; Mungthin, Mathirut; Tan-Ariya, Peerapan; Bualert, Lertwut; Naaglor, Tawee; Siriyasatien, Padet; Phumee, Atchara; Piyaraj, Phunlerd

2018-06-08

Leishmaniasis is a neglected tropical disease causing opportunistic infection among patients with HIV/AIDS. The fatal form of this disease is visceral leishmaniasis (VL). DNA of Leishmania can be detected in saliva, for which the collection is noninvasive and requires little expertise. This study aimed to evaluate the sensitivity and specificity of a nested-PCR to amplify the Internal Transcribed Spacer 1 (ITS1) to detect Leishmania DNA in paired saliva and buffy coat samples of 305 Thai patients with HIV/AIDS in Trang Hospital, Trang Province, southern Thailand. For asymptomatic Leishmania infection among Thai patients with HIV/AIDS, the sensitivity and specificity of the nested-PCR-ITS1 in buffy coat were 73.9 and 100%, respectively. However, the sensitivity in saliva was 26.1% and specificity was 100%. Using the nested-PCR-ITS1, saliva and buffy coat samples showed positive agreement in only 52.0% of patients. Saliva tested results with the nested-PCR-ITS1 showed positive agreement with the Direct Agglutination Test (DAT) in 46.5% of patients. Only 12.1% of the samples showed positive agreement for Leishmania infection among all the three tests: saliva, buffy coat and DAT results. Using nucleotide sequencing, at least three species of Leishmania infection were identified in saliva, i.e., L. siamensis (n = 28), L. martiniquensis (n = 9), and L. donovani complex (n = 1). As a result, buffy coat still appears to be a better specimen to diagnose asymptomatic VL infection among individuals with HIV. However, the use of both buffy coat and saliva together as clinical specimens would increase the sensitivity of Leishmania detection. Copyright © 2018 Elsevier B.V. All rights reserved.

Molecular surveillance of Theileria ovis, Theileria lestoquardi and Theileria annulata infection in sheep and ixodid ticks in Iran.

PubMed

Razmi, Gholamreza; Yaghfoori, Saeed

2013-01-01

A molecular study was undertaken to detect Theileria ovis, Theileria lestoquardi and Theileria annulata in sheep and tick vectors. Investigation was conducted from 2010 to 2011 in the south of Khorasan Razavi Province, Iran. A total of 150 blood samples were collected from 30 different sheep flocks. In addition, ixodid ticks were sampled from the same flocks. The stained blood smears were microscopically examined for the presence of piroplasms and a semi-nested polymerase chain reaction-restriction (PCR) was used for subsequent molecular speciation. Salivary glands were isolated from the ticks and subsequently analysed by semi-nested PCR. polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to differentiate between T. lestoquardi and T. annulata from PCR-positive samples. Theileria species infection was microscopically detected in 18.6% of blood smears. The presence of T. ovis and T. lestoquardi or T. annulata was detected by semi-nested PCR in 58.6% and 6.6% of blood samples respectively. In total, 169 ixodid ticks were collected from different areas of the province. The most prevalent ticks were Rhipicephalus turanicus (n = 155; 91.7% of the total), followed by Hyalomma anatolicum anatolicum (n = 8; 4.7%) and Hyalomma marginatum turanicum (n = 6; 3.5%). From an organ pooling of 33 ticks, three pools of salivary glands from R. turanicus were positive for Theileria species by semi-nested PCR. Of the three R. turanicus samples testing positive for Theileria species, two (6.1%) were positive for T. ovis and one (3.0%) for T. lestoquardi or T.annulata. Amongst the 11 PCR-positive samples for T. lestoquardi or T. annulata, 10 were positive for T. lestoquardi and one sample was positive for both T. lestoquardi and T. annulata using PCR-RFLP. The results also demonstrated that PCR-RFLP could be used for the detection of T. ovis. Based on the results, it can be concluded that T. ovis has a higher prevalence than T. lestoquardi, and that R. turanicus could be a possible vector for T. ovis and T. lestoquardi. Finally, the PCR-RFLP based on Msp1 restriction enzyme is a simple method for differentiation of Theileria species in sheep and ixodid ticks.

Comparison of a conventional and nested PCR for diagnostic confirmation and genotyping of Orientia tsutsugamushi.

PubMed

Janardhanan, Jeshina; Prakash, John Antony Jude; Abraham, Ooriapadickal C; Varghese, George M

2014-05-01

A nested polymerase chain reaction (PCR) targeting the 56-kDa antigen gene is currently the most commonly used molecular technique for confirmation of scrub typhus and genotyping of Orientia tsutsugamushi. In this study, we have compared the commonly used nested PCR (N-PCR) with a single-step conventional PCR (C-PCR) for amplification and genotyping. Eschar samples collected from 24 patients with scrub typhus confirmed by IgM enzyme-linked immunosorbent assay were used for DNA extraction following which amplifications were carried out using nested and C-PCR methods. The amplicons were sequenced and compared to other sequences in the database using BLAST. Conventional PCR showed a high positivity rate of 95.8% compared to the 75% observed using N-PCR. On sequence analysis, the N-PCR amplified region showed more variation among strains than the C-PCR amplified region. The C-PCR, which is more economical, provided faster and better results compared to N-PCR. Copyright © 2014 Elsevier Inc. All rights reserved.

Landscapes for Energy and Wildlife: Conservation Prioritization for Golden Eagles across Large Spatial Scales

PubMed Central

Tack, Jason D.; Fedy, Bradley C.

2015-01-01

Proactive conservation planning for species requires the identification of important spatial attributes across ecologically relevant scales in a model-based framework. However, it is often difficult to develop predictive models, as the explanatory data required for model development across regional management scales is rarely available. Golden eagles are a large-ranging predator of conservation concern in the United States that may be negatively affected by wind energy development. Thus, identifying landscapes least likely to pose conflict between eagles and wind development via shared space prior to development will be critical for conserving populations in the face of imposing development. We used publically available data on golden eagle nests to generate predictive models of golden eagle nesting sites in Wyoming, USA, using a suite of environmental and anthropogenic variables. By overlaying predictive models of golden eagle nesting habitat with wind energy resource maps, we highlight areas of potential conflict among eagle nesting habitat and wind development. However, our results suggest that wind potential and the relative probability of golden eagle nesting are not necessarily spatially correlated. Indeed, the majority of our sample frame includes areas with disparate predictions between suitable nesting habitat and potential for developing wind energy resources. Map predictions cannot replace on-the-ground monitoring for potential risk of wind turbines on wildlife populations, though they provide industry and managers a useful framework to first assess potential development. PMID:26262876

Landscapes for energy and wildlife: conservation prioritization for golden eagles across large spatial scales

USGS Publications Warehouse

Tack, Jason D.; Fedy, Bradley C.

2015-01-01

Proactive conservation planning for species requires the identification of important spatial attributes across ecologically relevant scales in a model-based framework. However, it is often difficult to develop predictive models, as the explanatory data required for model development across regional management scales is rarely available. Golden eagles are a large-ranging predator of conservation concern in the United States that may be negatively affected by wind energy development. Thus, identifying landscapes least likely to pose conflict between eagles and wind development via shared space prior to development will be critical for conserving populations in the face of imposing development. We used publically available data on golden eagle nests to generate predictive models of golden eagle nesting sites in Wyoming, USA, using a suite of environmental and anthropogenic variables. By overlaying predictive models of golden eagle nesting habitat with wind energy resource maps, we highlight areas of potential conflict among eagle nesting habitat and wind development. However, our results suggest that wind potential and the relative probability of golden eagle nesting are not necessarily spatially correlated. Indeed, the majority of our sample frame includes areas with disparate predictions between suitable nesting habitat and potential for developing wind energy resources. Map predictions cannot replace on-the-ground monitoring for potential risk of wind turbines on wildlife populations, though they provide industry and managers a useful framework to first assess potential development.

A survey of nested grid techniques and their potential for use within the MASS weather prediction model

NASA Technical Reports Server (NTRS)

Koch, Steven E.; Mcqueen, Jeffery T.

1987-01-01

A survey of various one- and two-way interactive nested grid techniques used in hydrostatic numerical weather prediction models is presented and the advantages and disadvantages of each method are discussed. The techniques for specifying the lateral boundary conditions for each nested grid scheme are described in detail. Averaging and interpolation techniques used when applying the coarse mesh grid (CMG) and fine mesh grid (FMG) interface conditions during two-way nesting are discussed separately. The survey shows that errors are commonly generated at the boundary between the CMG and FMG due to boundary formulation or specification discrepancies. Methods used to control this noise include application of smoothers, enhanced diffusion, or damping-type time integration schemes to model variables. The results from this survey provide the information needed to decide which one-way and two-way nested grid schemes merit future testing with the Mesoscale Atmospheric Simulation System (MASS) model. An analytically specified baroclinic wave will be used to conduct systematic tests of the chosen schemes since this will allow for objective determination of the interfacial noise in the kind of meteorological setting for which MASS is designed. Sample diagnostic plots from initial tests using the analytic wave are presented to illustrate how the model-generated noise is ascertained. These plots will be used to compare the accuracy of the various nesting schemes when incorporated into the MASS model.

Landscapes for Energy and Wildlife: Conservation Prioritization for Golden Eagles across Large Spatial Scales.

PubMed

Tack, Jason D; Fedy, Bradley C

2015-01-01

Proactive conservation planning for species requires the identification of important spatial attributes across ecologically relevant scales in a model-based framework. However, it is often difficult to develop predictive models, as the explanatory data required for model development across regional management scales is rarely available. Golden eagles are a large-ranging predator of conservation concern in the United States that may be negatively affected by wind energy development. Thus, identifying landscapes least likely to pose conflict between eagles and wind development via shared space prior to development will be critical for conserving populations in the face of imposing development. We used publically available data on golden eagle nests to generate predictive models of golden eagle nesting sites in Wyoming, USA, using a suite of environmental and anthropogenic variables. By overlaying predictive models of golden eagle nesting habitat with wind energy resource maps, we highlight areas of potential conflict among eagle nesting habitat and wind development. However, our results suggest that wind potential and the relative probability of golden eagle nesting are not necessarily spatially correlated. Indeed, the majority of our sample frame includes areas with disparate predictions between suitable nesting habitat and potential for developing wind energy resources. Map predictions cannot replace on-the-ground monitoring for potential risk of wind turbines on wildlife populations, though they provide industry and managers a useful framework to first assess potential development.

Sedimentology, geochemistry and rock magnetic properties of beach sands in Galapagos Islands - implications for nesting marine turtles

NASA Astrophysics Data System (ADS)

Perez-Cruz, L.; Urrutia-Fucugauchi, J.; Vazquez-Gutierrez, F.; Carranza-Edwards, A.

2007-12-01

Marine turtles are well known for their navigation ability in the open ocean and fidelity to nesting beaches. Green turtle adult females migrate from foraging areas to island nesting beaches, traveling hundreds or thousands of kilometers each way. The marine turtle breeding in the Galapagos Islands is the Green Sea Turtle (Chelonia mydas agassisi); fairly common throughout the islands but with nesting sites located at Las Bachas (Santa Cruz), Barahona and Quinta Playa (Isabela), Salinas (Baltra), Gardner Bay (Española) and Bartolomé Islet. In order to characterize and to identify the geochemical signature of nesting marine turtle beaches in Galapagos Islands, sedimentological, geochemical and rock magnetic parameters are used. A total of one hundred and twenty sand samples were collected in four beaches to relate compositional characteristics between equivalent areas, these are: Las Bachas, Salinas, Barahona and Quinta Playa. Grain size is evaluated using laser particle analysis (Model Coulter LS 230). Bulk ICP-MS geochemical analysis is performed, following trace elements are analyzed: Al, V, Cr, Co, Ni, Cu, Zn, Cd, Ba, Pb, Fe, Mn, K, Na, Mg, Sr, Ca and Hg; and low-field magnetic susceptibility is measured in all samples at low and high frequencies. Granulometric analysis showed that Barahona and Quinta Playa are characterized for fine grained sands. In contrast, Salinas and Las Bachas exhibit medium to coarse sands. Trace metals concentrations and magnetic susceptibility show different distribution patterns in the beach sands. Calcium is the most abundant element in the samples. In particular, Co, K, and Na show similar concentrations in the four beaches. Las Bachas beach shows highest concentrations of Pb and Hg (maximum values 101.1 and 118.5 mg/kg, respectively), we suggest that the enrichment corresponds to an anthropogenic signal. Salinas beach samples show high concentrations of Fe, V, Cr, Zn, Mn and the highest values of magnetic susceptibility (maximum 932 10-6 SI), we propose, a human activity influence less evident than in Bachas beach that could overlap the contribution of continent source. Quinta Playa sands show the maximum concentration of calcium and also high concentration of Fe and Mg, and relatively high values of magnetic susceptibility. Ca results from marine biogenic carbonates (mainly coral reefs). Barahona also show high concentrations in calcium that could be correlated with the presence of biogenous source around the beach.

Heartbeat detection in multimodal physiological signals using signal quality assessment based on sample entropy.

PubMed

Singh, Omkar; Sunkaria, Ramesh Kumar

2017-12-01

This paper presents a novel technique to identify heartbeats in multimodal data using electrocardiogram (ECG) and arterial blood pressure (ABP) signals. Multiple physiological signals such as ECG, ABP, and Respiration are often recorded in parallel from the activity of heart. These signals generally possess related information as they are generated by the same physical system. The ECG and ABP correspond to the same phenomenon of contraction and relaxation activity of heart. Multiple signals acquired from various sensors are generally processed independently, thus discarding the information from other measurements. In the estimation of heart rate and heart rate variability, the R peaks are generally identified from ECG signal. Efficient detection of R-peaks in electrocardiogram (ECG) is a key component in the estimation of clinically relevant parameters from ECG. However, when the signal is severely affected by undesired artifacts, this becomes a challenging task. Sometimes in clinical environment, other physiological signals reflecting the cardiac activity such as ABP signal are also acquired simultaneously. Under the availability of such multimodal signals, the accuracy of R peak detection methods can be improved using sensor-fusion techniques. In the proposed method, the sample entropy (SampEn) is used as a metric for assessing the noise content in the physiological signal and the R peaks in ECG and the systolic peaks in ABP signals are fused together to enhance the efficiency of heartbeat detection. The proposed method was evaluated on the 100 records from the computing in cardiology challenge 2014 training data set. The performance parameters are: sensitivity (Se) and positive predictivity (PPV). The unimodal R peaks detector achieved: Se gross = 99.40%, PPV gross = 99.29%, Se average = 99.37%, PPV average = 99.29%. Similarly unimodal BP delineator achieved Se gross = 99.93%, PPV gross = 99.99%, Se average = 99.93%, PPV average = 99.99% whereas, the proposed multimodal beat detector achieved: Se gross = 99.65%, PPV gross = 99.91%, Se average = 99.68%, PPV average = 99.91%.

Factors affecting hatch success of hawksbill sea turtles on Long Island, Antigua, West Indies.

PubMed

Ditmer, Mark Allan; Stapleton, Seth Patrick

2012-01-01

Current understanding of the factors influencing hawksbill sea turtle (Eretmochelys imbricata) hatch success is disparate and based on relatively short-term studies or limited sample sizes. Because global populations of hawksbills are heavily depleted, evaluating the parameters that impact hatch success is important to their conservation and recovery. Here, we use data collected by the Jumby Bay Hawksbill Project (JBHP) to investigate hatch success. The JBHP implements saturation tagging protocols to study a hawksbill rookery in Antigua, West Indies. Habitat data, which reflect the varied nesting beaches, are collected at egg deposition, and nest contents are exhumed and categorized post-emergence. We analyzed hatch success using mixed-model analyses with explanatory and predictive datasets. We incorporated a random effect for turtle identity and evaluated environmental, temporal and individual-based reproductive variables. Hatch success averaged 78.6% (SD: 21.2%) during the study period. Highly supported models included multiple covariates, including distance to vegetation, deposition date, individual intra-seasonal nest number, clutch size, organic content, and sand grain size. Nests located in open sand were predicted to produce 10.4 more viable hatchlings per clutch than nests located >1.5 m into vegetation. For an individual first nesting in early July, the fourth nest of the season yielded 13.2 more viable hatchlings than the initial clutch. Generalized beach section and inter-annual variation were also supported in our explanatory dataset, suggesting that gaps remain in our understanding of hatch success. Our findings illustrate that evaluating hatch success is a complex process, involving multiple environmental and individual variables. Although distance to vegetation and hatch success were inversely related, vegetation is an important component of hawksbill nesting habitat, and a more complete assessment of the impacts of specific vegetation types on hatch success and hatchling sex ratios is needed. Future research should explore the roles of sand structure, nest moisture, and local weather conditions.

Reproductive biology of Pleurodema guayapae (Anura: Leptodactylidae: Leiuperinae).

PubMed

Valetti, Julián Alonso; Grenat, Pablo Raúl; Baraquet, Mariana; Martino, Adolfo Ludovico

2014-03-01

Pleurodema guayapae is a species that inhabits saline environments and semidesert zones from central Argentina. To date, the knowledge about the reproductive biology of this species is very poor, and our aim is to contribute to its knowledge with the description of some important reproductive aspects. For this, field work was undertaken in an area near to Patquia, La Rioja province. Sampling was undertaken during three summer periods (2006-2007; 2007-2008; 2008-2009) in Chamical-Patquia area, where we could find reproductively active populations. We observed and described breeding sites, type of clutch, process of foam nest construction, clutch and egg number and sizes, and hatching time and stage. Behaviour observations were performed from the time that males began to call until the pairs ended up the foam nests building, and layed the eggs. Additionally, one amplected pair was observed and filmed in the process of foam nest construction, and four amplectant pairs were collected and separatelly placed in plastic containers, for nests observations in the laboratory. Hatching time was based on three different foam nests of known age. We found that P. guayapae populations were acoustically active only after a rainfall. Its breeding sites were represented by ephemeral ponds of fresh water, product of rains. The males emitted their calls inside or outside these ponds. A detailed description of the foam nest construction process by both females and males was made. The clutches were in dome-shaped foam nest type of 6-9cm in diameter and 1-3cm in height, some of which were in communal nests. The nests had an average of 1 137 pigmented eggs. This species showed a short hatching time. Our results allow us to conclude that this species should be considered an extreme explosive breeder. Our results are discussed with others obtained for related species.

Factors Affecting Hatch Success of Hawksbill Sea Turtles on Long Island, Antigua, West Indies

PubMed Central

Ditmer, Mark Allan; Stapleton, Seth Patrick

2012-01-01

Current understanding of the factors influencing hawksbill sea turtle (Eretmochelys imbricata) hatch success is disparate and based on relatively short-term studies or limited sample sizes. Because global populations of hawksbills are heavily depleted, evaluating the parameters that impact hatch success is important to their conservation and recovery. Here, we use data collected by the Jumby Bay Hawksbill Project (JBHP) to investigate hatch success. The JBHP implements saturation tagging protocols to study a hawksbill rookery in Antigua, West Indies. Habitat data, which reflect the varied nesting beaches, are collected at egg deposition, and nest contents are exhumed and categorized post-emergence. We analyzed hatch success using mixed-model analyses with explanatory and predictive datasets. We incorporated a random effect for turtle identity and evaluated environmental, temporal and individual-based reproductive variables. Hatch success averaged 78.6% (SD: 21.2%) during the study period. Highly supported models included multiple covariates, including distance to vegetation, deposition date, individual intra-seasonal nest number, clutch size, organic content, and sand grain size. Nests located in open sand were predicted to produce 10.4 more viable hatchlings per clutch than nests located >1.5 m into vegetation. For an individual first nesting in early July, the fourth nest of the season yielded 13.2 more viable hatchlings than the initial clutch. Generalized beach section and inter-annual variation were also supported in our explanatory dataset, suggesting that gaps remain in our understanding of hatch success. Our findings illustrate that evaluating hatch success is a complex process, involving multiple environmental and individual variables. Although distance to vegetation and hatch success were inversely related, vegetation is an important component of hawksbill nesting habitat, and a more complete assessment of the impacts of specific vegetation types on hatch success and hatchling sex ratios is needed. Future research should explore the roles of sand structure, nest moisture, and local weather conditions. PMID:22802928

Use of analyte-modulated modal power distribution in multimode optical fibers for simultaneous single-wavelength evanescent-wave refractometry and spectrometry.

PubMed

Potyrailo, R A; Ruddy, V P; Hieftje, G M

1999-11-01

A new method is described for the simultaneous determination of absorbance and refractive index of a sample medium. The method is based on measurement of the analyte-modulated modal power distribution (MPD) in a multimode waveguide. In turn, the MPD is quantified by the far-field spatial pattern and intensity of light, i.e., the Fraunhofer diffraction pattern (registered on a CCD camera), that emerges from a multimode optical fiber. Operationally, light that is sent down the fiber interacts with the surrounding analyte-containing medium by means of the evanescent wave at the fiber boundary. The light flux in the propagating beam and the internal reflection angles within the fiber are both affected by optical absorption connected with the analyte and by the refractive index of the analyte-containing medium. In turn, these angles are reflected in the angular divergence of the beam as it leaves the fiber. As a result, the Fraunhofer diffraction pattern of that beam yields two parameters that can, together, be used to deduce refractive index and absorbance. This MPD based detection offers important advantages over traditional evanescent-wave detection strategies which rely on recording only the total transmitted optical power or its lost fraction. First, simultaneous determination of sample refractive index and absorbance is possible at a single probe wavelength. Second, the sensitivity of refractometric and absorption measurements can be controlled simply, either by adjusting the distance between the end face of the fiber and the CCD detector or by monitoring selected modal groups at the fiber output. As a demonstration of these capabilities, several weakly absorbing solutions were examined, with refractive indices in the range from 1.3330 to 1.4553 and with absorption coefficients in the range 0-16 cm-1. The new detection strategy is likely to be important in applications in which sample coloration varies and when it is necessary to compensate for variations in the refractive index of a sample.

Characterization of alkanes, hopanes, and polycyclic aromatic hydrocarbons (PAHs) in tar-balls collected from the East Coast of Peninsular Malaysia.

PubMed

Chandru, Kuhan; Zakaria, Mohamad Pauzi; Anita, Sofia; Shahbazi, Azadeh; Sakari, Mahyar; Bahry, Pourya Shahpoury; Mohamed, Che Abd Rahim

2008-05-01

The East Coast of Peninsular Malaysia faces the South China Sea and is vulnerable to oil pollution because of intense petroleum production activities in the area. The South China Sea is also a favored route for supertankers carrying crude oil to the Far East. Consequently, oil spills can occur, causing pollution and contamination in the surrounding areas. Residual oil spills stranded on coastal beaches usually end up as tar-balls. Elucidating the sources of tar-balls using a molecular marker approach is essential in assessing environmental impacts and perhaps settling legal liabilities for affected parties. This study utilizes a multimodal molecular marker approach through the use of diagnostic ratios of alkanes, hopanes, and polycyclic aromatic hydrocarbons (PAHs) to determine the source, distribution and weathering of tar-balls. Hopane ratios (e.g., C29/C30, and summation C31-C35/C30 ratios) were used to identify the sources of tar-balls. The weathering effects were distinguished by using alkanes, namely the unresolved complex mixture (UCM) and low molecular weight/high molecular weight (L/H) ratios. Similarly, PAHs were also used for the determination of weathering processes undergone by the tar-balls. This multimodal molecular marker gave a very strong indication of the sources of tar-balls in this study. For example, 16 out of 17 samples originated from South East Asian Crude Oil (SEACO) with one sample from Merang, Terengganu originating from North Sea Oil (Troll). The TRME-2 sample may have come from a supertanker's ballast water discharge. The second possibility is that the tar-ball may have been transported via oceanographic currents. All 'weathered' sample characterizations were based on the presence of UCM and other ratios. The multimodal molecular marker approach applied in this study has enabled us to partially understand the transport behavior of tar-balls in the marine environment and has revealed insights into the weathering process of tar-balls.

Multimodal hyperspectral optical microscopy

DOE PAGES

Novikova, Irina V.; Smallwood, Chuck R.; Gong, Yu; ...

2017-09-02

We describe a unique and convenient approach to multimodal hyperspectral optical microscopy, herein achieved by coupling a portable and transferable hyperspectral imager to various optical microscopes. The experimental and data analysis schemes involved in recording spectrally and spatially resolved fluorescence, dark field, and optical absorption micrographs are illustrated through prototypical measurements targeting selected model systems. Namely, hyperspectral fluorescence micrographs of isolated fluorescent beads are employed to ensure spectral calibration of our detector and to gauge the attainable spatial resolution of our measurements; the recorded images are diffraction-limited. Moreover, spatially over-sampled absorption spectroscopy of a single lipid (18:1 Liss Rhod PE)more » layer reveals that optical densities on the order of 10-3 may be resolved by spatially averaging the recorded optical signatures. We also briefly illustrate two applications of our setup in the general areas of plasmonics and cell biology. Most notably, we deploy hyperspectral optical absorption microscopy to identify and image algal pigments within a single live Tisochrysis lutea cell. Overall, this work paves the way for multimodal multidimensional spectral imaging measurements spanning the realms of several scientific disciples.« less

Colocalization of cellular nanostructure using confocal fluorescence and partial wave spectroscopy.

PubMed

Chandler, John E; Stypula-Cyrus, Yolanda; Almassalha, Luay; Bauer, Greta; Bowen, Leah; Subramanian, Hariharan; Szleifer, Igal; Backman, Vadim

2017-03-01

A new multimodal confocal microscope has been developed, which includes a parallel Partial Wave Spectroscopic (PWS) microscopy path. This combination of modalities allows molecular-specific sensing of nanoscale intracellular structure using fluorescent labels. Combining molecular specificity and sensitivity to nanoscale structure allows localization of nanostructural intracellular changes, which is critical for understanding the mechanisms of diseases such as cancer. To demonstrate the capabilities of this multimodal instrument, we imaged HeLa cells treated with valinomycin, a potassium ionophore that uncouples oxidative phosphorylation. Colocalization of fluorescence images of the nuclei (Hoechst 33342) and mitochondria (anti-mitochondria conjugated to Alexa Fluor 488) with PWS measurements allowed us to detect a significant decrease in nuclear nanoscale heterogeneity (Σ), while no significant change in Σ was observed at mitochondrial sites. In addition, application of the new multimodal imaging approach was demonstrated on human buccal samples prepared using a cancer screening protocol. These images demonstrate that nanoscale intracellular structure can be studied in healthy and diseased cells at molecular-specific sites. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multimodal hyperspectral optical microscopy

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

Novikova, Irina V.; Smallwood, Chuck R.; Gong, Yu

We describe a unique and convenient approach to multimodal hyperspectral optical microscopy, herein achieved by coupling a portable and transferable hyperspectral imager to various optical microscopes. The experimental and data analysis schemes involved in recording spectrally and spatially resolved fluorescence, dark field, and optical absorption micrographs are illustrated through prototypical measurements targeting selected model systems. Namely, hyperspectral fluorescence micrographs of isolated fluorescent beads are employed to ensure spectral calibration of our detector and to gauge the attainable spatial resolution of our measurements; the recorded images are diffraction-limited. Moreover, spatially over-sampled absorption spectroscopy of a single lipid (18:1 Liss Rhod PE)more » layer reveals that optical densities on the order of 10-3 may be resolved by spatially averaging the recorded optical signatures. We also briefly illustrate two applications of our setup in the general areas of plasmonics and cell biology. Most notably, we deploy hyperspectral optical absorption microscopy to identify and image algal pigments within a single live Tisochrysis lutea cell. Overall, this work paves the way for multimodal multidimensional spectral imaging measurements spanning the realms of several scientific disciples.« less

Multimodal MSI in Conjunction with Broad Coverage Spatially Resolved MS2 Increases Confidence in Both Molecular Identification and Localization.

PubMed

Veličković, Dušan; Chu, Rosalie K; Carrell, Alyssa A; Thomas, Mathew; Paša-Tolić, Ljiljana; Weston, David J; Anderton, Christopher R

2018-01-02

One critical aspect of mass spectrometry imaging (MSI) is the need to confidently identify detected analytes. While orthogonal tandem MS (e.g., LC-MS 2 ) experiments from sample extracts can assist in annotating ions, the spatial information about these molecules is lost. Accordingly, this could cause mislead conclusions, especially in cases where isobaric species exhibit different distributions within a sample. In this Technical Note, we employed a multimodal imaging approach, using matrix assisted laser desorption/ionization (MALDI)-MSI and liquid extraction surface analysis (LESA)-MS 2 I, to confidently annotate and localize a broad range of metabolites involved in a tripartite symbiosis system of moss, cyanobacteria, and fungus. We found that the combination of these two imaging modalities generated very congruent ion images, providing the link between highly accurate structural information onfered by LESA and high spatial resolution attainable by MALDI. These results demonstrate how this combined methodology could be very useful in differentiating metabolite routes in complex systems.

Hepatitis E Virus in Wild Boar in Northwest Poland: Sensitivity of Methods of Detection.

PubMed

Dorn-In, Samart; Schwaiger, Karin; Twarużek, Magdalena; Grajewski, Jan; Gottschalk, Christoph; Gareis, Manfred

2017-02-01

In northwest Poland, 163 blood and 53 fecal samples of wild boars were collected in winter 2012/13 and 2013/14. All blood samples were tested for the presence of hepatitis E virus (HEV) ribonucleic acid (RNA) by two reverse transcription-polymerase chain reaction (RT-PCR) based methods and by anti-HEV IgG enzyme-linked immunosorbent assay (ELISA). About 17.2% of blood samples were seropositive. One-step nested RT-PCR turned out to be too insensitive (11.6% were positive). Therefore a two-step nested RT-PCR was applied where 25.8% of the blood samples were tested positive for HEV RNA. About 50.0% of blood samples positive in ELISA were also positive in two-step nested RT-PCR. The prevalence of HEV RNA in feces was 9.4%. Based on the results of blood (ELISA, PCR) and fecal (PCR) tests, the overall prevalence of HEV in wild boars in northwest Poland was 36.8%. There was no correlation between the ELISA results and the presence of HEV RNA in plasma or in feces. According to the sequencing results of 348 bp PCR products of HEV, there were four different subtypes identified. Reports on the prevalence of HEV in wild boar populations are varying due to different sensitivities of the detection methods. However, this study reveals based on a highly sensitive method that HEV is widely spread in wild boar populations in the northwestern region of Poland and posing a potential risk to the consumer of game meat.

Rapid Multiplex PCR Assay To Identify Respiratory Viral Pathogens: Moving Forward Diagnosing The Common Cold

PubMed Central

Gordon, Sarah M; Elegino-Steffens, Diane U; Agee, Willie; Barnhill, Jason; Hsue, Gunther

2013-01-01

Upper respiratory tract infections (URIs) can be a serious burden to the healthcare system. The majority of URIs are viral in etiology, but definitive diagnosis can prove difficult due to frequently overlapping clinical presentations of viral and bacterial infections, and the variable sensitivity, and lengthy turn-around time of viral culture. We tested new automated nested multiplex PCR technology, the FilmArray® system, in the TAMC department of clinical investigations, to determine the feasibility of replacing the standard viral culture with a rapid turn-around system. We conducted a feasibility study using a single-blinded comparison study, comparing PCR results with archived viral culture results from a convenience sample of cryopreserved archived nasopharyngeal swabs from acutely ill ED patients who presented with complaints of URI symptoms. A total of 61 archived samples were processed. Viral culture had previously identified 31 positive specimens from these samples. The automated nested multiplex PCR detected 38 positive samples. In total, PCR was 94.5% concordant with the previously positive viral culture results. However, PCR was only 63.4% concordant with the negative viral culture results, owing to PCR detection of 11 additional viral pathogens not recovered on viral culture. The average time to process a sample was 75 minutes. We determined that an automated nested multiplex PCR is a feasible alternative to viral culture in an acute clinical setting. We were able to detect at least 94.5% as many viral pathogens as viral culture is able to identify, with a faster turn-around time. PMID:24052914

An Automated Multi-Modal Serial Sectioning System for Characterization of Grain-Scale Microstructures in Engineering Materials (Preprint)

DTIC Science & Technology

2012-03-01

the three main sub-systems. The Mitsubishi RV12SVL 6-axis robot arm has a 54’’ reach, which allows it to readily move a 2” diameter stainless ... steel sample holder, Figure 2A, between sample exchange points on the Robo-Met.3D, the Tescan SEM, and an additional sample transfer stand that enables...Rowenhorst DJ, et al. (2006) Crystallographic and morphological analysis of coarse martensite : Combining EBSD and serial sectioning. Scripta

Detection of pathogenic Yersinia enterocolitica in foods and water by immunomagnetic separation, nested polymerase chain reactions, and colorimetric detection of amplified DNA.

PubMed Central

Kapperud, G; Vardund, T; Skjerve, E; Hornes, E; Michaelsen, T E

1993-01-01

A two-step polymerase chain reaction (PCR) procedure with two nested pairs of primers specific for the yadA gene of Yersinia enterocolitica was developed. The PCR assay identified all common pathogenic serogroups (O:3, O:5,27, O:8, O:9, O:13, and O:21) from three continents and differentiated pathogenic Y. enterocolitica from Y. pseudotuberculosis and from a variety of nonpathogenic yersiniae representing 25 serogroups and four species. The performance of the method was evaluated with seeded food and water samples. We compared two procedures for sample preparation prior to PCR: one was based on immunomagnetic separation of the target bacteria from the sample, using magnetic particles coated with immunoglobulin antibodies to Y. enterocolitica serogroup O:3, and the other method consisted of a series of centrifugation steps combined with proteinase treatment. Regardless of the method used, the PCR assay was capable of detecting 10 to 30 CFU/g of meat in 10(6)-fold excess of indigenous bacteria. When the samples were enriched overnight in a nonselective medium, the sensitivity was increased to approximately 2 CFU/g, except for samples with an extremely high background flora (> 10(7) CFU/g). We compared gel electrophoretic detection of PCR products with a colorimetric detection method designated DIANA (detection of immobilized amplified nucleic acids), which enabled easy visualization of amplified fragments in a microtiter plate format with an optical density reader. DIANA and gel electrophoresis showed complete concordance in their discrimination between positive and negative samples. The combination of immunomagnetic separation, nested PCR, and DIANA makes possible the development of a fully automated analytic process which requires a minimum of laboratory manipulations. Images PMID:8215366

Anadromous sea lampreys (Petromyzon marinus) are ecosystem engineers in a spawning tributary

USGS Publications Warehouse

Hogg, Robert S.; Coghlan, Stephen M.; Zydlewski, Joseph D.; Simon, Kevin S.

2014-01-01

Sea lampreys (Petromyzon marinus) disturb the substratum during nest construction and alter the physical habitat, potentially affecting other stream organisms. We quantified differences in depth, velocity, fine-sediment coverage, embeddedness, intragravel permeability and benthic invertebrate assemblages (density and diversity) among nest mounds, nest pits and undisturbed reference locations over a 4-month period after June spawning. In 2010 and 2011, immediate and persistent effects of nest construction were assessed in summer (July) and in autumn (late September to early October), respectively. Randomly selected nests were sampled annually (25 each in summer and autumn). Nest construction increased stream-bed complexity by creating and juxtaposing shallow, swift, rocky habitat patches with deep, slow, sandy habitat patches. Mounds had a 50–143% less cover of fine sediment, and a 30–62% reduction in embeddedness, compared to pits and reference locations. These physical changes persisted into the autumn (almost 4 months). Five insect families contributed 74% of the benthic invertebrate abundance: Chironomidae (27%), Hydropsychidae (26%), Heptageniidae (8%), Philopotamidae (7%) and Ephemerellidae (6%). Densities of Hydropsychidae, Philopotamidae and Heptageniidae were up to 10 times greater in mounds than in pits and adjacent reference habitat. In summer, mounds had twice the density of Chironomidae than did pits, and 1.5 times more than reference habitats, but densities were similar among the habitats in autumn. These results suggest that spawning sea lampreys are ecosystem engineers. The physical disturbance caused by nest-building activity was significant and persistent, increasing habitat heterogeneity and favouring pollution-sensitive benthic invertebrates and, possibly, drift-feeding fish.

Generation of light-sheet at the end of multimode fibre (Conference Presentation)

NASA Astrophysics Data System (ADS)

Plöschner, Martin; Kollárová, Véra; Dostál, Zbyněk.; Nylk, Jonathan; Barton-Owen, Thomas; Ferrier, David E. K.; Chmelik, Radim; Dholakia, Kishan; Cizmár, TomáÅ.¡

2017-02-01

Light-sheet fluorescence microscopy is quickly becoming one of the cornerstone imaging techniques in biology as it provides rapid, three-dimensional sectioning of specimens at minimal levels of phototoxicity. It is very appealing to bring this unique combination of imaging properties into an endoscopic setting and be able to perform optical sectioning deep in tissues. Current endoscopic approaches for delivery of light-sheet illumination are based on single-mode optical fibre terminated by cylindrical gradient index lens. Such configuration generates a light-sheet plane that is axially fixed and a mechanical movement of either the sample or the endoscope is required to acquire three-dimensional information about the sample. Furthermore, the axial resolution of this technique is limited to 5um. The delivery of the light-sheet through the multimode fibre provides better axial resolution limited only by its numerical aperture, the light-sheet is scanned holographically without any mechanical movement, and multiple advanced light-sheet imaging modalities, such as Bessel and structured illumination Bessel beam, are intrinsically supported by the system due to the cylindrical symmetry of the fibre. We discuss the holographic techniques for generation of multiple light-sheet types and demonstrate the imaging on a sample of fluorescent beads fixed in agarose gel, as well as on a biological sample of Spirobranchus Lamarcki.

Enhanced detection of tuberculous mycobacteria in animal tissues using a semi-nested probe-based real-time PCR.

PubMed

Costa, Pedro; Ferreira, Ana S; Amaro, Ana; Albuquerque, Teresa; Botelho, Ana; Couto, Isabel; Cunha, Mónica V; Viveiros, Miguel; Inácio, João

2013-01-01

Bovine tuberculosis has been tackled for decades by costly eradication programs in most developed countries, involving the laboratory testing of tissue samples from allegedly infected animals for detection of Mycobacterium tuberculosis complex (MTC) members, namely Mycobacterium bovis. Definitive diagnosis is usually achieved by bacteriological culture, which may take up to 6-12 weeks, during which the suspect animal carcass and herd are under sanitary arrest. In this work, a user-friendly DNA extraction protocol adapted for tissues was coupled with an IS6110-targeted semi-nested duplex real-time PCR assay to enhance the direct detection of MTC bacteria in animal specimens, reducing the time to achieve a diagnosis and, thus, potentially limiting the herd restriction period. The duplex use of a novel β-actin gene targeted probe, with complementary targets in most mammals, allowed the assessment of amplification inhibitors in the tissue samples. The assay was evaluated with a group of 128 fresh tissue specimens collected from bovines, wild boars, deer and foxes. Mycobacterium bovis was cultured from 57 of these samples. Overall, the full test performance corresponds to a diagnostic sensitivity and specificity of 98.2% (CIP95% 89.4-99.9%) and 88.7% (CIP95% 78.5-94.7%), respectively. An observed kappa coefficient was estimated in 0.859 (CI P95% 0.771-0.948) for the overall agreement between the semi-nested PCR assay and the bacteriological culture. Considering only bovine samples (n = 69), the diagnostic sensitivity and specificity were estimated in 100% (CIP95% 84.0-100%) and 97.7% (CIP95% 86.2-99.9%), respectively. Eight negative culture samples exhibiting TB-like lesions were detected by the semi-nested real-time PCR, thus emphasizing the increased potential of this molecular approach to detect MTC-infected animal tissues. This novel IS6110-targeted assay allows the fast detection of tuberculous mycobacteria in animal specimens with very high sensitivity and specificity, being amenable and cost effective for use in the routine veterinary diagnostic laboratory with further automation possibilities.

Loop mediated isothermal amplification (LAMP) accurately detects malaria DNA from filter paper blood samples of low density parasitaemias.

PubMed

Aydin-Schmidt, Berit; Xu, Weiping; González, Iveth J; Polley, Spencer D; Bell, David; Shakely, Delér; Msellem, Mwinyi I; Björkman, Anders; Mårtensson, Andreas

2014-01-01

Loop mediated isothermal amplification (LAMP) provides an opportunity for improved, field-friendly detection of malaria infections in endemic areas. However data on the diagnostic accuracy of LAMP for active case detection, particularly low-density parasitaemias, are lacking. We therefore evaluated the performance of a new LAMP kit compared with PCR using DNA from filter paper blood spots. Samples from 865 fever patients and 465 asymptomatic individuals collected in Zanzibar were analysed for Pan (all species) and Pf (P. falciparum) DNA with the Loopamp MALARIA Pan/Pf kit. Samples were amplified at 65°C for 40 minutes in a real-time turbidimeter and results were compared with nested PCR. Samples with discordant results between LAMP and nested PCR were analysed with real-time PCR. The real-time PCR corrected nested PCR result was defined as gold standard. Among the 117 (13.5%) PCR detected P. falciparum infections from fever patients (mean parasite density 7491/µL, range 6-782,400) 115, 115 and 111 were positive by Pan-LAMP, Pf-LAMP and nested PCR, respectively. The sensitivities were 98.3% (95%CI 94-99.8) for both Pan and Pf-LAMP. Among the 54 (11.6%) PCR positive samples from asymptomatic individuals (mean parasite density 10/µL, range 0-4972) Pf-LAMP had a sensitivity of 92.7% (95%CI 80.1-98.5) for detection of the 41 P. falciparum infections. Pan-LAMP had sensitivities of 97% (95%CI 84.2-99.9) and 76.9% (95%CI 46.2-95) for detection of P. falciparum and P. malariae, respectively. The specificities for both Pan and Pf-LAMP were 100% (95%CI 99.1-100) in both study groups. Both components of the Loopamp MALARIA Pan/Pf detection kit revealed high diagnostic accuracy for parasite detection among fever patients and importantly also among asymptomatic individuals of low parasite densities from minute blood volumes preserved on filter paper. These data support LAMPs potential role for improved detection of low-density malaria infections in pre-elimination settings.

Loop Mediated Isothermal Amplification (LAMP) Accurately Detects Malaria DNA from Filter Paper Blood Samples of Low Density Parasitaemias

PubMed Central

González, Iveth J.; Polley, Spencer D.; Bell, David; Shakely, Delér; Msellem, Mwinyi I.; Björkman, Anders; Mårtensson, Andreas

2014-01-01

Background Loop mediated isothermal amplification (LAMP) provides an opportunity for improved, field-friendly detection of malaria infections in endemic areas. However data on the diagnostic accuracy of LAMP for active case detection, particularly low-density parasitaemias, are lacking. We therefore evaluated the performance of a new LAMP kit compared with PCR using DNA from filter paper blood spots. Methods and Findings Samples from 865 fever patients and 465 asymptomatic individuals collected in Zanzibar were analysed for Pan (all species) and Pf (P. falciparum) DNA with the Loopamp MALARIA Pan/Pf kit. Samples were amplified at 65°C for 40 minutes in a real-time turbidimeter and results were compared with nested PCR. Samples with discordant results between LAMP and nested PCR were analysed with real-time PCR. The real-time PCR corrected nested PCR result was defined as gold standard. Among the 117 (13.5%) PCR detected P. falciparum infections from fever patients (mean parasite density 7491/µL, range 6–782,400) 115, 115 and 111 were positive by Pan-LAMP, Pf-LAMP and nested PCR, respectively. The sensitivities were 98.3% (95%CI 94–99.8) for both Pan and Pf-LAMP. Among the 54 (11.6%) PCR positive samples from asymptomatic individuals (mean parasite density 10/µL, range 0–4972) Pf-LAMP had a sensitivity of 92.7% (95%CI 80.1–98.5) for detection of the 41 P. falciparum infections. Pan-LAMP had sensitivities of 97% (95%CI 84.2–99.9) and 76.9% (95%CI 46.2–95) for detection of P. falciparum and P. malariae, respectively. The specificities for both Pan and Pf-LAMP were 100% (95%CI 99.1–100) in both study groups. Conclusion Both components of the Loopamp MALARIA Pan/Pf detection kit revealed high diagnostic accuracy for parasite detection among fever patients and importantly also among asymptomatic individuals of low parasite densities from minute blood volumes preserved on filter paper. These data support LAMPs potential role for improved detection of low-density malaria infections in pre-elimination settings. PMID:25105591

Human motion tracking by temporal-spatial local gaussian process experts.

PubMed

Zhao, Xu; Fu, Yun; Liu, Yuncai

2011-04-01

Human pose estimation via motion tracking systems can be considered as a regression problem within a discriminative framework. It is always a challenging task to model the mapping from observation space to state space because of the high-dimensional characteristic in the multimodal conditional distribution. In order to build the mapping, existing techniques usually involve a large set of training samples in the learning process which are limited in their capability to deal with multimodality. We propose, in this work, a novel online sparse Gaussian Process (GP) regression model to recover 3-D human motion in monocular videos. Particularly, we investigate the fact that for a given test input, its output is mainly determined by the training samples potentially residing in its local neighborhood and defined in the unified input-output space. This leads to a local mixture GP experts system composed of different local GP experts, each of which dominates a mapping behavior with the specific covariance function adapting to a local region. To handle the multimodality, we combine both temporal and spatial information therefore to obtain two categories of local experts. The temporal and spatial experts are integrated into a seamless hybrid system, which is automatically self-initialized and robust for visual tracking of nonlinear human motion. Learning and inference are extremely efficient as all the local experts are defined online within very small neighborhoods. Extensive experiments on two real-world databases, HumanEva and PEAR, demonstrate the effectiveness of our proposed model, which significantly improve the performance of existing models.

Mercury concentrations in tissues of Florida bald eagles

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

Wood, P.B.; Wood, J.M.; White, J.H.

1996-01-01

We collected 48 blood and 61 feather samples from nestling bald eagles at 42 nests and adult feather samples from 20 nests in north and central Florida during 1991-93. We obtained 32 liver, 10 feather, and 5 blood samples from 33 eagle carcasses recovered in Florida during 1987-93. For nestlings, mercury concentrations in blood (GM = 0.16 ppm wet wt) and feather (GM = 3.23 ppm) samples were correlated (r = 0.69, P = 0.0001). Although nestlings had lower mercury concentrations in feathers than did adults (GM = 6.03 ppm), the feather mercury levels in nestlings and adults from themore » same nest were correlated (r = 0.63, P < 0.02). Mercury concentrations in blood of captive adult eagles (GM = 0.23 ppm) was similar to Florida nestlings but some Florida nestlings had blood mercury concentrations up to 0.61 ppm, more than twice as high as captive adults. Feather mercury concentrations in both nestlings and adults exceeded those in captive eagles, but concentrations in all tissues were similar to, or lower than, those in bald eagles from other wild populations. Although mercury concentrations in Florida eagles are below those that cause mortality, they are in the range of concentrations that can cause behavioral changes or reduce reproduction. We recommend periodic monitoring of mercury in Florida bald eagles for early detection of mercury increases before negative effects on reproduction occur. 26 refs., 5 figs., 2 tabs.« less

[Detection of human parvovirus B19, human bocavirus and human parvovirus 4 infections in blood samples among 95 patients with liver disease in Nanjing by nested PCR].

PubMed

Tong, Rui; Zhou, Wei-Min; Liu, Xi-Jun; Wang, Yue; Lou, Yong-Liang; Tan, Wen-Jie

2013-04-01

To analyze the infection of human parvovirus B19, human bocavirus (HBoV) and human parvovirus 4 (PARV4) in blood samples among patients with liver disease in Nanjing by molecular detection. Nested PCR assays were designed and validated to detect B19, HBoV and PARV4, respectively. The assays were used to screen three parvoviruses in blood samples from 95 patients with different liver disease in Nanjing. The parvovirus infection was analyzed statistically. The detection limits were 10 copies of genomic DNA equivalents per reaction for each assays and the good specificity were observed. The frequency of B19 and HBoV were 2/95 (2.1%) and 9/95 (9.5%) in blood samples respectively. No PARV4 was detected. HBoV was detected in 3/5 patients with drug-induced hepatitis. Both B19 and HBoV infection were detected in blood from patients with liver disease.

Detection of Bovine Leukemia Virus in Brains of Cattle with a Neurological Syndrome: Pathological and Molecular Studies

PubMed Central

D'Angelino, Rubens Henrique Ramos; Pituco, Edviges Maristela; Villalobos, Eliana Monteforte Cassaro; Harakava, Ricardo; Gregori, Fábio

2013-01-01

Bovine leukemia virus (BLV) was investigated in the central nervous system (CNS) of cattle with neurological syndrome. A total of 269 CNS samples were submitted to nested-PCR (BLV env gene gp51), and the viral genotypes were identified. The nested-PCR was positive in 4.8% (13/269) CNS samples, with 2.7% (2/74) presenting at histological examination lesions of nonpurulent meningoencephalitis (NPME), whereas 5.6% (11/195) not presenting NPME (P > 0.05). No samples presented lymphosarcoma. The PCR products (437 bp) were sequenced and submitted to phylogenetic analysis by neighbor-joining and maximum composite likelihood methods, and genotypes 1, 5, and 6 were detected, corroborating other South American studies. The genotype 6 barely described in Brazil and Argentina was more frequently detected in this study. The identity matrices showed maximum similarity (100%) among some samples of this study and one from Argentina (FJ808582), recovered from GenBank. There was no association among the genotypes and NPME lesions. PMID:23710448

Molecular identification of Coccidioides spp. in soil samples from Brazil

PubMed Central

2011-01-01

Background Since 1991 several outbreaks of acute coccidioidomycosis (CM) were diagnosed in the semi-arid Northeast of Brazil, mainly related to disturbance of armadillo burrows caused by hunters while digging them for the capture of these animals. This activity causes dust contaminated with arthroconidia of Coccidioides posadasii, which, once inhaled, cause the mycosis. We report on the identification of C. posadasii in soil samples related to outbreaks of CM. Results Twenty four soil samples had their DNA extracted and subsequently submitted to a semi-nested PCR technique using specific primers. While only 6 (25%) soil samples were positive for C. posadasii by mice inoculation, all (100%) were positive by the molecular tool. Conclusion This methodology represents a simple, sensitive and specific molecular technique to determine the environmental distribution of Coccidioides spp. in endemic areas, but cannot distinguish the species. Moreover, it may be useful to identify culture isolates. Key-words: 1. Coccidioidomycosis. 2. Coccidioides spp. 3. C. posadasii. 4. Semi-arid. 5. Semi-nested PCR PMID:21575248

Transition from Propagating Polariton Solitons to a Standing Wave Condensate Induced by Interactions

NASA Astrophysics Data System (ADS)

Sich, M.; Chana, J. K.; Egorov, O. A.; Sigurdsson, H.; Shelykh, I. A.; Skryabin, D. V.; Walker, P. M.; Clarke, E.; Royall, B.; Skolnick, M. S.; Krizhanovskii, D. N.

2018-04-01

We explore phase transitions of polariton wave packets, first, to a soliton and then to a standing wave polariton condensate in a multimode microwire system, mediated by nonlinear polariton interactions. At low excitation density, we observe ballistic propagation of the multimode polariton wave packets arising from the interference between different transverse modes. With increasing excitation density, the wave packets transform into single-mode bright solitons due to effects of both intermodal and intramodal polariton-polariton scattering. Further increase of the excitation density increases thermalization speed, leading to relaxation of the polariton density from a solitonic spectrum distribution in momentum space down to low momenta, with the resultant formation of a nonequilibrium condensate manifested by a standing wave pattern across the whole sample.

Transition from Propagating Polariton Solitons to a Standing Wave Condensate Induced by Interactions.

PubMed

Sich, M; Chana, J K; Egorov, O A; Sigurdsson, H; Shelykh, I A; Skryabin, D V; Walker, P M; Clarke, E; Royall, B; Skolnick, M S; Krizhanovskii, D N

2018-04-20

We explore phase transitions of polariton wave packets, first, to a soliton and then to a standing wave polariton condensate in a multimode microwire system, mediated by nonlinear polariton interactions. At low excitation density, we observe ballistic propagation of the multimode polariton wave packets arising from the interference between different transverse modes. With increasing excitation density, the wave packets transform into single-mode bright solitons due to effects of both intermodal and intramodal polariton-polariton scattering. Further increase of the excitation density increases thermalization speed, leading to relaxation of the polariton density from a solitonic spectrum distribution in momentum space down to low momenta, with the resultant formation of a nonequilibrium condensate manifested by a standing wave pattern across the whole sample.

Multimodality hard-x-ray imaging of a chromosome with nanoscale spatial resolution

DOE PAGES

Yan, Hanfei; Nazaretski, Evgeny; Lauer, Kenneth R.; ...

2016-02-05

Here, we developed a scanning hard x-ray microscope using a new class of x-ray nano-focusing optic called a multilayer Laue lens and imaged a chromosome with nanoscale spatial resolution. The combination of the hard x-ray's superior penetration power, high sensitivity to elemental composition, high spatial-resolution and quantitative analysis creates a unique tool with capabilities that other microscopy techniques cannot provide. Using this microscope, we simultaneously obtained absorption-, phase-, and fluorescence-contrast images of Pt-stained human chromosome samples. The high spatial-resolution of the microscope and its multi-modality imaging capabilities enabled us to observe the internal ultra-structures of a thick chromosome without sectioningmore » it.« less

Multimodality hard-x-ray imaging of a chromosome with nanoscale spatial resolution

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

Yan, Hanfei; Nazaretski, Evgeny; Lauer, Kenneth R.

Here, we developed a scanning hard x-ray microscope using a new class of x-ray nano-focusing optic called a multilayer Laue lens and imaged a chromosome with nanoscale spatial resolution. The combination of the hard x-ray's superior penetration power, high sensitivity to elemental composition, high spatial-resolution and quantitative analysis creates a unique tool with capabilities that other microscopy techniques cannot provide. Using this microscope, we simultaneously obtained absorption-, phase-, and fluorescence-contrast images of Pt-stained human chromosome samples. The high spatial-resolution of the microscope and its multi-modality imaging capabilities enabled us to observe the internal ultra-structures of a thick chromosome without sectioningmore » it.« less

Fast Physically Accurate Rendering of Multimodal Signatures of Distributed Fracture in Heterogeneous Materials.

PubMed

Visell, Yon

2015-04-01

This paper proposes a fast, physically accurate method for synthesizing multimodal, acoustic and haptic, signatures of distributed fracture in quasi-brittle heterogeneous materials, such as wood, granular media, or other fiber composites. Fracture processes in these materials are challenging to simulate with existing methods, due to the prevalence of large numbers of disordered, quasi-random spatial degrees of freedom, representing the complex physical state of a sample over the geometric volume of interest. Here, I develop an algorithm for simulating such processes, building on a class of statistical lattice models of fracture that have been widely investigated in the physics literature. This algorithm is enabled through a recently published mathematical construction based on the inverse transform method of random number sampling. It yields a purely time domain stochastic jump process representing stress fluctuations in the medium. The latter can be readily extended by a mean field approximation that captures the averaged constitutive (stress-strain) behavior of the material. Numerical simulations and interactive examples demonstrate the ability of these algorithms to generate physically plausible acoustic and haptic signatures of fracture in complex, natural materials interactively at audio sampling rates.

Detection of Legionella spp. by a nested-PCR assay in air samples of a wastewater treatment plant and downwind distances in Isfahan

PubMed Central

Mirzaee, Seyyed Abbas; Nikaeen, Mahnaz; Hajizadeh, Yaghob; Nabavi, BiBi Fatemeh; Hassanzadeh, Akbar

2015-01-01

Background: Wastewater contains a variety of pathogens and bio -aerosols generated during the wastewater treatment process, which could be a potential health risk for exposed individuals. This study was carried out to detect Legionella spp. in the bio -aerosols generated from different processes of a wastewater treatment plant (WWTP) in Isfahan, Iran, and the downwind distances. Materials and Methods: A total of 54 air samples were collected and analyzed for the presence of Legionella spp. by a nested- polymerase chain reaction (PCR) assay. A liquid impingement biosampler was used to capture bio -aerosols. The weather conditions were also recorded. Results: Legionella were detected in 6% of the samples, including air samples above the aeration tank (1/9), belt filter press (1/9), and 250 m downwind (1/9). Conclusion: The result of this study revealed the presence of Legionella spp. in air samples of a WWTP and downwind distance, which consequently represent a potential health risk to the exposed individuals. PMID:25802817

Comparison of milk culture, direct and nested polymerase chain reaction (PCR) with fecal culture based on samples from dairy herds infected with Mycobacterium avium subsp. paratuberculosis

PubMed Central

Gao, Anli; Odumeru, Joseph; Raymond, Melinda; Hendrick, Steven; Duffield, Todd; Mutharia, Lucy

2009-01-01

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne’s disease in cattle and other farm ruminants, and is also a suspected pathogen of Crohn’s disease in humans. Development of diagnostic methods for MAP infection has been a challenge over the last few decades. The objective of this study was to investigate the relationship between different methods for detection of MAP in milk and fecal samples. A total of 134 milk samples and 110 feces samples were collected from 146 individual cows in 14 MAP-infected herds in southwestern Ontario. Culture, IS900 polymerase chain reaction (PCR) and nested PCR methods were used for detecting MAP in milk; results were compared with those of fecal culture. A significant relationship was found between milk culture, direct PCR, and nested PCR (P < 0.05). The fecal culture results were not related to any of the 3 assay methods used for the milk samples (P > 0.10). Although fecal culture showed a higher sensitivity than the milk culture method, the difference was not significant (P = 0.2473). The number of MAP colony-forming units (CFU) isolated by culture from fecal samples was, on average, higher than that isolated from milk samples (P = 0.0083). There was no significant correlation between the number of CFU cultured from milk and from feces (Pearson correlation coefficient = 0.1957, N = 63, P = 0.1243). The animals with high numbers of CFU in milk culture may not be detected by fecal culture at all, and vise versa. A significant proportion (29% to 41%) of the positive animals would be missed if only 1 culture method, instead of both milk and feces, were to be used for diagnosis. This suggests that the shedding of MAP in feces and milk is not synchronized. Most of the infected cows were low-level shedders. The proportion of low-level shedders may even be underestimated because MAP is killed during decontamination, thus reducing the chance of detection. Therefore, to identify suspected Johne’s-infected animals using the tests in this study, both milk and feces samples should be collected in duplicate to enhance the diagnostic rate. The high MAP kill rate identified in the culture methods during decontamination may be compensated for by using the nested PCR method, which had a higher sensitivity than the IS900 PCR method used. PMID:19337397

[A novel TaqMan® MGB probe for specifically detecting Streptococcus mutans].

PubMed

Zheng, Hui; Lin, Jiu-Xiang; DU, Ning; Chen, Feng

2013-10-18

To design a new TaqMan® MGB probe for improving the specificity of Streptococcus mutans's detection. We extracted six DNA samples from different streptococcal strains for PCR reaction. Conventional nested PCR and TaqMan® MGB real-time PCR were applied independently. The first round of nested PCR was carried out with the bacterial universal primers, while a second PCR was conducted by using primers specific for the 16S rRNA gene of Streptococcus mutans. The TaqMan® MGB probe for Streptococcus mutans was designed from sequence analyses, and the primers were the same as nested PCR. Streptococcus mutans DNA with 2.5 mg/L was sequentially diluted at 5-fold intervals to 0.16 μg/L. Standard DNA samples were used to generate standard curves by TaqMan® MGB real-time PCR. In the nested PCR, the primers specific for Streptococcus mutans also detected Streptococcus gordonii with visible band of 282 bp, giving false-positive results. In the TaqMan® MGB real-time PCR reaction, only Streptococcus mutans was detected. The detection limitation of TaqMan® MGB real-time PCR for Streptococcus mutans 16S rRNA gene was 20 μg/L. We designed a new TaqMan® MGB probe, and successfully set up a PCR based method for detecting oral Streptococcus mutans. TaqMan® MGB real-time PCR is a both specific and sensitive bacterial detection method.

Coevolutionary diversification creates nested-modular structure in phage–bacteria interaction networks

PubMed Central

Beckett, Stephen J.; Williams, Hywel T. P.

2013-01-01

Phage and their bacterial hosts are the most diverse and abundant biological entities in the oceans, where their interactions have a major impact on marine ecology and ecosystem function. The structure of interaction networks for natural phage–bacteria communities offers insight into their coevolutionary origin. At small phylogenetic scales, observed communities typically show a nested structure, in which both hosts and phages can be ranked by their range of resistance and infectivity, respectively. A qualitatively different multi-scale structure is seen at larger phylogenetic scales; a natural assemblage sampled from the Atlantic Ocean displays large-scale modularity and local nestedness within each module. Here, we show that such ‘nested-modular’ interaction networks can be produced by a simple model of host–phage coevolution in which infection depends on genetic matching. Negative frequency-dependent selection causes diversification of hosts (to escape phages) and phages (to track their evolving hosts). This creates a diverse community of bacteria and phage, maintained by kill-the-winner ecological dynamics. When the resulting communities are visualized as bipartite networks of who infects whom, they show the nested-modular structure characteristic of the Atlantic sample. The statistical significance and strength of this observation varies depending on whether the interaction networks take into account the density of the interacting strains, with implications for interpretation of interaction networks constructed by different methods. Our results suggest that the apparently complex community structures associated with marine bacteria and phage may arise from relatively simple coevolutionary origins. PMID:24516719

What's in a Day? A Guide to Decomposing the Variance in Intensive Longitudinal Data

PubMed Central

de Haan-Rietdijk, Silvia; Kuppens, Peter; Hamaker, Ellen L.

2016-01-01

In recent years there has been a growing interest in the use of intensive longitudinal research designs to study within-person processes. Examples are studies that use experience sampling data and autoregressive modeling to investigate emotion dynamics and between-person differences therein. Such designs often involve multiple measurements per day and multiple days per person, and it is not clear how this nesting of the data should be accounted for: That is, should such data be considered as two-level data (which is common practice at this point), with occasions nested in persons, or as three-level data with beeps nested in days which are nested in persons. We show that a significance test of the day-level variance in an empty three-level model is not reliable when there is autocorrelation. Furthermore, we show that misspecifying the number of levels can lead to spurious or misleading findings, such as inflated variance or autoregression estimates. Throughout the paper we present instructions and R code for the implementation of the proposed models, which includes a novel three-level AR(1) model that estimates moment-to-moment inertia and day-to-day inertia. Based on our simulations we recommend model selection using autoregressive multilevel models in combination with the AIC. We illustrate this method using empirical emotion data from two independent samples, and discuss the implications and the relevance of the existence of a day level for the field. PMID:27378986

Measuring the effect of mercury exposure on common loon productivity in Wisconsin

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

Meyer, M.W.; Hartigan, J.; Woodford, J.

1994-12-31

In 1991, the Wisconsin DNR conducted a pilot study to determine the extent of mercury (Hg) exposure in common loons (Gavia immer) breeding in Wisconsin. Loons are at risk to elevated mercury exposure in Wisconsin because they often nest on acidified, low alkalinity lakes. Fish from these lakes bioaccumulate methyl-Hg to a greater extent than biota from neutral pH lakes. Using nightlighting techniques, 35 adult loons were captured on 22 northern Wisconsin lakes (pH = 5.0--8.7) in 1991. Blood and feather samples were collected for Hg analysis. There was a highly significant negative linear relationship between adult loon blood clotmore » Hg and lake pH (r{sup 2} = 0.38, F = 15.27, P < 0.001); indicating loons nesting on low pH lakes receive greater mercury exposure than loons nesting on neutral pH lakes. The relationship was greater amongst adult males (r{sup 2} = 0.56) than among adult females (r{sup 2} = 0.36). The research effort was expanded in 1992 and 1993; 253 loons have been captured to date on 62 lakes in northern Wisconsin. The mercury content of feather and blood samples is being measured. Individual loons were also fitted with unique colored leg bands. Reproductive performance, annual return rates, and nesting behavior of adult loons with the greatest Hg exposure is being compared to that of adult loons with the least Hg exposure. The preliminary results from 1991--93 field seasons will be presented.« less

What's in a Day? A Guide to Decomposing the Variance in Intensive Longitudinal Data.

PubMed

de Haan-Rietdijk, Silvia; Kuppens, Peter; Hamaker, Ellen L

2016-01-01

In recent years there has been a growing interest in the use of intensive longitudinal research designs to study within-person processes. Examples are studies that use experience sampling data and autoregressive modeling to investigate emotion dynamics and between-person differences therein. Such designs often involve multiple measurements per day and multiple days per person, and it is not clear how this nesting of the data should be accounted for: That is, should such data be considered as two-level data (which is common practice at this point), with occasions nested in persons, or as three-level data with beeps nested in days which are nested in persons. We show that a significance test of the day-level variance in an empty three-level model is not reliable when there is autocorrelation. Furthermore, we show that misspecifying the number of levels can lead to spurious or misleading findings, such as inflated variance or autoregression estimates. Throughout the paper we present instructions and R code for the implementation of the proposed models, which includes a novel three-level AR(1) model that estimates moment-to-moment inertia and day-to-day inertia. Based on our simulations we recommend model selection using autoregressive multilevel models in combination with the AIC. We illustrate this method using empirical emotion data from two independent samples, and discuss the implications and the relevance of the existence of a day level for the field.

A multimodal imaging platform with integrated simultaneous photoacoustic microscopy, optical coherence tomography, optical Doppler tomography and fluorescence microscopy

NASA Astrophysics Data System (ADS)

Dadkhah, Arash; Zhou, Jun; Yeasmin, Nusrat; Jiao, Shuliang

2018-02-01

Various optical imaging modalities with different optical contrast mechanisms have been developed over the past years. Although most of these imaging techniques are being used in many biomedical applications and researches, integration of these techniques will allow researchers to reach the full potential of these technologies. Nevertheless, combining different imaging techniques is always challenging due to the difference in optical and hardware requirements for different imaging systems. Here, we developed a multimodal optical imaging system with the capability of providing comprehensive structural, functional and molecular information of living tissue in micrometer scale. This imaging system integrates photoacoustic microscopy (PAM), optical coherence tomography (OCT), optical Doppler tomography (ODT) and fluorescence microscopy in one platform. Optical-resolution PAM (OR-PAM) provides absorption-based imaging of biological tissues. Spectral domain OCT is able to provide structural information based on the scattering property of biological sample with no need for exogenous contrast agents. In addition, ODT is a functional extension of OCT with the capability of measurement and visualization of blood flow based on the Doppler effect. Fluorescence microscopy allows to reveal molecular information of biological tissue using autofluoresce or exogenous fluorophores. In-vivo as well as ex-vivo imaging studies demonstrated the capability of our multimodal imaging system to provide comprehensive microscopic information on biological tissues. Integrating all the aforementioned imaging modalities for simultaneous multimodal imaging has promising potential for preclinical research and clinical practice in the near future.

Multimodal exercise intervention improves frontal cognitive functions and gait in Alzheimer's disease: a controlled trial.

PubMed

Coelho, Flávia Gomes de Melo; Andrade, Larissa Pires; Pedroso, Renata Valle; Santos-Galduroz, Ruth Ferreira; Gobbi, Sebastião; Costa, José Luiz Riani; Gobbi, Lilian Teresa Bucken

2013-01-01

The objective of the present study was to investigate the effect of a multimodal exercise intervention on frontal cognitive functions and kinematic gait parameters in patients with Alzheimer's disease. A sample of elderly patients with Alzheimer's disease (n=27) were assigned to a training group (n=14; aged 78.0±7.3 years) and a control group (n=13; aged 77.1±7.4 years). Multimodal exercise intervention includes motor activities and cognitive tasks simultaneously. The participants attended a 1-h session three times a week for 16 weeks, and the control participants maintained their regular daily activities during the same period. The frontal cognitive functions were evaluated using the Frontal Assessment Battery, the Clock Drawing Test and the Symbol Search Subtest. The kinematic parameters of gait-cadence, stride length and stride speed were analyzed under two conditions: (i) free gait (single task); and (ii) gait with frontal cognitive task (walking and counting down from 20--dual task). The patients in the intervention group significantly increased the scores in frontal cognitive variables, Frontal Assessment Battery (P<0.001) and Symbol Search Subtest (P<0.001) after the 16-week period. The control group decreased the scores in the Clock Drawing Test (P=0.001) and increased the number of counting errors during the dual task (P=0.008) after the same period. The multimodal exercise intervention improved the frontal cognitive functions in patients with Alzheimer's disease. © 2012 Japan Geriatrics Society.

Molecular analysis of dolphin morbillivirus: A new sensitive detection method based on nested RT-PCR.

PubMed

Centelleghe, Cinzia; Beffagna, Giorgia; Zanetti, Rossella; Zappulli, Valentina; Di Guardo, Giovanni; Mazzariol, Sandro

2016-09-01

Cetacean Morbillivirus (CeMV) has been identified as the most pathogenic virus for cetaceans. Over the past three decades, this RNA virus has caused several outbreaks of lethal disease in odontocetes and mysticetes worldwide. Isolation and identification of CeMV RNA is very challenging in whales because of the poor preservation status frequently shown by tissues from stranded animals. Nested reverse transcription polymerase chain reaction (nested RT-PCR) is used instead of conventional RT-PCR when it is necessary to increase the sensitivity and the specificity of the reaction. This study describes a new nested RT-PCR technique useful to amplify small amounts of the cDNA copy of Cetacean morbillivirus (CeMV) when it is present in scant quantity in whales' biological specimens. This technique was used to analyze different tissues (lung, brain, spleen and other lymphoid tissues) from one under human care seal and seven cetaceans stranded along the Italian coastline between October 2011 and September 2015. A well-characterized, 200 base pair (bp) fragment of the dolphin Morbillivirus (DMV) haemagglutinin (H) gene, obtained by nested RT-PCR, was sequenced and used to confirm DMV positivity in all the eight marine mammals under study. In conclusion, this nested RT-PCR protocol can represent a sensitive detection method to identify CeMV-positive, poorly preserved tissue samples. Furthermore, this is also a rather inexpensive molecular technique, relatively easy to apply. Copyright © 2016 Elsevier B.V. All rights reserved.

Development of an In-House Multiplex Nested RT-PCR Method for Detecting Acute HIV-1 Infection in High Risk Populations.

PubMed

Liu, Zhiying; Li, Wei; Xu, Meng; Sheng, Bo; Yang, Zixuan; Jiao, Yanmei; Zhang, Tong; Mou, Danlei; Chen, Dexi; Wu, Hao

2015-01-01

The detection of acute HIV infection (AHI) among high risk populations can help reduce secondary transmission of HIV. The nucleic acid testing (NAT) can shorten the test window period by up to 7-12 days. In this study, we describe an in-house NAT based on the multiplex nested RT-PCR method to detect the HIV RNA. We also evaluated it in a high risk cohort in Beijing. Four primer pairs were designed and evaluated for the detection of different HIV-1 subtypes in group M. Multiplex RT-PCR and nested PCR were performed. The sensitivity, specialty, primers compatibility among HIV subtypes were evaluated simultaneously. In an MSM cohort in Beijing during a 3-year period, a total of 11,808 blood samples that were negative by ELISA or indeterminate by Western blot were analyzed by this multiplex nested RT-PCR with pooling strategy. The multiplex nested RT-PCR was successfully applied for the detection of at least six HIV-1 subtypes. The sensitivity was 40 copies/ml and the specificity was 100%. A total of 29 people were tested HIV-1 positive with acute infection in a MSM cohort of Beijing during a 3 years period. This multiplex nested RT-PCR provides a useful tool for the rapid detection of acute HIV-1 infection. When used in combination with the 3(rd) generation ELISA, it can improve the detection rate of HIV infection, especially in the source limited regions.

Compositional changes in bee and wasp communities along Neotropical mountain altitudinal gradient.

PubMed

Perillo, Lucas Neves; Neves, Frederico de Siqueira; Antonini, Yasmine; Martins, Rogério Parentoni

2017-01-01

Climate conditions tend to differ along an altitudinal gradient, resulting in some species groups' patterns of lower species richness with increasing altitude. While this pattern is well understood for tropical mountains, studies investigating possible determinants of variation in beta-diversity at its different altitudes are scarce. We sampled bee and wasp communities (Hymenoptera: Aculeata) along an altitudinal gradient (1,000-2,000 m.a.s.l.) in a tropical mountainous region of Brazil. Trap nests and Moericke traps were established at six sampling points, with 200 m difference in altitude between each point. We obtained average climate data (1970-2000) from Worldclim v2 for altitudes at each sampling site. Nest traps captured 17 bee and wasp species from six families, and Moericke traps captured 124 morphospecies from 13 families. We found a negative correlation between altitude and species richness and abundance. Temperature, precipitation, water vapor pressure, and wind speed influenced species richness and abundance, and were correlated with altitude. β-diversity was primarily determined by species turnover as opposed to nestedness, and Aculeate community similarity was higher for more similar altitudinal ranges. Moericke traps seem to be more efficient for altitudinal surveys compared to nest traps. We found high occurrence of singleton and doubleton species at all altitudes, highlighting the need for long-term studies to efficiently assess hymenopteran diversity in these environments.

Detection of Helicobacter spp. DNA in the oral cavity of dogs.

PubMed

Recordati, Camilla; Gualdi, Valentina; Tosi, Sabrina; Facchini, Roberto Vailati; Pengo, Graziano; Luini, Mario; Simpson, Kenneth W; Scanziani, Eugenio

2007-01-31

The mode of acquisition of gastric Helicobacter spp. infection in dogs has not been determined. It is suspected that oral-oral and faecal-oral transmission may be involved. The present study sought to determine if Helicobacter spp. DNA is present in the oral cavity of healthy and vomiting dogs. Thirty-eight pet dogs (27 vomiting and 11 clinically healthy) were studied. The presence of Helicobacter spp. was determined by single and nested PCR evaluation of DNA extracted from saliva, dental plaque and gastric biopsy samples. Helicobacter spp. DNA was detected by nested PCR in 36 (94.7%) gastric biopsies, 17 (44.7%) dental plaque and 19 (50%) saliva samples out of the 38 dogs examined. Overall 27 (71.1%) dogs screened by nested PCR were found to harbour Helicobacter spp. DNA in the oral cavity (dental plaque and/or saliva). There was no significant difference in the prevalence of Helicobacter spp. DNA in the oral cavity of vomiting and healthy dogs, and the time from vomiting to oral sampling did not have significant impact. This study confirms the high prevalence of gastric Helicobacter spp. infection in dogs, and reveals that Helicobacter spp. DNA is detectable in the oral cavity of over 70% of dogs. These findings support the possibility of oral-oral transmission between dogs and that the canine oral cavity may act as source of non-pylori Helicobacter spp. infection for humans.

Clinical Evaluation of a Loop-Mediated Amplification Kit for Diagnosis of Imported Malaria

PubMed Central

Polley, Spencer D.; González, Iveth J.; Mohamed, Deqa; Daly, Rosemarie; Bowers, Kathy; Watson, Julie; Mewse, Emma; Armstrong, Margaret; Gray, Christen; Perkins, Mark D.; Bell, David; Kanda, Hidetoshi; Tomita, Norihiro; Kubota, Yutaka; Mori, Yasuyoshi; Chiodini, Peter L.; Sutherland, Colin J.

2013-01-01

Background. Diagnosis of malaria relies on parasite detection by microscopy or antigen detection; both fail to detect low-density infections. New tests providing rapid, sensitive diagnosis with minimal need for training would enhance both malaria diagnosis and malaria control activities. We determined the diagnostic accuracy of a new loop-mediated amplification (LAMP) kit in febrile returned travelers. Methods. The kit was evaluated in sequential blood samples from returned travelers sent for pathogen testing to a specialist parasitology laboratory. Microscopy was performed, and then malaria LAMP was performed using Plasmodium genus and Plasmodium falciparum–specific tests in parallel. Nested polymerase chain reaction (PCR) was performed on all samples as the reference standard. Primary outcome measures for diagnostic accuracy were sensitivity and specificity of LAMP results, compared with those of nested PCR. Results. A total of 705 samples were tested in the primary analysis. Sensitivity and specificity were 98.4% and 98.1%, respectively, for the LAMP P. falciparum primers and 97.0% and 99.2%, respectively, for the Plasmodium genus primers. Post hoc repeat PCR analysis of all 15 tests with discrepant results resolved 4 results in favor of LAMP, suggesting that the primary analysis had underestimated diagnostic accuracy. Conclusions. Malaria LAMP had a diagnostic accuracy similar to that of nested PCR, with a greatly reduced time to result, and was superior to expert microscopy. PMID:23633403

Methods of detecting and counting raptors: A review

USGS Publications Warehouse

Fuller, M.R.; Mosher, J.A.; Ralph, C. John; Scott, J. Michael

1981-01-01

Most raptors are wide-ranging, secretive, and occur at relatively low densities. These factors, in conjunction with the nocturnal activity of owls, cause the counting of raptors by most standard census and survey efforts to be very time consuming and expensive. This paper reviews the most common methods of detecting and counting raptors. It is hoped that it will be of use to the ever-increasing number of biologists, land-use planners, and managers that must determine the occurrence, density, or population dynamics of raptors. Road counts of fixed station or continuous transect design are often used to sample large areas. Detection of spontaneous or elicited vocalizations, especially those of owls, provides a means of detecting and estimating raptor numbers. Searches for nests are accomplished from foot surveys, observations from automobiles and boats, or from aircraft when nest structures are conspicuous (e.g., Osprey). Knowledge of nest habitat, historic records, and inquiries of local residents are useful for locating nests. Often several of these techniques are combined to help find nest sites. Aerial searches have also been used to locate or count large raptors (e.g., eagles), or those that may be conspicuous in open habitats (e.g., tundra). Counts of birds entering or leaving nest colonies or colonial roosts have been attempted on a limited basis. Results from Christmas Bird Counts have provided an index of the abundance of some species. Trapping and banding generally has proven to be an inefficient method of detecting raptors or estimating their populations. Concentrations of migrants at strategically located points around the world afford the best opportunity to count many rap tors in a relatively short period of time, but the influence of many unquantified variables has inhibited extensive interpretation of these counts. Few data exist to demonstrate the effectiveness of these methods. We believe more research on sampling techniques, rather than complete counts or intensive searches, will provide adequate yet affordable estimates of raptor numbers in addition to providing methods for detecting the presence of raptors on areas of interest to researchers and managers.

Novel approach based on one-tube nested PCR and a lateral flow strip for highly sensitive diagnosis of tuberculous meningitis.

PubMed

Sun, Yajuan; Chen, Jiajun; Li, Jia; Xu, Yawei; Jin, Hui; Xu, Na; Yin, Rui; Hu, Guohua

2017-01-01

Rapid and sensitive detection of Mycobacterium tuberculosis (M. Tb) in cerebrospinal fluid is crucial in the diagnosis of tuberculous meningitis (TBM), but conventional diagnostic technologies have limited sensitivity and specificity or are time-consuming. In this work, a novel, highly sensitive molecular diagnostic method, one-tube nested PCR-lateral flow strip test (OTNPCR-LFST), was developed for detecting M. tuberculosis. This one-tube nested PCR maintains the sensitivity of conventional two-step nested PCR and reduces both the chance of cross-contamination and the time required for analysis. The PCR product was detected by a lateral flow strip assay, which provided a basis for migration of the test to a point-of-care (POC) microfluidic format. The developed assay had an improved sensitivity compared with traditional PCR, and the limit of detection was up to 1 fg DNA isolated from M. tuberculosis. The assay was also specific for M. tuberculosis, and no cross-reactions were found in other non-target bacteria. The application of this technique to clinical samples was successfully evaluated, and OTNPCR-LFST showed 89% overall sensitivity and 100% specificity for TBM patients. This one-tube nested PCR-lateral flow strip assay is useful for detecting M. tuberculosis in TBM due to its rapidity, high sensitivity and simple manipulation.

Development of a novel single tube nested PCR for enhanced detection of cytomegalovirus DNA from dried blood spots.

PubMed

Atkinson, C; Emery, V C; Griffiths, P D

2014-02-01

Newborn screening for congenital cytomegalovirus (CCMV) using dried blood spots (DBS) has been proposed because many developed countries have DBS screening programmes in place for other diseases. The aim of this study was to develop a rapid, single tube nested polymerase chain reaction (PCR) method for enhanced detection of CMV from DBS compared to existing (single target) real time PCRs. The new method was compared with existing real time PCRs for sensitivity and specificity. Overall sensitivity of the single target PCR assays in both asymptomatic and symptomatic infants with laboratory confirmed congenital CMV was 69% (CMV PCR or culture positive before day 21 of life). In contrast, the single tube nested assay had an increased sensitivity of 81% with100% specificity. Overall the assay detected CMV from a DBS equivalent to an original blood sample which contained 500IU/ml. In conclusion this single tube nested methodology allows simultaneous amplification and detection of CMV DNA in 1.5h removing the associated contamination risk of a two step nested PCR. Owing to its increased sensitivity, it has the potential to be used as a screening assay and ultimately allow early identification and intervention for children with congenital CMV. Copyright © 2013 Elsevier B.V. All rights reserved.

Detection of fungi by conventional methods and semi-nested PCR in patients with presumed fungal keratitis.

PubMed

Haghani, I; Amirinia, F; Nowroozpoor-Dailami, K; Shokohi, T

2015-06-01

Fungal keratitis is a suppurative, ulcerative, and sight-threatening infection of the cornea that sometimes leads to blindness. The aims of this study were: recuperating facilities for laboratory diagnosis, determining the causative microorganisms, and comparing conventional laboratory diagnostic tools and semi-nested PCR. Sampling was conducted in patients with suspected fungal keratitis. Two corneal scrapings specimens, one for direct smear and culture and the other for semi- nested PCR were obtained. Of the 40 expected cases of mycotic keratitis, calcofluor white staining showed positivity in 25%, culture in 17.5%, KOH in 10%, and semi-nested PCR in 27.5%. The sensitivities of semi-nested PCR, KOH, and CFW were 57.1%, 28.5%, and 42% while the specificities were 78.7%, 94%, and 78.7%, respectively. The time taken for PCR assay was 4 to 8 hours, whereas positive fungal cultures took at least 5 to 7 days. Due to the increasing incidence of fungal infections in people with weakened immune systems, uninformed using of topical corticosteroids and improper use of contact lens, fast diagnosis and accurate treatment of keratomycosis seems to be essential . Therefore, according to the current study, molecular methods can detect mycotic keratitis early and correctly leading to appropriate treatment.

Lack of spatial genetic structure among nesting and wintering King Eiders

USGS Publications Warehouse

Pearce, J.M.; Talbot, S.L.; Pierson, Barbara J.; Petersen, M.R.; Scribner, K.T.; Dickson, D.L.; Mosbech, A.

2004-01-01

The King Eider (Somateria spectabilis) has been delineated into two broadly distributed breeding populations in North America (the western and eastern Arctic) on the basis of banding data and their use of widely separated Pacific and Atlantic wintering areas. Little is known about the level of gene flow between these two populations. Also unknown is whether behavioral patterns common among migratory waterfowl, such as site fidelity to wintering areas and pair formation at these sites, have existed for sufficient time to create a population structure defined by philopatry to wintering rather than to nesting locations. We used six nuclear microsatellite DNA loci and cytochrome b mitochondrial DNA sequence data to estimate the extent of spatial genetic differentiation among nesting and wintering areas of King Eiders across North America and adjacent regions. Estimates of interpopulation variance in microsatellite allele and mtDNA haplotype frequency were both low and nonsignificant based on samples from three wintering and four nesting areas. Results from nested clade analysis, mismatch distributions, and coalescent-based analyses suggest historical population growth and gene flow that collectively may have homogenized gene frequencies. The presence of several unique mtDNA haplotypes among birds wintering near Greenland suggests that gene flow may now be more limited between the western and eastern Arctic, which is consistent with banding data.

Use of the superpopulation approach to estimate breeding population size: An example in asynchronously breeding birds

USGS Publications Warehouse

Williams, K.A.; Frederick, P.C.; Nichols, J.D.

2011-01-01

Many populations of animals are fluid in both space and time, making estimation of numbers difficult. Much attention has been devoted to estimation of bias in detection of animals that are present at the time of survey. However, an equally important problem is estimation of population size when all animals are not present on all survey occasions. Here, we showcase use of the superpopulation approach to capture-recapture modeling for estimating populations where group membership is asynchronous, and where considerable overlap in group membership among sampling occasions may occur. We estimate total population size of long-legged wading bird (Great Egret and White Ibis) breeding colonies from aerial observations of individually identifiable nests at various times in the nesting season. Initiation and termination of nests were analogous to entry and departure from a population. Estimates using the superpopulation approach were 47-382% larger than peak aerial counts of the same colonies. Our results indicate that the use of the superpopulation approach to model nesting asynchrony provides a considerably less biased and more efficient estimate of nesting activity than traditional methods. We suggest that this approach may also be used to derive population estimates in a variety of situations where group membership is fluid. ?? 2011 by the Ecological Society of America.

Ecosystem engineering of harvester ants: effects on vegetation in a sagebrush-steppe ecosystem

USGS Publications Warehouse

Gosselin, Elyce N; Holbrook, Joseph D.; Huggler, Katey; Brown, Emily; Vierling, Kerri T.; Arkle, Robert; Pilliod, David S.

2016-01-01

Harvester ants are influential in many ecosystems because they distribute and consume seeds, remove vegetation, and redistribute soil particles and nutrients. Understanding the interaction between harvester ants and plant communities is important for management and restoration efforts, particularly in systems altered by fire and invasive species such as the sagebrush-steppe. Our objective was to evaluate how vegetation cover changed as a function of distance from Owyhee harvester ant (Pogonomyrmex salinus) nests within a sagebrush-steppe ecosystem. We sampled 105 harvester ant nests within southern Idaho, USA, that occurred in different habitats: annual grassland, perennial grassland, and native shrubland. The influence of Owyhee harvester ants on vegetation was larger at the edge of ant nests, but the relationship was inconsistent among plant species. Percent cover was positively associated with distance from harvester ant nests for plant species that were considered undesirable food sources and were densely distributed. However, percent cover was negatively associated with distance-from-nests for patchily distributed and desirable plant species. For some plant species, there was no change in cover associated with distance-from-nests. Total vegetation cover was associated with distance-from-nests in the shrubland habitat but not in the 2 grasslands. The dominant plant species in the shrubland habitat was a densely distributed shrub (winterfat, Krascheninnikovia lanata) that was defoliated by harvester ants. Our results suggest that Owyhee harvester ants increase spatial heterogeneity in plant communities through plant clearing, but the direction and magnitude of effect will likely be contingent on the dominant vegetation groups. This information may inform future management and plant restoration efforts in sagebrush-steppe by directly considering the islands of influence associated with harvester ant engineering.

Osprey: worldwide sentinel species for assessing and monitoring environmental contamination in rivers, lakes, reservoirs, and estuaries.

PubMed

Grove, Robert A; Henny, Charles J; Kaiser, James L

2009-01-01

In the United States, many fish and wildlife species have been used nationwide to monitor environmental contaminant exposure and effects, including carcasses of the bald eagle (Haliaeetus leucocephalus), the only top avian predator regularly used in the past. Unfortunately, bald eagles are sensitive to investigator intrusion at the nest. Thus, the osprey (Pandion haliaetus) is evaluated as a potential sentinel species for aquatic ecosystems. Several characteristics support the choice of the osprey as a sentinel species, including: (1) fish-eating diet atop the aquatic food web, (2) long-lived with strong nest fidelity, (3) adapts to human landscapes (potentially the most contaminated), (4) tolerates short-term nest disturbance, (5) nests spatially distributed at regular intervals, (6) highly visible nests easily located for study, (7) ability to accumulate most, if not all, lipophilic contaminants, (8) known sensitivity to many contaminants, and (9) nearly a worldwide distribution. These osprey traits have been instrumental in successfully using the species to understand population distribution, abundance, and changes over time; the effects of various contaminants on reproductive success; how contaminants in prey (fish on biomass basis) contribute to egg concentrations (i.e., biomagnification factors); and spatial residue patterns. Data summarized include nesting population surveys, detailed nesting studies, and chemical analyses of osprey egg, organ, blood, and feather samples for contaminants that bioaccumulate and/or biomagnify in aquatic food webs; and biochemical evaluations of blood and various organs. Studies in the United States, Canada, Mexico, Europe, and elsewhere have shown the osprey to be a useful sentinel species for monitoring selected environmental contaminants, including some emerging contaminants in lakes, reservoirs, rivers, and estuaries.

Metal concentrations, foraging distances, and fledging success of great blue herons nesting along the Hanford Reach of the Columbia River.

PubMed

Tiller, Brett L; Marco, J D; Rickard, W H

2005-05-01

An ecological risk assessment of the spatial distribution of metal concentrations along the Hanford Reach of the free-flowing Columbia River in southcentral Washington, identified great blue herons, Ardea herodias, at potential risk through the ingestion of contaminated riverine biota, especially fish. We measured metal concentrations in livers of pre-flight herons from the Hanford Reach and excrement samples taken from the same nests. Nests were distributed among three colonies situated upstream and downstream from nine retired plutonium production reactors along the river where metals in reactor coolant waters had been released directly into the river or disposed to shoreline retention basins and ditches. Distances traveled by parent herons to foraging areas along the river shore were determined by visually tracking parent birds as they flew from nests to upriver and downriver foraging sites. Foraging flight distances varied between colonies with mean distances ranging between 0.7 and 3.1 km. Cadmium, Cr, and Pb concentrations were higher in excrement than in the livers of pre-flight herons but the opposite was noted for Cu, Hg, and Zn. Highest metal concentrations of Cr, Cu, Zn, Cd, and Pb, were measured in excrement taken from heron nests at the colony located upstream from all reactors. These results were consistent with metal concentrations reported in river sediment from the same regions, indicating excrement from the heron nests may be a useful indicator of dietary uptake of metals by herons. Fledging success and eggshell thickness measurements were used as an index of health of the local heron population. The results indicate that the reproductive health of great blue herons nesting along the Hanford Reach is among the highest reported in the continental United States.

Belted kingfishers: Under surveillance and sampled in the privacy of their own burrow

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

Baron, L.A.; Ashwood, T.L.

The belted kingfisher, a common piscivore of the Oak Ridge Reservation (ORR), bioaccumulates contaminants from consumption of aquatic prey. Three kingfisher carcasses found near contaminated streams on the ORR were analyzed. Mercury, cadmium, and selenium bioaccumulated within the liver, kidney, and feathers. Additionally, PCB-1254 accumulated in muscle and lipid tissue, while Cesium-137 accumulated within the muscle and whole body. These contaminant levels have been shown to produce a variety of toxicological effects (i.e., reproductive impairment, central nervous system dysfunction) within other species of birds. In addition to use of this data for ecological risk assessment, kingfishers can also be monitoredmore » as a viable bioindicator species reflecting environmental contaminant levels over time. However, current sampling methods of burrow excavation or the use of mist nets can be detrimental to the reproductive success of the birds. The authors present a method for obtaining adequate samples of feathers and other remnants (i.e., egg shells, dried regurgitant) found in the burrow during or following the nesting season. The collection of samples following surveillance of the burrow and its contents was performed with the use of a 15 ft-long flexible, portable probe containing a video camera. Once sighted with the probe, contents of the burrow were collected by insertion of an additional tube attached to a hand held vacuum cleaner (Dirt Devil{reg_sign}). Feathers collected from a nest at an uncontaminated site contained selenium, lead and mercury. Cesium-137 was found in an egg shell collected from a nest at a radiologically contaminated site. Close-up photos of a kingfisher mother incubating her eggs and nestlings within two burrows will also be shown. This surveillance and sampling technique can also be used for monitoring other burrowing terrestrial species.« less

A survey of microbial community diversity in marine sediments impacted by petroleum hydrocarbons from the Gulf of Mexico and Atlantic shorelines, Texas to Florida

USGS Publications Warehouse

Lisle, John T.; Stellick, Sarah H.

2011-01-01

Microbial community genomic DNA was extracted from sediment samples collected along the Gulf of Mexico and Atlantic coasts from Texas to Florida. Sample sites were identified as being ecologically sensitive and (or) as having high potential of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon blowout. The diversity within the microbial communities associated with the collected sediments provides a baseline dataset to which microbial community-diversity data from impacted sites could be compared. To determine the microbial community diversity in the samples, genetic fingerprints were generated and compared. Specific sequences within the community genomic DNA were first amplified using the polymerase chain reaction (PCR) with a primer set that provides possible resolution to the species level. A second nested PCR was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. The nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Samples with similar fingerprints were grouped and compared to oil-fingerprint data from the same sites (Rosenbauer and others, 2011). The microbial community fingerprints were generally grouped into sites that had been shown to contain background concentrations of non-Deepwater Horizon oil. However, these groupings also included sites where no oil signature was detected. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the Gulf of Mexico and Atlantic coasts from Texas to Florida.

A Versatile High-Vacuum Cryo-transfer System for Cryo-microscopy and Analytics

PubMed Central

Tacke, Sebastian; Krzyzanek, Vladislav; Nüsse, Harald; Wepf, Roger Albert; Klingauf, Jürgen; Reichelt, Rudolf

2016-01-01

Cryogenic microscopy methods have gained increasing popularity, as they offer an unaltered view on the architecture of biological specimens. As a prerequisite, samples must be handled under cryogenic conditions below their recrystallization temperature, and contamination during sample transfer and handling must be prevented. We present a high-vacuum cryo-transfer system that streamlines the entire handling of frozen-hydrated samples from the vitrification process to low temperature imaging for scanning transmission electron microscopy and transmission electron microscopy. A template for cryo-electron microscopy and multimodal cryo-imaging approaches with numerous sample transfer steps is presented. PMID:26910419

Isotope analysis reveals foraging area dichotomy for atlantic leatherback turtles.

PubMed

Caut, Stéphane; Fossette, Sabrina; Guirlet, Elodie; Angulo, Elena; Das, Krishna; Girondot, Marc; Georges, Jean-Yves

2008-03-26

The leatherback turtle (Dermochelys coriacea) has undergone a dramatic decline over the last 25 years, and this is believed to be primarily the result of mortality associated with fisheries bycatch followed by egg and nesting female harvest. Atlantic leatherback turtles undertake long migrations across ocean basins from subtropical and tropical nesting beaches to productive frontal areas. Migration between two nesting seasons can last 2 or 3 years, a time period termed the remigration interval (RI). Recent satellite transmitter data revealed that Atlantic leatherbacks follow two major dispersion patterns after nesting season, through the North Gulf Stream area or more eastward across the North Equatorial Current. However, information on the whole RI is lacking, precluding the accurate identification of feeding areas where conservation measures may need to be applied. Using stable isotopes as dietary tracers we determined the characteristics of feeding grounds of leatherback females nesting in French Guiana. During migration, 3-year RI females differed from 2-year RI females in their isotope values, implying differences in their choice of feeding habitats (offshore vs. more coastal) and foraging latitude (North Atlantic vs. West African coasts, respectively). Egg-yolk and blood isotope values are correlated in nesting females, indicating that egg analysis is a useful tool for assessing isotope values in these turtles, including adults when not available. Our results complement previous data on turtle movements during the first year following the nesting season, integrating the diet consumed during the year before nesting. We suggest that the French Guiana leatherback population segregates into two distinct isotopic groupings, and highlight the urgent need to determine the feeding habitats of the turtle in the Atlantic in order to protect this species from incidental take by commercial fisheries. Our results also emphasize the use of eggs, a less-invasive sampling material than blood, to assess isotopic data and feeding habits for adult female leatherbacks.

Maternal health status correlates with nest success of leatherback sea turtles (Dermochelys coriacea) from Florida.

PubMed

Perrault, Justin R; Miller, Debra L; Eads, Erica; Johnson, Chris; Merrill, Anita; Thompson, Larry J; Wyneken, Jeanette

2012-01-01

Of the seven sea turtle species, the critically endangered leatherback sea turtle (Dermochelys coriacea) exhibits the lowest and most variable nest success (i.e., hatching success and emergence success) for reasons that remain largely unknown. In an attempt to identify or rule out causes of low reproductive success in this species, we established the largest sample size (n = 60-70 for most values) of baseline blood parameters (protein electrophoresis, hematology, plasma biochemistry) for this species to date. Hematologic, protein electrophoretic and biochemical values are important tools that can provide information regarding the physiological condition of an individual and population health as a whole. It has been proposed that the health of nesting individuals affects their reproductive output. In order to establish correlations with low reproductive success in leatherback sea turtles from Florida, we compared maternal health indices to hatching success and emergence success of their nests. As expected, hatching success (median = 57.4%) and emergence success (median = 49.1%) in Floridian leatherbacks were low during the study period (2007-2008 nesting seasons), a trend common in most nesting leatherback populations (average global hatching success = ∼50%). One protein electrophoretic value (gamma globulin protein) and one hematologic value (red blood cell count) significantly correlated with hatching success and emergence success. Several maternal biochemical parameters correlated with hatching success and/or emergence success including alkaline phosphatase activity, blood urea nitrogen, calcium, calcium:phosphorus ratio, carbon dioxide, cholesterol, creatinine, and phosphorus. Our results suggest that in leatherbacks, physiological parameters correlate with hatching success and emergence success of their nests. We conclude that long-term and comparative studies are needed to determine if certain individuals produce nests with lower hatching success and emergence success than others, and if those individuals with evidence of chronic suboptimal health have lower reproductive success.

Isotope Analysis Reveals Foraging Area Dichotomy for Atlantic Leatherback Turtles

PubMed Central

Angulo, Elena; Das, Krishna; Girondot, Marc

2008-01-01

Background The leatherback turtle (Dermochelys coriacea) has undergone a dramatic decline over the last 25 years, and this is believed to be primarily the result of mortality associated with fisheries bycatch followed by egg and nesting female harvest. Atlantic leatherback turtles undertake long migrations across ocean basins from subtropical and tropical nesting beaches to productive frontal areas. Migration between two nesting seasons can last 2 or 3 years, a time period termed the remigration interval (RI). Recent satellite transmitter data revealed that Atlantic leatherbacks follow two major dispersion patterns after nesting season, through the North Gulf Stream area or more eastward across the North Equatorial Current. However, information on the whole RI is lacking, precluding the accurate identification of feeding areas where conservation measures may need to be applied. Methodology/Principal Findings Using stable isotopes as dietary tracers we determined the characteristics of feeding grounds of leatherback females nesting in French Guiana. During migration, 3-year RI females differed from 2-year RI females in their isotope values, implying differences in their choice of feeding habitats (offshore vs. more coastal) and foraging latitude (North Atlantic vs. West African coasts, respectively). Egg-yolk and blood isotope values are correlated in nesting females, indicating that egg analysis is a useful tool for assessing isotope values in these turtles, including adults when not available. Conclusions/Significance Our results complement previous data on turtle movements during the first year following the nesting season, integrating the diet consumed during the year before nesting. We suggest that the French Guiana leatherback population segregates into two distinct isotopic groupings, and highlight the urgent need to determine the feeding habitats of the turtle in the Atlantic in order to protect this species from incidental take by commercial fisheries. Our results also emphasize the use of eggs, a less-invasive sampling material than blood, to assess isotopic data and feeding habits for adult female leatherbacks. PMID:18365003

Maternal Health Status Correlates with Nest Success of Leatherback Sea Turtles (Dermochelys coriacea) from Florida

PubMed Central

Perrault, Justin R.; Miller, Debra L.; Eads, Erica; Johnson, Chris; Merrill, Anita; Thompson, Larry J.; Wyneken, Jeanette

2012-01-01

Of the seven sea turtle species, the critically endangered leatherback sea turtle (Dermochelys coriacea) exhibits the lowest and most variable nest success (i.e., hatching success and emergence success) for reasons that remain largely unknown. In an attempt to identify or rule out causes of low reproductive success in this species, we established the largest sample size (n = 60–70 for most values) of baseline blood parameters (protein electrophoresis, hematology, plasma biochemistry) for this species to date. Hematologic, protein electrophoretic and biochemical values are important tools that can provide information regarding the physiological condition of an individual and population health as a whole. It has been proposed that the health of nesting individuals affects their reproductive output. In order to establish correlations with low reproductive success in leatherback sea turtles from Florida, we compared maternal health indices to hatching success and emergence success of their nests. As expected, hatching success (median = 57.4%) and emergence success (median = 49.1%) in Floridian leatherbacks were low during the study period (2007–2008 nesting seasons), a trend common in most nesting leatherback populations (average global hatching success = ∼50%). One protein electrophoretic value (gamma globulin protein) and one hematologic value (red blood cell count) significantly correlated with hatching success and emergence success. Several maternal biochemical parameters correlated with hatching success and/or emergence success including alkaline phosphatase activity, blood urea nitrogen, calcium, calcium∶phosphorus ratio, carbon dioxide, cholesterol, creatinine, and phosphorus. Our results suggest that in leatherbacks, physiological parameters correlate with hatching success and emergence success of their nests. We conclude that long-term and comparative studies are needed to determine if certain individuals produce nests with lower hatching success and emergence success than others, and if those individuals with evidence of chronic suboptimal health have lower reproductive success. PMID:22359635

Molecular characterization of Orientia tsutsugamushi serotypes causing scrub typhus outbreak in southern region of Andhra Pradesh, India.

PubMed

Usha, K; Kumar, E; Kalawat, Usha; Kumar, B Siddhartha; Chaudhury, A; Gopal, D V R Sai

2016-10-01

Scrub typhus is a vector-borne zoonotic infection caused by Orientiatsutsugamushi. Local epidemiology of the circulating serotypes of scrub typhus is not available from most parts of India. We conducted this study for the diagnosis of scrub typhus using IgM ELISA and to detect O. tsutsugamushi serotypes circulating in southern Andhra Pradesh, India. Samples were collected from patients clinically suspected to have scrub typhus and were subjected to IgM ELISA to measure IgM antibodies against O. tsutsugamushi. Nested polymerase chain reaction (PCR) was performed targeting strain-specific regions in ELISA-positive samples. Of a total of 663 samples, 258 (38.91%) were found to be positive by IgM ELISA. Serotypes could be detected in 230 (34.69%) samples only. Only two serotypes, Karp and Kawasaki, were found in the serum samples, with the former being predominant. The dual infection of Karp and Kawasaki serotypes was found in seven patients. Other serotypes such as Gilliam, Kuroki and Kato were not detected in the samples. The nested PCR products proved useful in presumptively identifying the endemic O. tsutsugamushi serotypes. The present study could be significant in understanding scrub typhus epidemiology in this region.

Mercury, cadmium, lead, and selenium in three waterbird species nesting in Galveston Bay, Texas, USA

USGS Publications Warehouse

King, K.A.; Cromartie, E.

1986-01-01

Heavy metal and selenium concentrations were determined in Olivaceous Cormorants (Phalacrocorax olivaceus ), Laughing gulls (Larus atricilla ), and Black Skimmers (Rynchops niger ) nesting in Galveston Bay, Texas, during 1980-81. Lead was detected at low levels in a small proportion of the liver samples. Mercury was present in all livers sampled, the highest levels being found in cormorants (7.8 ppm) and skimmers (16 ppm). Concentrations were considerably lower than those reported in birds from mercury-contaminated lakes in northern United States and Canada. Cadmium and selenium were detected in 93 and 95% of the kidneys. Cadmium was highest in gulls and skimmers with a maximum value of 16 ppm. Selenium levels were similar among species except for higher concentrations in gulls collected in 1981.

Antagonistic interactions between garden yeasts and microfungal garden pathogens of leaf-cutting ants.

PubMed

Rodrigues, Andre; Cable, Rachel N; Mueller, Ulrich G; Bacci, Maurício; Pagnocca, Fernando C

2009-10-01

We investigate the diversity of yeasts isolated in gardens of the leafcutter ant Atta texana. Repeated sampling of gardens from four nests over a 1-year time period showed that gardens contain a diverse assemblage of yeasts. The yeast community in gardens consisted mostly of yeasts associated with plants or soil, but community composition changed between sampling periods. In order to understand the potential disease-suppressing roles of the garden yeasts, we screened isolates for antagonistic effects against known microfungal garden contaminants. In vitro assays revealed that yeasts inhibited the mycelial growth of two strains of Escovopsis (a specialized attine garden parasite), Syncephalastrum racemosum (a fungus often growing in gardens of leafcutter lab nests), and the insect pathogen Beauveria bassiana. These garden yeasts add to the growing list of disease-suppressing microbes in attine nests that may contribute synergistically, together with actinomycetes and Burkholderia bacteria, to protect the gardens and the ants against diseases. Additionally, we suggest that garden immunity against problem fungi may therefore derive not only from the presence of disease-suppressing Pseudonocardia actinomycetes, but from an enrichment of multiple disease-suppressing microorganisms in the garden matrix.

Genetic variability in captive populations of the stingless bee Tetragonisca angustula.

PubMed

Santiago, Leandro R; Francisco, Flávio O; Jaffé, Rodolfo; Arias, Maria C

2016-08-01

Low genetic variability has normally been considered a consequence of animal husbandry and a major contributing factor to declining bee populations. Here, we performed a molecular analysis of captive and wild populations of the stingless bee Tetragonisca angustula, one of the most commonly kept species across South America. Microsatellite analyses showed similar genetic variability between wild and captive populations However, captive populations showed lower mitochondrial genetic variability. Male-mediated gene flow, transport and division of nests are suggested as the most probable explanations for the observed patterns of genetic structure. We conclude that increasing the number of colonies kept through nest divisions does not negatively affect nuclear genetic variability, which seems to be maintained by small-scale male dispersal and human-mediated nest transport. However, the transport of nests from distant localities should be practiced with caution given the high genetic differentiation observed between samples from western and eastern areas. The high genetic structure verified is the result of a long-term evolutionary process, and bees from distant localities may represent unique evolutionary lineages.

PCDDs, PCDFs, PCBs, OC pesticides and mercury in fish and osprey eggs from Willamette River, Oregon (1993, 2001 and 2006) with calculated biomagnification factors

USGS Publications Warehouse

Henny, C.J.; Kaiser, J.L.; Grove, R.A.

2009-01-01

The osprey (Pandion haliaetus) population nesting along the main stem Willamette River and lower Santiam River was first studied to evaluate contaminants and reproductive rates in 1993 when 78 occupied nests were present. By 2001, the population increased to 234 occupied nests, a 13.7% annual rate of population increase. A sample egg was collected from each of a series of nests along the Upper River (river mile 55-187) in 1993, 2001 and 2006 to evaluate trends of persistent contaminants (organochlorine [OC] pesticides, polychlorinated biphenyls [PCBs], polychlorinated dibenzo-p-dioxins [PCDDs], and polychlorinated dibenzofurans [PCDFs]). Nearly all OC pesticide residues decreased significantly, e.g., p, p?-DDE (DDE) from 2,350 to 1,353 to 210 ??g/kg wet weight (ww). PCBs followed a similar pattern over time, e.g., ???PCBs 688 to 245 to 182 ??g/kg ww, while PCDDs and PCDFs showed a more precipitous decline (often 85-95%) between 1993 and 2001, with no egg analyses warranted in 2006. During 2001-2002, sample osprey eggs were also collected from nests at three Headwater Reservoirs and two lower reaches (Newberg Pool and Tidal Portland) of the Willamette River, as well as the lower portion of the Santiam River to evaluate spatial residue patterns. Significant differences were seldom detected among the different sampling areas for OC pesticides (probably due to small sample sizes), although higher concentrations were often seen in the lower reaches, e.g., DDE 901 ??g/kg ww (Headwater Reservoirs), 1,353 (Upper River), 1,384 (Newberg Pool) and 2,676 (Tidal Portland). PCB congener concentrations in eggs were usually higher in the Tidal Portland reach than at other locations and often significantly higher than at the Headwater Reservoirs or Upper River. Mercury (first analyzed in eggs in 2001), PCDDs and PCDFs were extremely low in 2001/2002 with no significant spatial patterns. Whole fish composite samples of largescale sucker (Catastomus macrocheilus) and northern pikeminnow (Ptychocheilus oregonensis), which account for about 90% of the biomass in the diet of this osprey population, were also collected from the Willamette River in 1993 and 2001 and analyzed for the same contaminants as osprey eggs. Contaminant residues in fish from the Upper River decreased between 1993 and 2001, paralleling findings for osprey eggs. Likewise, spatial patterns for fish residues paralleled findings for osprey eggs from the different reaches in 2001. A second empirical estimate of biomagnification factors (BMFs) from fish to osprey eggs for OC pesticides, PCBs, PCDDs and PCDFs (ww and lipid weight [lw] basis) was calculated based on residue data collected in 2001. The two independent BMF estimates (1993 and 2001) for each contaminant from the Upper River provide a measure of consistency, e.g., DDE (ww) 87 and 79, (lw) 103 and 112; ???PCBs (ww) 11 and 8.4, (lw) 13 and 12. Mercury did not biomagnify from fish to osprey eggs (BMF = 0.60). Legacy contaminants investigated had limited (perhaps only DDE), if any, effects on reproductive success of the increasing osprey population nesting along the Willamette River by 2001. ?? 2008 U.S. Government.

Comparison of Virginia's multimodal transportation corridors using cost and demographic analyses.

DOT National Transportation Integrated Search

2006-01-01

This effort was performed in support of VTrans2025, Virginia's long-range multimodal transportation plan, and the VTrans2025 Multimodal Advisory Committee. The effort develops a preliminary approach to evaluating multimodal and highway-only corridor ...

Dynamical Casimir Effect for Gaussian Boson Sampling.

PubMed

Peropadre, Borja; Huh, Joonsuk; Sabín, Carlos

2018-02-28

We show that the Dynamical Casimir Effect (DCE), realized on two multimode coplanar waveg-uide resonators, implements a gaussian boson sampler (GBS). The appropriate choice of the mirror acceleration that couples both resonators translates into the desired initial gaussian state and many-boson interference in a boson sampling network. In particular, we show that the proposed quantum simulator naturally performs a classically hard task, known as scattershot boson sampling. Our result unveils an unprecedented computational power of DCE, and paves the way for using DCE as a resource for quantum simulation.

Bloodmeal Host Congregation and Landscape Structure Impact the Estimation of Female Mosquito (Diptera: Culicidae) Abundance Using Dry Ice-Baited Traps

PubMed Central

THIEMANN, TARA; NELMS, BRITTANY; REISEN, WILLIAM K.

2011-01-01

Vegetation patterns and the presence of large numbers of nesting herons and egrets significantly altered the number of host-seeking Culex tarsalis Coquillett (Diptera: Culicidae) collected at dry ice-baited traps. The numbers of females collected per trap night at traps along the ecotone of Eucalyptus stands with and without a heron colony were always greater or equal to numbers collected at traps within or under canopy. No Cx. tarsalis were collected within or under Eucaplytus canopy during the peak heron nesting season, even though these birds frequently were infected with West Nile virus and large number of engorged females could be collected at resting boxes. These data indicate a diversion of host-seeking females from traps to nesting birds reducing sampling efficiency. PMID:21661310