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Sample records for nested reverse transcription-pcr

  1. Detection of dengue virus RNA in blood clots by multiplex nested reverse transcription-PCR%多重套式RT-PCR检测患者凝血块中登革病毒RNA

    Institute of Scientific and Technical Information of China (English)

    张拥军; 黄萌; 翁育伟; 郑友限; 王金章

    2012-01-01

    目的 建立简便、灵敏、适合于全部血清型登革病毒核酸检测的多重套式RT- PCR体系,检测临床样品中登革病毒RNA,作为实验室辅助诊断的依据.方法 利用登革病毒标准株核酸,建立多重RT- PCR检测方法.提取患者凝血块总RNA,分别用一步法RT- PCR及多重套式RT PCR检测.结果 通过对检测体系进行优化,多重RT- PCR能够同时检测4种血清型登革病毒核酸.采用多重套式RT- PCR方法,从8例登革热患者凝血块中有4例检测到病毒RNA,而其它核酸检测方法仅检出1例阳性.结论 多重套式RT-PCR的方法能够从临床凝血块样品中检测到登革病毒核酸,并同时进行血清学分型,简化了登革病毒核酸检测步骤,有利于对临床样品开展病毒核酸检测.%Dengue is the most common vector borne viral disease of humans globally.Detection of viral RNA from suspected patient specimens is rapid,specific and confirmative in laboratory diagnosis of dengue infections during the acute phase.In this study,a multiplex nested reverse transcription PCR (RT-PCR) system was established for clinical specimens.While other nucleic acid amplification tests showed relatively low sensitivity,the multiplex nested RT PCR assay detected 4 cases among blood clots from 8 serologically confirmed dengue patients.These results suggested that blood clots of dengue patients could be used in laboratory diagnosis,and that the multiplex nested RT PCR assay,which simplified the detection procedure,could facilitate viral RNA detection of specimens in clinical laboratories.

  2. Single-Reaction Multiplex Reverse Transcription PCR for Detection of Zika, Chikungunya, and Dengue Viruses.

    Science.gov (United States)

    Waggoner, Jesse J; Gresh, Lionel; Mohamed-Hadley, Alisha; Ballesteros, Gabriela; Davila, Maria Jose Vargas; Tellez, Yolanda; Sahoo, Malaya K; Balmaseda, Angel; Harris, Eva; Pinsky, Benjamin A

    2016-07-01

    Clinical manifestations of Zika virus, chikungunya virus, and dengue virus infections can be similar. To improve virus detection, streamline molecular workflow, and decrease test costs, we developed and evaluated a multiplex real-time reverse transcription PCR for these viruses.

  3. Single-Reaction Multiplex Reverse Transcription PCR for Detection of Zika, Chikungunya, and Dengue Viruses

    OpenAIRE

    Waggoner, Jesse J.; Gresh, Lionel; Mohamed-Hadley, Alisha; Ballesteros, Gabriela; Davila, Maria Jose Vargas; Tellez, Yolanda; Sahoo, Malaya K.; Balmaseda, Angel; Harris, Eva; Pinsky, Benjamin A.

    2016-01-01

    Clinical manifestations of Zika virus, chikungunya virus, and dengue virus infections can be similar. To improve virus detection, streamline molecular workflow, and decrease test costs, we developed and evaluated a multiplex real-time reverse transcription PCR for these viruses.

  4. Detection of Babesia microti parasites by highly sensitive 18S rRNA reverse transcription PCR.

    Science.gov (United States)

    Hanron, Amelia E; Billman, Zachary P; Seilie, Annette M; Chang, Ming; Murphy, Sean C

    2017-03-01

    Babesia are increasingly appreciated as a cause of transfusion-transmitted infection. Sensitive methods are needed to screen blood products. We report herein that B. microti 18S rRNA is over 1,000-fold more abundant than its coding genes, making reverse transcription PCR (RT-PCR) much more sensitive than PCR. Babesia 18S rRNA may be useful for screening the blood supply.

  5. Detection of All Species of the Genus Alphavirus by Reverse Transcription-PCR with Diagnostic Sensitivity▿

    OpenAIRE

    Grywna, K.; Kupfer, B.; Panning, M.; Drexler, J. F.; Emmerich, P.; Drosten, C.; Kummerer, B. M.

    2010-01-01

    Clinical arbovirus screening requires exclusion of a broad range of viruses with as few assays as possible. We present a reverse transcription-PCR (RT-PCR) for the detection of all species of the genus Alphavirus qualified for exclusion screening (limit of detection [LOD], 5 to 100 RNA copies per reaction across all Alphavirus species; detection of viremia down to ca. 10,000 copies per ml).

  6. Reverse Transcription-PCR Analysis of the Regulation of the Manganese Peroxidase Gene Family

    OpenAIRE

    Gettemy, Jessica M.; Ma, Biao; Alic, Margaret; Gold, Michael H.

    1998-01-01

    Manganese peroxidase (MnP) gene expression in the lignin-degrading fungus Phanerochaete chrysosporium is regulated by nutrient nitrogen levels and by Mn(II), the substrate for the enzyme, as well as by heat shock and other factors. Reverse transcription-PCR (RT-PCR) of total RNA can distinguish the mRNAs of each of the three sequenced P. chrysosporium mnp genes, i.e., mnp1, mnp2, and mnp3. Quantitative RT-PCR demonstrates that each of the three transcripts is present at a similar low basal le...

  7. Application of anti-listerial bacteriocins: monitoring enterocin expression by multiplex relative reverse transcription-PCR.

    Science.gov (United States)

    Williams, D Ross; Chanos, Panagiotis

    2012-12-01

    Listeriosis is a deadly food-borne disease, and its incidence may be limited through the biotechnological exploitation of a number of anti-listerial biocontrol agents. The most widely used of these agents are bacteriocins and the Class II enterocins are characterized by their activity against Listeria. Enterocins are primarily produced by enterococci, particularly Enterococcus faecium and many strains have been described, often encoding multiple bacteriocins. The use of these strains in food will require that they are free of virulence functions and that they exhibit a high level expression of anti-listerial enterocins in fermentation conditions. Multiplex relative RT (reverse transcription)-PCR is a technique that is useful in the discovery of advantageous expression characteristics among enterocin-producing strains. It allows the levels of individual enterocin gene expression to be monitored and determination of how expression is altered under different growth conditions.

  8. How Many Microorganisms Are Present? Quantitative Reverse Transcription PCR (qRT-PCR)

    Science.gov (United States)

    Price, Andy; Álvarez, Laura Acuña; Whitby, Corinne; Larsen, Jan

    Quantitative reverse transcription PCR (qRT-PCR) is a variation of conventional quantitative or real-time PCR, whereby mRNA is first converted into the complementary DNA (cDNA) by reverse transcription, the cDNA is then subsequently quantified by qPCR. The use of mRNA as the initial template allows the quantification of gene transcripts, rather than gene copy numbers. mRNA is only produced by actively metabolising cells and is produced by its corresponding gene to provide a 'blueprint' in order for a cell to manufacture a specific protein. Conventional qPCR detects not only DNA present in actively metabolising cells but also inactive and dead cells. qRT-PCR has the advantage that only actively metabolising cells are detected, hence provides a more reliable measure of microbial activity in oilfield samples. When qRT-PCR is combined with primers and probes for specific genes, the activity of microbial processes important in the oilfield, such as sulphate reduction, methanogenesis and nitrate reduction can be monitored.

  9. Detection of Zika Virus in Desiccated Mosquitoes by Real-Time Reverse Transcription PCR and Plaque Assay

    Science.gov (United States)

    Savage, Harry M.

    2017-01-01

    We assayed Zika virus–infected mosquitoes stored at room temperature for <30 days for live virus by using plaque assay and virus RNA by using real-time reverse transcription PCR. Viable virus was detected in samples stored <10 days, and virus RNA was detected in samples held for 30 days. PMID:28075325

  10. Standardized positive controls for detection of norovirus by reverse transcription PCR

    Directory of Open Access Journals (Sweden)

    Oh SeHwan

    2011-05-01

    Full Text Available Abstract Background Norovirus is one of the most common causes of nonbacterial gastroenteritis in humans. Rapid spread by contaminated food and person-to-person transmission through the fecal-oral route are characteristics of norovirus epidemiology and result in high morbidity in vulnerable patient populations. Therefore, detection of norovirus is a major public health concern. Currently, the most common method for detecting and differentiating among norovirus strains in clinical and environmental samples is reverse transcription PCR (RT-PCR. Standardized positive controls used in RT-PCR assays to detect norovirus are designed to overcome the problem of false-negative results due to PCR inhibitors and suboptimal reaction conditions. Results In the current study, four types of RNA transcripts were produced from plasmids: norovirus GI-5 and GII-4 capsid regions with human rotavirus (VP7 gene derived fragment insertions, and norovirus GI-6 and GII-4 capsid regions with hepatitis A virus (VP1/P2A gene derived fragment insertions. These size-distinguishable products were used as positive controls under the RT-PCR assay conditions used to detect NoV in stool and groundwater samples. Their reliability and reproducibility was confirmed by multiple sets of experiments. Conclusions These standardized products may contribute to the reliable and accurate diagnosis by RT-PCR of norovirus outbreaks, when conducted by laboratories located in different regions.

  11. Critical analysis of rhinovirus RNA load quantification by real-time reverse transcription-PCR.

    Science.gov (United States)

    Schibler, Manuel; Yerly, Sabine; Vieille, Gaël; Docquier, Mylène; Turin, Lara; Kaiser, Laurent; Tapparel, Caroline

    2012-09-01

    Rhinoviruses are the most frequent cause of human respiratory infections, and quantitative rhinovirus diagnostic tools are needed for clinical investigations. Although results obtained by real-time reverse-transcription PCR (RT-PCR) assays are frequently converted to viral RNA loads, this presents several limitations regarding accurate virus RNA quantification, particularly given the need to reliably quantify all known rhinovirus genotypes with a single assay. Using an internal extraction control and serial dilutions of an in vitro-transcribed rhinovirus RNA reference standard, we validated a quantitative one-step real-time PCR assay. We then used chimeric rhinovirus genomes with 5'-untranslated regions (5'UTRs) originating from the three rhinovirus species and from one enterovirus to estimate the impact of the 5'UTR diversity. Respiratory specimens from infected patients were then also analyzed. The assay quantification ability ranged from 4.10 to 9.10 log RNA copies/ml, with an estimated error margin of ±10%. This variation was mainly linked to target variability and interassay variability. Taken together, our results indicate that our assay can reliably estimate rhinovirus RNA load, provided that the appropriate error margin is used. In contrast, due to the lack of a universal rhinovirus RNA standard and the variability related to sample collection procedures, accurate absolute rhinovirus RNA quantification in respiratory specimens is currently hardly feasible.

  12. VP4 and VP7 genotyping by reverse transcription-PCR of human rotavirus in mexican children with acute diarrhea.

    Science.gov (United States)

    Rodríguez Castillo, A; Villa, A V; Ramírez González, J E; Mayén Pimentel, E; Melo Munguía, M; Díaz De Jesús, B; Olivera Díaz, H; García Lozano, H

    2000-10-01

    Dual typing (VP4 and VP7) of rotavirus obtained from 257 Mexican children during three epidemiological seasons was performed by reverse transcription-PCR. The P1G1 genotype was the most prevalent (40%), followed by P1G3 (19%) and P2G2 (16%). Thirty-one specimens (12%) presented mixed infections, while some genotypes were not found. This is the first dual typing of isolates from diarrhea cases in Mexico.

  13. Development and Validation of a Multiplex Reverse Transcription PCR Assay for Simultaneous Detection of Three Papaya Viruses

    OpenAIRE

    Tuo, Decai; Shen, Wentao; Yang, Yong; Yan, Pu; Li, Xiaoying; Zhou, Peng

    2014-01-01

    Papaya ringspot virus (PRSV), Papaya leaf distortion mosaic virus (PLDMV), and Papaya mosaic virus (PapMV) produce similar symptoms in papaya. Each threatens commercial production of papaya on Hainan Island, China. In this study, a multiplex reverse transcription PCR assay was developed to detect simultaneously these three viruses by screening combinations of mixed primer pairs and optimizing the multiplex RT-PCR reaction conditions. A mixture of three specific primer pairs was used to amplif...

  14. On-chip single-copy real-time reverse-transcription PCR in isolated picoliter droplets

    Energy Technology Data Exchange (ETDEWEB)

    Beer, N R; Wheeler, E; Lee-Houghton, L; Watkins, N; Nasarabadi, S; Hebert, N; Leung, P; Arnold, D; Bailey, C; Colston, B

    2007-12-19

    The first lab-on-chip system for picoliter droplet generation and RNA isolation, followed by reverse transcription, and PCR amplification with real-time fluorescence detection in the trapped droplets has been developed. The system utilized a shearing T-junction in a fused silica device to generate a stream of monodisperse picoliter-scale droplets that were isolated from the microfluidic channel walls and each other by the oil phase carrier. An off-chip valving system stopped the droplets on-chip, allowing thermal cycling for reverse transcription and subsequent PCR amplification without droplet motion. This combination of the established real-time reverse transcription-PCR assay with digital microfluidics is ideal for isolating single-copy RNA and virions from a complex environment, and will be useful in viral discovery and gene-profiling applications.

  15. Application of Reverse Transcription-PCR and Real-Time PCR in Nanotoxicity Research

    Science.gov (United States)

    Mo, Yiqun; Wan, Rong; Zhang, Qunwei

    2016-01-01

    Reverse transcription-polymerase chain reaction (RT-PCR) is a relatively simple and inexpensive technique to determine the expression level of target genes and is widely used in biomedical science research including nanotoxicology studies for semiquantitative analysis. Real-time PCR allows for the detection of PCR amplification in the exponential growth phase of the reaction and is much more quantitative than traditional RT-PCR. Although a number of kits and reagents for RT-PCR and real-time PCR are commercially available, the basic principles are the same. Here, we describe the procedures for total RNA isolation by using TRI Reagent, for reverse transcription (RT) by M-MLV reverse transcriptase, and for PCR by GoTaq® DNA Polymerase. And real-time PCR will be performed on an iQ5 multicolor real-time PCR detection system by using iQ™ SYBR Green Supermix. PMID:22975959

  16. Detection of Human Picornaviruses by Multiplex Reverse Transcription-PCR and Liquid Hybridization

    OpenAIRE

    Jokela, Pia; Joki-Korpela, Päivi; Maaronen, Marita; Glumoff, Virpi; Hyypiä, Timo

    2005-01-01

    A qualitative multiplex reverse transcription (RT)-PCR and liquid hybridization assay for the detection of human enteroviruses, rhinoviruses, parechoviruses, and Aichi virus was developed. Furthermore, a separate assay for the recognition of hepatitis A virus was established to complement the test pattern so that all human picornaviruses were covered. The amplicons, which represented the 5′ untranslated regions of the viral RNA genomes, were identified in liquid hybridization reactions with g...

  17. Development of a neutralization assay for influenza virus using an endpoint assessment based on quantitative reverse-transcription PCR.

    Directory of Open Access Journals (Sweden)

    Belete Teferedegne

    Full Text Available A microneutralization assay using an ELISA-based endpoint assessment (ELISA-MN is widely used to measure the serological response to influenza virus infection and vaccination. We have developed an alternative microneutralization assay for influenza virus using a quantitative reverse transcription PCR-based endpoint assessment (qPCR-MN in order to improve upon technical limitations associated with ELISA-MN. For qPCR-MN, infected MDCK-London cells in 96-well cell-culture plates are processed with minimal steps such that resulting samples are amenable to high-throughput analysis by downstream one-step quantitative reverse transcription PCR (qRT-PCR; SYBR Green chemistry with primers targeting a conserved region of the M1 gene of influenza A viruses. The growth curves of three recent vaccine strains demonstrated that the qRT-PCR signal detected at 6 hours post-infection reflected an amplification of at least 100-fold over input. Using ferret antisera, we have established the feasibility of measuring virus neutralization at 6 hours post-infection, a duration likely confined to a single virus-replication cycle. The neutralization titer for qPCR-MN was defined as the highest reciprocal serum dilution necessary to achieve a 90% inhibition of the qRT-PCR signal; this endpoint was found to be in agreement with ELISA-MN using the same critical reagents in each assay. qPCR-MN was robust with respect to assay duration (6 hours vs. 12 hours. In addition, qPCR-MN appeared to be compliant with the Percentage Law (i.e., virus neutralization results appear to be consistent over an input virus dose ranging from 500 to 12,000 TCID(50. Compared with ELISA-MN, qPCR-MN might have inherent properties conducive to reducing intra- and inter-laboratory variability while affording suitability for automation and high-throughput uses. Finally, our qRT-PCR-based approach may be broadly applicable to the development of neutralization assays for a wide variety of viruses.

  18. Multiplex, Quantitative, Reverse Transcription PCR Detection of Influenza Viruses Using Droplet Microfluidic Technology

    Directory of Open Access Journals (Sweden)

    Ravi Prakash

    2014-12-01

    Full Text Available Quantitative, reverse transcription, polymerase chain reaction (qRT-PCR is facilitated by leveraging droplet microfluidic (DMF system, which due to its precision dispensing and sample handling capabilities at microliter and lower volumes has emerged as a popular method for miniaturization of the PCR platform. This work substantially improves and extends the functional capabilities of our previously demonstrated single qRT-PCR micro-chip, which utilized a combination of electrostatic and electrowetting droplet actuation. In the reported work we illustrate a spatially multiplexed micro-device that is capable of conducting up to eight parallel, real-time PCR reactions per usage, with adjustable control on the PCR thermal cycling parameters (both process time and temperature set-points. This micro-device has been utilized to detect and quantify the presence of two clinically relevant respiratory viruses, Influenza A and Influenza B, in human samples (nasopharyngeal swabs, throat swabs. The device performed accurate detection and quantification of the two respiratory viruses, over several orders of RNA copy counts, in unknown (blind panels of extracted patient samples with acceptably high PCR efficiency (>94%. The multi-stage qRT-PCR assays on eight panel patient samples were accomplished within 35–40 min, with a detection limit for the target Influenza virus RNAs estimated to be less than 10 RNA copies per reaction.

  19. Design and Assessment of a Real Time Reverse Transcription-PCR Method to Genotype Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae).

    Science.gov (United States)

    A real-time, reverse transcription-PCR (RT-qPCR) assay was developed to differentiate the four genogroups of male-specific ssRNA coliphages (FRNA) (family Leviviridae). As FRNA display a trend of source-specificity (human sewage or animal waste) at the genogroup level, this assa...

  20. Development of a multiplex reverse transcription-PCR assay for simultaneous detection of garlic viruses

    Institute of Scientific and Technical Information of China (English)

    HU Xin-xi; LEI Yan; WANG Pei; TANG Lin-fei; HE Chang-zheng; SONG Yong; XIONG Xing-yao; NIE Xian-zhou

    2015-01-01

    A preliminary screening for garlic viruses in garlic plants in Hunan, China, using existing monoplex (simplex) reverse tran-scription-polymerase chain reaction (RT-PCR) procedures detected four viruses/virus groups. These viruses/virus groups were Onion yel ow dwarf virus (OYDV), Leek yel ow stripe virus (LYSV), Shal ot latent virus (SLV) and al exiviruses (e.g., garlic viruses A, B, C, D, E, X). Sequence analysis of the projected al exivirus amplicons revealed the al exivirus in the infected garlic plants was Garlic virus D (GarV-D), which shared 92–97%sequence identities with various isolates from the world. A multiplex RT-PCR (mRT-PCR) was therefore developed to simultaneously detect and differentiate the four viruses/virus groups. To achieve this, four primer pairs targeting al exiviruses, OYDV, LYSV and SLV were designed. The anticipated amplicon sizes are 183 bp (al exiviruses), 265 bp (OYDV), 404 bp (LYSV) and 592 bp (SLV), respectively. Al primer pairs produced virus-speciifc fragments in both simplex and multiplex formats, thus conifrming the efifcacy of the newly developed mRT-PCR for detection of these viruses. The mRT-PCR further was evaluated by applying it to garlic plant samples col ected in two geographic locations in Hunan. Al exiviruses, OYDV, LYSV and SLV were detected in 50.9, 40.3, 28.3 and 58.5%of leaf samples, respectively;and mixed infections with two or more viruses accounted for 54%of the garlic samples. The results obtained by mRT-PCR were conifrmed by simplex RT-PCR assays. In conclusion, this newly devel-oped mRT-PCR provides a rapid, sensitive and reliable method for the detection and identiifcation of major garlic viruses.

  1. Evaluation of Altona Diagnostics RealStar Zika Virus Reverse Transcription-PCR Test Kit for Zika Virus PCR Testing.

    Science.gov (United States)

    L'Huillier, Arnaud G; Lombos, Ernesto; Tang, Elaine; Perusini, Stephen; Eshaghi, Alireza; Nagra, Sandeep; Frantz, Christine; Olsha, Romy; Kristjanson, Erik; Dimitrova, Kristina; Safronetz, David; Drebot, Mike; Gubbay, Jonathan B

    2017-05-01

    With the emerging Zika virus (ZIKV) epidemic, accessible real-time reverse transcription-PCR (rRT-PCR) assays are needed to streamline testing. The commercial Altona Diagnostics RealStar ZIKV rRT-PCR test kit (Altona PCR) has been approved for emergency use authorization by the U.S. FDA. Our aim was to verify the Altona PCR by comparing it to the CDC-designed dual-target ZIKV rRT-PCR reference assay (reference PCR) and describe the demographics of patients tested for ZIKV by rRT-PCR in Ontario, Canada. A large set of clinical specimens was tested for ZIKV by the Altona PCR and the reference PCR. Positive or equivocal specimens underwent PCR and Sanger sequencing targeting the ZIKV NS5 gene. A total of 671 serum specimens were tested by the reference PCR: 58 (8.6%) were positive, 193 (28.8%) were equivocal, and 420 (62.6%) were negative. Ninety percent of the reference PCR-positive patients were tested in the first 5 days after symptom onset. The Altona PCR was performed on 284/671 specimens tested by the reference PCR. The Altona PCR was positive for 53/58 (91%) reference PCR-positive specimens and 16/193 (8%) reference PCR-equivocal specimens; the ZIKV NS5 PCR was positive for all 68 Altona PCR-positive specimens and negative for all 181 Altona PCR-negative specimens that underwent the NS5 PCR. The Altona PCR has very good sensitivity (91%) and specificity (97%) compared to the reference PCR. The Altona PCR can be used for ZIKV diagnostic testing and has less extensive verification requirements than a laboratory-developed test. Copyright © 2017 American Society for Microbiology.

  2. Development and validation of a multiplex reverse transcription PCR assay for simultaneous detection of three papaya viruses.

    Science.gov (United States)

    Tuo, Decai; Shen, Wentao; Yang, Yong; Yan, Pu; Li, Xiaoying; Zhou, Peng

    2014-10-21

    Papaya ringspot virus (PRSV), Papaya leaf distortion mosaic virus (PLDMV), and Papaya mosaic virus (PapMV) produce similar symptoms in papaya. Each threatens commercial production of papaya on Hainan Island, China. In this study, a multiplex reverse transcription PCR assay was developed to detect simultaneously these three viruses by screening combinations of mixed primer pairs and optimizing the multiplex RT-PCR reaction conditions. A mixture of three specific primer pairs was used to amplify three distinct fragments of 613 bp from the P3 gene of PRSV, 355 bp from the CP gene of PLDMV, and 205 bp from the CP gene of PapMV, demonstrating the assay's specificity. The sensitivity of the multiplex RT-PCR was evaluated by showing plasmids containing each of the viral target genes with 1.44 × 103, 1.79 × 103, and 1.91 × 102 copies for the three viruses could be detected successfully. The multiplex RT-PCR was applied successfully for detection of three viruses from 341 field samples collected from 18 counties of Hainan Island, China. Rates of single infections were 186/341 (54.5%), 93/341 (27.3%), and 3/341 (0.9%), for PRSV, PLDMV, and PapMV, respectively; 59/341 (17.3%) of the samples were co-infected with PRSV and PLDMV, which is the first time being reported in Hainan Island. This multiplex RT-PCR assay is a simple, rapid, sensitive, and cost-effective method for detecting multiple viruses in papaya and can be used for routine molecular diagnosis and epidemiological studies in papaya.

  3. Development and Validation of a Multiplex Reverse Transcription PCR Assay for Simultaneous Detection of Three Papaya Viruses

    Directory of Open Access Journals (Sweden)

    Decai Tuo

    2014-10-01

    Full Text Available Papaya ringspot virus (PRSV, Papaya leaf distortion mosaic virus (PLDMV, and Papaya mosaic virus (PapMV produce similar symptoms in papaya. Each threatens commercial production of papaya on Hainan Island, China. In this study, a multiplex reverse transcription PCR assay was developed to detect simultaneously these three viruses by screening combinations of mixed primer pairs and optimizing the multiplex RT-PCR reaction conditions. A mixture of three specific primer pairs was used to amplify three distinct fragments of 613 bp from the P3 gene of PRSV, 355 bp from the CP gene of PLDMV, and 205 bp from the CP gene of PapMV, demonstrating the assay’s specificity. The sensitivity of the multiplex RT-PCR was evaluated by showing plasmids containing each of the viral target genes with 1.44 × 103, 1.79 × 103, and 1.91 × 102 copies for the three viruses could be detected successfully. The multiplex RT-PCR was applied successfully for detection of three viruses from 341 field samples collected from 18 counties of Hainan Island, China. Rates of single infections were 186/341 (54.5%, 93/341 (27.3%, and 3/341 (0.9%, for PRSV, PLDMV, and PapMV, respectively; 59/341 (17.3% of the samples were co-infected with PRSV and PLDMV, which is the first time being reported in Hainan Island. This multiplex RT-PCR assay is a simple, rapid, sensitive, and cost-effective method for detecting multiple viruses in papaya and can be used for routine molecular diagnosis and epidemiological studies in papaya.

  4. Utility of IgM ELISA, TaqMan real-time PCR, reverse transcription PCR, and RT-LAMP assay for the diagnosis of Chikungunya fever.

    Science.gov (United States)

    Reddy, Vijayalakshmi; Ravi, Vasanthapuram; Desai, Anita; Parida, Manmohan; Powers, Ann M; Johnson, Barbara W

    2012-11-01

    Chikungunya fever a re-emerging infection with expanding geographical boundaries, can mimic symptoms of other infections like dengue, malaria which makes the definitive diagnosis of the infection important. The present study compares the utility of four laboratory diagnostic methods viz. IgM capture ELISA, an in house reverse transcription PCR for the diagnosis of Chikungunya fever, TaqMan real-time PCR, and a one step reverse transcription-loop mediated isothermal amplification assay (RT-LAMP). Out of the 70 serum samples tested, 29 (41%) were positive for Chikungunya IgM antibody by ELISA and 50 (71%) samples were positive by one of the three molecular assays. CHIKV specific nucleic acid was detected in 33/70 (47%) by reverse transcription PCR, 46/70 (66%) by TaqMan real-time PCR, and 43/70 (62%) by RT-LAMP assay. A majority of the samples (62/70; 89%) were positive by at least one of the four assays used in the study. The molecular assays were more sensitive for diagnosis in the early stages of illness (2-5 days post onset) when antibodies were not detectable. In the later stages of illness, the IgM ELISA is a more sensitive diagnostic test. In conclusion we recommend that the IgM ELISA be used as an initial screening test followed one of the molecular assays in samples that are collected in the early phase of illness and negative for CHIKV IgM antibodies. Such as approach would enable rapid confirmation of the diagnosis and implementation of public health measures especially during outbreaks. Copyright © 2012 Wiley Periodicals, Inc.

  5. Detection of norovirus, sapovirus, and human astrovirus in fecal specimens using a multiplex reverse transcription-PCR with fluorescent dye-labeled primers.

    Science.gov (United States)

    Shigemoto, Naoki; Fukuda, Shinji; Tanizawa, Yukie; Kuwayama, Masaru; Ohara, Sachiko; Seno, Masato

    2011-05-01

    We applied a multiplex reverse transcription-PCR with fluorescent dye-labeled primers (fluorescent multiplex RT-PCR) for noroviruses (NoV), sapovirus (SaV), and human astrovirus (HAstV) to diagnose 71 outbreaks of acute gastroenteritis during July 2007 and May 2010 in Hiroshima prefecture. In this assay, the green, red, yellow, and blue fluorescence for NoV genogroup I, NoV genogroup II, SaV, and HAstV, respectively, were indicated on an agarose gel under ultraviolet light. In 61 virus-positive outbreaks confirmed by fluorescent multiplex RT-PCR, detection rates of outbreaks for NoVs, SaV, and HAstV were 96.7%, 3.3%, and 0%, respectively. © 2011 The Societies and Blackwell Publishing Asia Pty Ltd.

  6. Improved Safety for Molecular Diagnosis of Classical Rabies Viruses by Use of a TaqMan Real-Time Reverse Transcription-PCR "Double Check" Strategy

    DEFF Research Database (Denmark)

    Hoffmann, B.; Freuling, C. M.; Wakeley, P. R.

    2010-01-01

    by a combined assay that detected all samples as positive. In addition, the introduction of labeled positive controls (LPC) increased the diagnostic safety of the single as well as the combined assay. Based on the newly developed, alternative assay for the detection of rabies virus and the application of LPCs......To improve the diagnosis of classical rabies virus with molecular methods, a validated, ready-to-use, real-time reverse transcription-PCR (RT-PCR) assay was developed. In a first step, primers and 6-carboxyfluorescien-labeled TaqMan probes specific for rabies virus were selected from the consensus...... sequence of the nucleoprotein gene of 203 different rabies virus sequences derived from GenBank. The selected primer-probe combination was highly specific and sensitive. During validation using a sample set of rabies virus strains from the virus archives of the Friedrich-Loeffler-Institut (FLI; Germany...

  7. Rapid and specific detection of Lassa virus by reverse transcription-PCR coupled with oligonucleotide array hybridization.

    Science.gov (United States)

    Olschläger, Stephan; Günther, Stephan

    2012-07-01

    To facilitate sequence-specific detection of DNA amplified in a diagnostic reverse transcription (RT)-PCR for Lassa virus, we developed an array featuring 47 oligonucleotide probes for post-PCR hybridization of the amplicons. The array procedure may be performed with low-tech equipment and does not take longer than agarose gel detection.

  8. Evaluation of reverse transcription-PCR protocols based on the fusion gene for diagnosis of bovine respiratory syncytial virus infections

    OpenAIRE

    Selim A.; Gaede W.

    2013-01-01

    Bovine respiratory syncytial virus (BRSV) is a pneumovirus in the family paramyxoviridae, is an important cause of acute respiratory disease in postweaning calves and feedlot cattle. The real-time reverse transcriptase PCR protocols were developed to detect BRSV infection in infected animals. The sensitivity of RT-PCR protocols based on fusion gene were evaluated using different Mastermixes such as Qiagen One Step RT-PCR (Qiagen) for conventional RT-PCR, Su...

  9. Simultaneous detection of four garlic viruses by multiplex reverse transcription PCR and their distribution in Indian garlic accessions.

    Science.gov (United States)

    Majumder, S; Baranwal, V K

    2014-06-01

    Indian garlic is infected with Onion yellow dwarf virus (OYDV), Shallot latent virus (SLV), Garlic common latent virus (GarCLV) and allexiviruses. Identity and distribution of garlic viruses in various garlic accessions from different geographical regions of India were investigated. OYDV and allexiviruses were observed in all the garlic accessions, while SLV and GarCLV were observed only in a few accessions. A multiplex reverse transcription (RT)-PCR method was developed for the simultaneous detection and identification of OYDV, SLV, GarCLV and Allexivirus infecting garlic accessions in India. This multiplex protocol standardized in this study will be useful in indexing of garlic viruses and production of virus free seed material.

  10. External Quality Assessment for the Detection of Measles Virus by Reverse Transcription-PCR Using Armored RNA.

    Directory of Open Access Journals (Sweden)

    Dong Zhang

    Full Text Available In recent years, nucleic acid tests for detection of measles virus RNA have been widely applied in laboratories belonging to the measles surveillance system of China. An external quality assessment program was established by the National Center for Clinical Laboratories to evaluate the performance of nucleic acid tests for measles virus. The external quality assessment panel, which consisted of 10 specimens, was prepared using armored RNAs, complex of noninfectious MS2 bacteriophage coat proteins encapsulated RNA of measles virus, as measles virus surrogate controls. Conserved sequences amplified from a circulating measles virus strain or from a vaccine strain were encapsulated into these armored RNAs. Forty-one participating laboratories from 15 provinces, municipalities, or autonomous regions that currently conduct molecular detection of measles virus enrolled in the external quality assessment program, including 40 measles surveillance system laboratories and one diagnostic reagent manufacturer. Forty laboratories used commercial reverse transcription-quantitative PCR kits, with only one laboratory applying a conventional PCR method developed in-house. The results indicated that most of the participants (38/41, 92.7% were able to accurately detect the panel with 100% sensitivity and 100% specificity. Although a wide range of commercially available kits for nucleic acid extraction and reverse transcription polymerase chain reaction were used by the participants, only two false-negative results and one false-positive result were generated; these were generated by three separate laboratories. Both false-negative results were obtained with tests performed on specimens with the lowest concentration (1.2 × 104 genomic equivalents/mL. In addition, all 18 participants from Beijing achieved 100% sensitivity and 100% specificity. Overall, we conclude that the majority of the laboratories evaluated have reliable diagnostic capacities for the detection

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

    Science.gov (United States)

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

    2017-01-01

    Nasopharyngeal swabs (NPSs) are being widely used as specimens for multiplex real-time reverse transcription (RT)-PCR for respiratory virus detection. However, it remains unclear whether NPS specimens are optimal for all viruses targeted by multiplex RT-PCR. In addition, the procedure to obtain NPS specimens causes coughing in most patients, which possibly increases the risk of nosocomial spread of viruses. In this study, paired NPS and saliva specimens were collected from 236 adult male patients with suspected acute respiratory illnesses. Specimens were tested for 16 respiratory viruses by multiplex real-time RT-PCR. Among the specimens collected from the 236 patients, at least 1 respiratory virus was detected in 183 NPS specimens (77.5%) and 180 saliva specimens (76.3%). The rates of detection of respiratory viruses were comparable for NPS and saliva specimens (P = 0.766). Nine virus species and 349 viruses were isolated, 256 from NPS specimens and 273 from saliva specimens (P = 0.1574). Adenovirus was detected more frequently in saliva samples (P saliva samples was excluded by direct sequencing. In conclusion, neither of the sampling methods was consistently more sensitive than the other. We suggest that these cost-effective methods for detecting respiratory viruses in mixed NPS-saliva specimens might be valuable for future studies. Copyright © 2016 American Society for Microbiology.

  12. Improved detection of Lassa virus by reverse transcription-PCR targeting the 5' region of S RNA.

    Science.gov (United States)

    Olschläger, Stephan; Lelke, Michaela; Emmerich, Petra; Panning, Marcus; Drosten, Christian; Hass, Meike; Asogun, Danny; Ehichioya, Deborah; Omilabu, Sunday; Günther, Stephan

    2010-06-01

    The method of choice for the detection of Lassa virus is reverse transcription (RT)-PCR. However, the high degree of genetic variability of the virus poses a problem with the design of RT-PCR assays that will reliably detect all strains. Recently, we encountered difficulties in detecting some strains from Liberia and Nigeria in a commonly used glycoprotein precursor (GPC) gene-specific RT-PCR assay (A. H. Demby, J. Chamberlain, D. W. Brown, and C. S. Clegg, J. Clin. Microbiol. 32:2898-2903, 1994), which prompted us to revise the protocol. The design of the new assay, the GPC RT-PCR/2007 assay, took into account 62 S RNA sequences from all countries where Lassa fever is endemic, including 40 sequences generated from the strains in our collection. The analytical sensitivity of the new assay was determined with 11 strains from Sierra Leone, Liberia, Ivory Coast, and Nigeria by probit analysis; the viral loads detectable with a probability of 95% ranged from 342 to 2,560 S RNA copies/ml serum, which corresponds to 4 to 30 S RNA copies/assay. The GPC RT-PCR/2007 assay was validated with 77 serum samples and 1 cerebrospinal fluid sample from patients with laboratory-confirmed Lassa fever. The samples mainly originated from Liberia and Nigeria and included strains difficult to detect in the assay of 1994. The GPC RT-PCR/2007 assay detected virus in all clinical specimens (100% sensitivity). In conclusion, a new RT-PCR assay, based in part on the protocol developed by Demby et al. in 1994, for the detection of Lassa virus is described. Compared to the assay developed in 1994, the GPC RT-PCR/2007 assay offers improved sensitivity for the detection of Liberian and Nigerian Lassa virus strains.

  13. Reverse transcription PCR-based detection of Crimean-Congo hemorrhagic fever virus isolated from ticks of domestic ruminants in Kurdistan province of Iran.

    Science.gov (United States)

    Fakoorziba, Mohammad Reza; Golmohammadi, Parvaneh; Moradzadeh, Rahmatollah; Moemenbellah-Fard, Mohammad Djaefar; Azizi, Kourosh; Davari, Behrooz; Alipour, Hamzeh; Ahmadnia, Sara; Chinikar, Sadegh

    2012-09-01

    Crimean-Congo hemorrhagic fever (CCHF) is a potentially fatal viral vector-borne zoonosis which has a mortality rate of up to 30% without treatment in humans. CCHF virus is transmitted to humans by ticks, predominantly from the Hyalomma genus. Following the report of two confirmed and one suspected death due to CCHF virus in Kurdistan province of Iran in 2007, this study was undertaken to determine the fauna of hard ticks on domestic ruminants (cattle, sheep, and goats) and their possible infection with CCHF virus using reverse transcription PCR technique. This is the first detection of CCHF virus in ticks from the Kurdistan province of Iran. Overall, 414 ixodid ticks were collected from two districts in this province. They represented four genera from which 10 separate species were identified. The Hyalomma genus was the most abundant tick genus (70%). It was the only genus shown to be infected with the CCHF virus using RT-PCR technique. The number of ticks positive for CCHF virus was 5 out of 90 (5.6%) adult ticks. The three remaining genera (Haemaphysalis, Rhipicephalus, and Dermacentor) were all negative following molecular survey. Four of the five virally-infected ticks were from cattle mainly in the Sanandaj district. We concluded that CCHF virus is present in the Hyalomma ticks on domestic ruminants (cattle) in Kurdistan province of Iran.

  14. To Normalize the Using of Quantitative Real-time Reverse Transcription PCR%Real time RT-qPCR 检测规范化

    Institute of Scientific and Technical Information of China (English)

    马俊彦; 林俊

    2010-01-01

    Real time RT-qPCR(real-time quantitatire reverse transcription-PCR)是一种快速、简便、准确、灵敏、成本低廉的基因检测技术,被认为是目前检测基因在转录水平表达的金标准.研究发现Real time RT-qPCR的检测结果会受到实验设计、引物、模板的质量、内参的选择及数据分析的方法等多个因素的影响,规范实验设计及操作是得到可靠结论的前提和必要条件.对近年来国内外涉及Real time RT-qPCR整个实验流程及数据发表的一些规范及标准进行综述,以便规范实验设计及操作,加强实验质量控制,促进研究结果的推广,和更好地发挥其应用价值.

  15. Preliminary results on ghrelin mRNA quantification in buffalo calves during fasting and refeeding by real-time reverse transcription PCR assay

    Directory of Open Access Journals (Sweden)

    G. Neglia

    2010-02-01

    Full Text Available The aim of this trial was to evaluate ghrelin response to milk administration in 20 days old buffalo calves. The trial was carried out on 5 female buffalo calves with a mean age of 21.2±2.8 days. Five blood samples were collected from each animal into EDTA tubes, starting at 07.00 until 15.00, at 2-h intervals. At 09.00, after the second blood sample, replaced milk was administered to the calves. Blood samples were immediately placed at 4°C until processing, which was performed on the same day. We used real-time reverse transcription PCR system to detect the expression of ghrelin mRNA levels in blood of buffalo calves. Two calves showed a low ghrelin concentration at the start of the trial (Group A = low ghrelin concentration and three calves a high ghrelin concentration (Group B = high ghrelin concentration. Ghrelin expression was significantly higher either two hours (P<0.01 and just before feeding (P<0.05 in Group B vs. Group A. However, in both cases, a significant (P<0.05 difference was observed within each group between -2 and 6 hours after feeding. Therefore, ghrelin concentration tended to increase in animals that showed low levels and, similarly, it lowered in animals that showed high concentration. If these results will be confirmed, may represent the evidence that also in buffalo calves the ghrelin system may affect feed intake. Further studies are needed in order to better evaluate the ghrelin system in buffalo calves.

  16. Quantitative real-time reverse transcription-PCR analysis reveals stable and prolonged neurotoxin cluster gene activity in a Clostridium botulinum type E strain at refrigeration temperature.

    Science.gov (United States)

    Chen, Ying; Korkeala, Hannu; Lindén, Jere; Lindström, Miia

    2008-10-01

    The relative expression levels of six botulinum neurotoxin cluster genes in a group II Clostridium botulinum type E strain grown at 10 or 30 degrees C were investigated using quantitative real-time reverse transcription-PCR. An enzyme-linked immunosorbent assay was used to confirm neurotoxin expression. Distinct mRNA and toxin production patterns were observed at the two temperatures. The average relative mRNA levels at 10 degrees C were higher than (ntnh and p47), similar to (botE), or lower than (orfx1, orfx2, orfx3) those at 30 degrees C. The maximum botE expression levels and average neurotoxin levels at 10 degrees C were 45 to 65% of those at 30 degrees C. The relative mRNA levels at 10 degrees C declined generally slowly within 8 days, as opposed to the rapid decline observed at 30 degrees C within 24 h. Distinct expression patterns of the six genes at the two temperatures suggest that the type E neurotoxin cluster genes are transcribed as two tricistronic operons at 30 degrees C, whereas at 10 degrees C monocistronic (botE or orfx1 alone) and bicistronic (ntnh-p47 and orfx2-orfx3) transcription may dominate. Thus, type E botulinum neurotoxin production may be involved with various temperature-dependent regulatory events. In light of group II C. botulinum type E being a dangerous food-borne pathogen, these findings may be important in terms of the safety of refrigerated packaged foods of extended durability.

  17. Simultaneous detection of papaya ringspot virus, papaya leaf distortion mosaic virus, and papaya mosaic virus by multiplex real-time reverse transcription PCR.

    Science.gov (United States)

    Huo, P; Shen, W T; Yan, P; Tuo, D C; Li, X Y; Zhou, P

    2015-12-01

    Both the single infection of papaya ringspot virus (PRSV), papaya leaf distortion mosaic virus (PLDMV) or papaya mosaic virus (PapMV) and double infection of PRSV and PLDMV or PapMV which cause indistinguishable symptoms, threaten the papaya industry in Hainan Island, China. In this study, a multiplex real-time reverse transcription PCR (RT-PCR) was developed to detect simultaneously the three viruses based on their distinctive melting temperatures (Tms): 81.0±0.8°C for PRSV, 84.7±0.6°C for PLDMV, and 88.7±0.4°C for PapMV. The multiplex real-time RT-PCR method was specific and sensitive in detecting the three viruses, with a detection limit of 1.0×10(1), 1.0×10(2), and 1.0×10(2) copies for PRSV, PLDMV, and PapMV, respectively. Indeed, the reaction was 100 times more sensitive than the multiplex RT-PCR for PRSV, and 10 times more sensitive than multiplex RT-PCR for PLDMV. Field application of the multiplex real-time RT-PCR demonstrated that some non-symptomatic samples were positive for PLDMV by multiplex real-time RT-PCR but negative by multiplex RT-PCR, whereas some samples were positive for both PRSV and PLDMV by multiplex real-time RT-PCR assay but only positive for PLDMV by multiplex RT-PCR. Therefore, this multiplex real-time RT-PCR assay provides a more rapid, sensitive and reliable method for simultaneous detection of PRSV, PLDMV, PapMV and their mixed infections in papaya.

  18. Reference genes for high-throughput quantitative reverse transcription-PCR analysis of gene expression in organs and tissues of Eucalyptus grown in various environmental conditions.

    Science.gov (United States)

    Cassan-Wang, Hua; Soler, Marçal; Yu, Hong; Camargo, Eduardo Leal O; Carocha, Victor; Ladouce, Nathalie; Savelli, Bruno; Paiva, Jorge A P; Leplé, Jean-Charles; Grima-Pettenati, Jacqueline

    2012-12-01

    Interest in the genomics of Eucalyptus has skyrocketed thanks to the recent sequencing of the genome of Eucalyptus grandis and to a growing number of large-scale transcriptomic studies. Quantitative reverse transcription-PCR (RT-PCR) is the method of choice for gene expression analysis and can now also be used as a high-throughput method. The selection of appropriate internal controls is becoming of utmost importance to ensure accurate expression results in Eucalyptus. To this end, we selected 21 candidate reference genes and used high-throughput microfluidic dynamic arrays to assess their expression among a large panel of developmental and environmental conditions with a special focus on wood-forming tissues. We analyzed the expression stability of these genes by using three distinct statistical algorithms (geNorm, NormFinder and ΔCt), and used principal component analysis to compare methods and rankings. We showed that the most stable genes identified depended not only on the panel of biological samples considered but also on the statistical method used. We then developed a comprehensive integration of the rankings generated by the three methods and identified the optimal reference genes for 17 distinct experimental sets covering 13 organs and tissues, as well as various developmental and environmental conditions. The expression patterns of Eucalyptus master genes EgMYB1 and EgMYB2 experimentally validated our selection. Our findings provide an important resource for the selection of appropriate reference genes for accurate and reliable normalization of gene expression data in the organs and tissues of Eucalyptus trees grown in a range of conditions including abiotic stresses.

  19. Multiplex Reverse Transcription-PCR for Simultaneous Detection of Beet Necrotic Yellow Vein Virus, Beet Soilborne Virus, and Beet Virus Q and Their Vector Polymyxa betae KESKIN on Sugar Beet

    OpenAIRE

    Meunier, Alexandre; Schmit, Jean-François; Stas, Arnaud; Kutluk, Nazli; Bragard, Claude

    2003-01-01

    Three soilborne viruses transmitted by Polymyxa betae KESKIN in sugar beet have been described: Beet necrotic yellow vein virus (BNYVV), the agent of rhizomania, Beet soilborne virus (BSBV), and Beet virus Q (BVQ). A multiplex reverse transcription-PCR technique was developed to simultaneously detect BNYVV, BSBV, and BVQ, together with their vector, P. betae. The detection threshold of the test was up to 128 times greater than that of an enzyme-linked immunosorbent assay. Systematic associati...

  20. Multiplex Reverse Transcription-PCR for Simultaneous Detection of Beet Necrotic Yellow Vein Virus, Beet Soilborne Virus, and Beet Virus Q and Their Vector Polymyxa betae KESKIN on Sugar Beet

    OpenAIRE

    Meunier, Alexandre; Schmit, Jean-François; Stas, Arnaud; Kutluk, Nazli; Bragard, Claude

    2003-01-01

    Three soilborne viruses transmitted by Polymyxa betae KESKIN in sugar beet have been described: Beet necrotic yellow vein virus (BNYVV), the agent of rhizomania, Beet soilborne virus (BSBV), and Beet virus Q (BVQ). A multiplex reverse transcription-PCR technique was developed to simultaneously detect BNYVV, BSBV, and BVQ, together with their vector, P. betae. The detection threshold of the test was up to 128 times greater than that of an enzyme-linked immunosorbent assay. Systematic associati...

  1. New in situ capture quantitative (real-time) reverse transcription-PCR method as an alternative approach for determining inactivation of Tulane virus.

    Science.gov (United States)

    Wang, Dapeng; Xu, Shuxia; Yang, David; Young, Glenn M; Tian, Peng

    2014-04-01

    Human noroviruses (HuNoVs) are the major cause of epidemic nonbacterial gastroenteritis. Although quantitative (real-time) reverse transcription-PCR (qRT-PCR) is widely used for detecting HuNoVs, it only detects the presence of viral RNA and does not indicate viral infectivity. Human blood group antigens (HBGAs) have been identified as receptors/co-receptors for both HuNoVs and Tulane virus (TV) and are crucial for viral infection. We propose that viral infectivity can be evaluated with a molecular assay based on receptor-captured viruses. In this study, we employed TV as an HuNoV surrogate to validate the HBGA-based capture qRT-PCR method against the 50% tissue culture infectious dose (TCID50) method. We employed type B HBGA on an immuno-well module to concentrate TV, followed by amplification of the captured viral genome by in situ qRT-PCR. We first demonstrated that this in situ capture qRT-PCR (ISC-qRT-PCR) method could effectively concentrate and detect TV. We then treated TV under either partial or full inactivation conditions and measured the remaining infectivity by ISC-qRT-PCR and a tissue culture-based amplification method (TCID50). We found that the ISC-qRT-PCR method could be used to evaluate virus inactivation deriving from damage to the capsid and study interactions between the capsid and viral receptor. Heat, chlorine, and ethanol treatment primarily affect the capsid structure, which in turns affects the ability of the capsid to bind to viral receptors. Inactivation of the virus by these methods could be reflected by the ISC-qRT-PCR method and confirmed by TCID50 assay. However, the loss of the infectivity caused by damage to the viral genome (such as that from UV irradiation) could not be effectively reflected by this method. Despite this limitation, the ISC-qRT-PCR provides an alternative approach to determine inactivation of Tulane virus. A particular advantage of the ISC-qRT-PCR method is that it is also a faster and easier method to effectively

  2. Real-time quantitative reverse transcription-PCR analysis of expression stability of Actinobacillus pleuropneumoniae housekeeping genes during in vitro growth under iron-depleted conditions

    DEFF Research Database (Denmark)

    Nielsen, K. K.; Boye, Mette

    2005-01-01

    The aims of the present investigation were to develop and test a sensitive and reproducible method for the study of gene expression in the porcine lung pathogen Actinobacillus pleuropneumoniae by real-time quantitative reverse transcription (RT)-PCR and to evaluate a number of suitable internal...... up-regulation under iron-restricted conditions compared to bacteria grown in medium with sufficient iron. The observed expression patterns of the genes of interest were consistent with previous observations. This study therefore lends further support to the use of real-time quantitative RT...

  3. Detection and subtyping (H5 and H7) of avian type A influenza virus by reverse transcription-PCR and PCR-ELISA

    DEFF Research Database (Denmark)

    Munch, M.; Nielsen, L.P.; Handberg, Kurt

    2001-01-01

    Avian influenza virus infections are a major cause of morbidity and rapid identification of the virus has important clinical, economical and epidemiological implications. We have developed a one-tube Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) for the rapid diagnosis of avian influenza...... catching probe confirming the NP influenza A origin. The PCR-ELISA was about 100 times more sensitive than detection of PCR products by agarose gel electrophoresis. RT-PCR and detection by PCR-ELISA is comparable in sensitivity to virus propagation in eggs. We also designed primers for the detection...... A. A panel of reference influenza strains from various hosts including avian species, human, swine and horse were evaluated in a one tube RT-PCR using primers designed for the amplification of a 218 bp fragment of the NP gene. The PCR products were detected by PCR-ELISA by use of an internal...

  4. Detection, differentiation, and VP1 sequencing of duck hepatitis A virus type 1 and type 3 by a 1-step duplex reverse-transcription PCR assay.

    Science.gov (United States)

    Wen, X J; Cheng, A C; Wang, M S; Jia, R Y; Zhu, D K; Chen, S; Liu, M F; Liu, F; Chen, X Y

    2014-09-01

    Duck hepatitis A virus (DHAV) is an infectious pathogen causing fatal duck viral hepatitis in ducklings. Although both the inactivated vaccines and live attenuated vaccines have been used to protect ducklings, DHAV-1 and DHAV-3 still cause significant serious damage to the duck industry in China and South Korea. For rapid detection, differentiation, and epidemic investigation of DHAV in China, a genotype-specific 1-step duplex reverse-transcription (RT) PCR assay was established in this study. The sensitivity and specificity of the developed RT-PCR assay was evaluated with nucleic acids extracted from 2 DHAV reference strains, and 9 other infectious viruses and bacteria. The genotype-specific primers amplified different size DNA fragments encompassing the complete VP1 gene of the DHAV-1 or DHAV-3. The assay detected the liver samples collected from experimentally infected ducklings and dead ducklings collected from different regions of China. Sequence analysis of these DNA fragments indicated that VP1 sequences of DHAV-1 can be used to distinguish wild type and vaccine strains. The phylogenetic analysis of VP1 sequences indicated that the developed RT-PCR assay can be used for epidemic investigation of DHAV-1 and DHAV-3. The developed RT-PCR assay can be used as a specific molecular tool for simultaneous detection, differentiation, and sequencing the VP1 gene of DHAV-1 and DHAV-3, which can be used for understanding the epidemiology and evolution of DHAV. © 2014 Poultry Science Association Inc.

  5. Molecular detection of the clostridia in an anaerobic biohydrogen fermentation system by hydrogenase mRNA-targeted reverse transcription-PCR.

    Science.gov (United States)

    Chang, Jui-Jen; Chen, Wei-En; Shih, Shiou-Yun; Yu, Sian-Jhong; Lay, Jiunn-Jyi; Wen, Fu-Shyan; Huang, Chieh-Chen

    2006-05-01

    Molecular biological approaches were developed to monitor the potential biohydrogen-producing clostridia in an anaerobic semisolid fermentation system that used brewery yeast waste as the fermentation substrate. The denaturing gradient gel electrophoresis with 16S rDNA gene-targeted polymerase chain reaction (PCR) analysis was employed to confirm the existence of clostridia in the system. Remarkably, reproducible nucleotide sequences of clostridia were obtained from different hydrogen production stages by using hydrogenase gene-targeted reverse transcription (RT)-PCR. These RNA-based information suggested that the predominant hydrogen-producing strains possess either a specific Clostridium pasteurianum-like or a specific Clostridium saccharobutylicum-like hydrogenase sequence. Comparison of the hydrogenase gene-targeted sequence profiles between PCR and RT-PCR revealed that the specific C. pasteurianum-like hydrogenase harboring bacterial strains were dominant in both mRNA and bacterial population level. On the other hand, the specific C. saccharobutylicum-like hydrogenase harboring strains expressed high level of hydrogenase mRNA but may not be dominant in population. Furthermore, quantitative real-time RT-PCR analysis showed the expression pattern of the clostridial hydrogenase mRNA and may serve as an activity index for the system.

  6. High-resolution magic angle spinning 1H NMR spectroscopy and reverse transcription-PCR analysis of apoptosis in a rat glioma.

    Science.gov (United States)

    Griffin, Julian L; Blenkiron, Cherie; Valonen, Piia K; Caldas, Carlos; Kauppinen, Risto A

    2006-03-01

    The functional genomic approaches of transcriptomics, proteomics and metabolomics aim to measure the mRNA, protein or metabolite complement of a cell, tissue or organism. In this study we have investigated the compatibility of transcriptional analysis, using Reverse Transcription (RT)-PCR, and metabolite analysis, by high-resolution magic angle spinning (HRMAS) 1H NMR spectroscopy, in BT4C rat glioma following the induction of programmed cell death. The metabolite and transcriptional changes that accompanied apoptosis were examined at 0, 4 and 8 days of ganciclovir/thymidine kinase gene therapy. Despite the high spinning speeds employed during HRMAS 1H NMR spectroscopy of one-half of the tumor samples, RT-PCR analysis of the pro-apoptotic transcripts Bcl-2, BAK-1, caspase-9 and FAS was possible, producing similar results to those detected in the unspun half of the tumors. Furthermore, the expression of FAS was inversely correlated with some of the key metabolic changes across the time period examined including the increases CH=CH and CH=CHCH2 lipid resonances which accompany apoptosis. This study demonstrates how combined transcriptomic and metabolomic studies of tumors can be used to understand the molecular events that accompany well documented metabolic perturbations during cell death processes.

  7. Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays.

    Directory of Open Access Journals (Sweden)

    Curi Kim

    Full Text Available BACKGROUND: Many acute respiratory illness surveillance systems collect and test nasopharyngeal (NP and/or oropharyngeal (OP swab specimens, yet there are few studies assessing the relative measures of performance for NP versus OP specimens. METHODS: We collected paired NP and OP swabs separately from pediatric and adult patients with influenza-like illness or severe acute respiratory illness at two respiratory surveillance sites in Kenya. The specimens were tested for eight respiratory viruses by real-time reverse transcription-polymerase chain reaction (qRT-PCR. Positivity for a specific virus was defined as detection of viral nucleic acid in either swab. RESULTS: Of 2,331 paired NP/OP specimens, 1,402 (60.1% were positive for at least one virus, and 393 (16.9% were positive for more than one virus. Overall, OP swabs were significantly more sensitive than NP swabs for adenovirus (72.4% vs. 57.6%, p<0.01 and 2009 pandemic influenza A (H1N1 virus (91.2% vs. 70.4%, p<0.01. NP specimens were more sensitive for influenza B virus (83.3% vs. 61.5%, p = 0.02, parainfluenza virus 2 (85.7%, vs. 39.3%, p<0.01, and parainfluenza virus 3 (83.9% vs. 67.4%, p<0.01. The two methods did not differ significantly for human metapneumovirus, influenza A (H3N2 virus, parainfluenza virus 1, or respiratory syncytial virus. CONCLUSIONS: The sensitivities were variable among the eight viruses tested; neither specimen was consistently more effective than the other. For respiratory disease surveillance programs using qRT-PCR that aim to maximize sensitivity for a large number of viruses, collecting combined NP and OP specimens would be the most effective approach.

  8. Assessment of the inhibitory effect of ribavirin on the rainbow trout rhabdovirus VHSV by real-time reverse-transcription PCR.

    Science.gov (United States)

    Marroquí, Laura; Estepa, Amparo; Perez, Luis

    2007-05-16

    Viral hemorrhagic septicemia virus (VHSV) is one of the most ubiquitous viruses in salmonid aquaculture in Europe. This infectious disease results in significant losses in the farming industry and therefore effective therapeutic agents are needed to control outbreaks caused by this pathogen. Thus, accurate methods to test new antiviral compounds need to be developed. Our goal was to establish a model system for testing novel antivirals with potential applications to aquaculture. In a previous study, a TaqMan real-time RT-PCR assay was designed to detect and quantitate VHSV in rainbow trout tissues [Chico, V., Gomez, N., Estepa, A., Perez, L., 2006. Rapid detection and quantitation of viral hemorrhagic septicemia virus in experimentally challenged rainbow trout by real-time RT-PCR. J. Virol. Methods 132, 154-159]. In this report, we applied the real-time RT-PCR assay to the evaluation of the inhibitory effect of ribavirin, a well-known broad spectrum antiviral drug, in a cell culture system. When added from the beginning of the infection, ribavirin caused a dose-dependent reduction of VHSV RNA accumulation. Real-time RT-PCR measurements showed 99.8% inhibition at 25 microg/ml ribavirin, with an IC50 of 0.43 microg/ml. Ribavirin maintained its inhibitory activity against VHSV when added at 6 h post-infection. Quantitation of N protein messenger RNA and plus-stranded RNA showed a substantial decrease of viral transcription in ribavirin-treated cells. Partial reversion of the effect of ribavirin by addition of GTP was observed, confirming that ribavirin targets the synthesis of guanidine nucleotides in the cells. This is the first report of a real-time PCR-based assay for addressing the efficacy and mechanism of action of an antiviral agent for rainbow trout.

  9. A comparative study of microbial diversity and community structure in marine sediments using poly(A tailing and reverse transcription PCR

    Directory of Open Access Journals (Sweden)

    Tatsuhiko eHoshino

    2013-06-01

    Full Text Available To obtain a better understanding of metabolically active microbial communities, we tested a molecular ecological approach using poly(A tailing of environmental 16S rRNA, followed by full-length complementary DNA (cDNA synthesis and sequencing to eliminate potential biases caused by mismatching of PCR primer sequences. The RNA pool tested was extracted from marine sediments of the Yonaguni Knoll IV hydrothermal field in the southern Okinawa Trough. The sequences obtained using the ploy(A tailing method were compared statistically and phylogenetically with those obtained using conventional reverse transcription-polymerase chain reaction (RT-PCR with published domain-specific primers. Both methods indicated that Deltaproteobacteria are predominant in sediment (>85% of the total sequence read. The poly(A tailing method indicated that Desulfobacterales were the predominant deltaproteobacteria, while most of the sequences in libraries constructed using RT-PCR were derived from Desulfuromonadales. This discrepancy may have been due to low coverage of Desulfobacterales by the primers used. A comparison of library diversity indices indicated that the poly(A tailing method retrieves more phylogenetically diverse sequences from the environment. The four archaeal 16S rRNA sequences that were obtained using the poly(A tailing method formed deeply branching lineages that were related to Candidatus Parvarchaeum and the Ancient Archaeal Group. These results clearly demonstrate that poly(A tailing followed by cDNA sequencing is a powerful and less biased molecular ecological approach for the study of metabolically active microbial communities.

  10. RT-PCR检测金黄色葡萄球菌%Reverse transcription-PCR assay for detection of viable Staphylococcus aureus

    Institute of Scientific and Technical Information of China (English)

    罗予; 李杰; 刘娜

    2011-01-01

    目的 探讨检测金黄色葡萄球菌及其活菌的RT-PCR方法 .方法 用RT-PCR方法 对金黄色葡萄球菌的spa基因进行检测,并做灵敏度和特异性测定,用RT-PCR检测细菌灭活前后的spa基因.结果 用spa基因检测金黄色葡萄球菌灵敏度为1.5×104 CFU/mL;Spa引物能特异性扩增出金黄色葡萄球菌的标准株和14株临床株的目的 片段,对大肠埃希菌、铜绿假单胞菌、表皮葡萄球菌和化脓性链球菌则无特异性扩增条带,而对白色念珠菌有较弱条带扩出;细菌灭活前可以检测出目的 基因,灭活后4℃放置24、48和72 h均无目的 基因片段扩出.结论可以用spa基因对金黄色葡萄球菌进行活菌检测.%Objective To observe the effect of reverse transcription-polymerase chain reaction (RT-PCR) in detecting viable Staphylococcus aureus using. Method The spa gene of Staphylococcus aweus was detected by mRNA-based RT-PCR both before and after inactivation. The sensitivity and specificity of the RT-PCR method were determined. Result The Special fragment of Staphylococcus aureus was extended by the pair of primers. There was no crossreaction with E. Coli, Pseudomonas aeruginosa, Staphylococcus epidermidis, Pyogenic streptococcus. The sensitivity of detection was 1.5 x 10* CFU/mL. mRNA from uninactivated cells was detected, while in inactivated cells,. mRNA became undetectable when dead cells were held at 4 ℃ temperature for over 24 h. Conclusion This gene can be used to detect viable Staphylococcus aureus.

  11. Reverse-transcription PCR (RT-PCR).

    Science.gov (United States)

    Bachman, Julia

    2013-01-01

    RT-PCR is commonly used to test for genetic diseases and to characterize gene expression in various tissue types, cell types, and over developmental time courses. This serves as a form of expression profiling, but typically as a candidate approach. RT-PCR is also commonly used to clone cDNAs for further use with other molecular biology techniques (e.g., see Oligo(dT)-primed RT-PCR isolation of polyadenylated RNA degradation intermediates and Circularized RT-PCR (cRT-PCR): analysis of RNA 5' ends, 3' ends, and poly(A) tails).

  12. TaqMan real-time reverse transcription-PCR assay for universal detection and quantification of avian hepatitis E virus from clinical samples in the presence of a heterologous internal control RNA.

    Science.gov (United States)

    Troxler, Salome; Marek, Ana; Prokofieva, Irina; Bilic, Ivana; Hess, Michael

    2011-04-01

    Avian hepatitis E virus (HEV) isolates could be separated into at least three genotypes. In this study, the development of the first duplex TaqMan real-time reverse transcription-PCR (RT-PCR) assay for detection and quantification of avian HEV is presented. Primers and probes binding within relatively conserved open reading frame 3 (ORF3) were designed. Tenfold dilution series of in vitro-transcribed avian HEV RNA were used as the standard for quantification. A 712-bp region of the green fluorescent protein gene was transcribed in vitro and used as a heterologous internal control for both RNA isolation and real-time RT-PCR. The duplex real-time RT-PCR for avian HEV had an efficiency of 1.04, a regression squared value of 0.996, and a sensitivity of approximately 3.6 × 10(3) copies per reaction mixture when in vitro-transcribed RNA was used as the template. The presence of in vitro-transcribed heterologous internal control RNA did not affect amplification of avian HEV RNA compared to that achieved by the single assay. The sensitivity of the real-time RT-PCR assay was comparable to that of conventional RT-PCR, and it was shown to be highly specific, as tissues from uninfected chickens, mammalian HEVs, and other viral genomes did not produce positive signals. All tested field samples with virus belonging to different avian HEV genotypes were successfully detected with this new duplex TaqMan real-time RT-PCR assay.

  13. Evaluation of transcription levels of inlA, inlB, hly, bsh and prfA genes in Listeria monocytogenes strains using quantitative reverse-transcription PCR and ability of invasion into human CaCo-2 cells.

    Science.gov (United States)

    Tamburro, Manuela; Sammarco, Michela Lucia; Ammendolia, Maria Grazia; Fanelli, Incoronata; Minelli, Fabio; Ripabelli, Giancarlo

    2015-03-01

    Listeria monocytogenes virulence depends on the activity of well-characterized virulence factors. In this study, transcription levels of inlA, inlB, hly, bsh and prfA genes in L. monocytogenes strains, and the ability of invasion into CaCo-2 cells were investigated. Serotyping, multiplex-PCR for serovar identification and restriction fragment analysis of inlA were performed. Transcription levels and invasiveness were evaluated by quantitative reverse-transcription PCR and by in vitro assays, respectively. The isolates were of serovars 1/2a, 4b, 1/2c, 1/2b and 3a. Full-length inlA profiles were found for nine of ten clinical isolates, while five of seven cultures from foods showed truncated profile. The analysis of transcription levels of virulence factors encoding genes demonstrated a substantial inter-strain heterogeneity, with clinical strains showing higher levels for almost all genes than isolates from food. A correlation between transcription levels of inlA and inlB, as well as between bsh and prfA, was observed. Significant differences between clinical strains and food isolates in the invasion of CaCo-2 cells were found. Analysis of gene transcription and invasiveness of human cells suggests different virulence phenotypes among L. monocytogenes populations, and this characterization could be a useful tool for risk assessment purposes and for the development of public health strategies. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Newly emerging mutations in the matrix genes of the human influenza A(H1N1)pdm09 and A(H3N2) viruses reduce the detection sensitivity of real-time reverse transcription-PCR.

    Science.gov (United States)

    Yang, Ji-Rong; Kuo, Chuan-Yi; Huang, Hsiang-Yi; Wu, Fu-Ting; Huang, Yi-Lung; Cheng, Chieh-Yu; Su, Yu-Ting; Chang, Feng-Yee; Wu, Ho-Sheng; Liu, Ming-Tsan

    2014-01-01

    New variants of the influenza A(H1N1)pdm09 and A(H3N2) viruses were detected in Taiwan between 2012 and 2013. Some of these variants were not detected in clinical specimens using a common real-time reverse transcription-PCR (RT-PCR) assay that targeted the conserved regions of the viral matrix (M) genes. An analysis of the M gene sequences of the new variants revealed that several newly emerging mutations were located in the regions where the primers or probes of the real-time RT-PCR assay bind; these included three mutations (G225A, T228C, and G238A) in the A(H1N1)pdm09 virus, as well as one mutation (C163T) in the A(H3N2) virus. These accumulated mismatch mutations, together with the previously identified C154T mutation of the A(H1N1)pdm09 virus and the C153T and G189T mutations of the A(H3N2) virus, result in a reduced detection sensitivity for the real-time RT-PCR assay. To overcome the loss of assay sensitivity due to mismatch mutations, we established a real-time RT-PCR assay using degenerate nucleotide bases in both the primers and probe and successfully increased the sensitivity of the assay to detect circulating variants of the human influenza A viruses. Our observations highlight the importance of the simultaneous use of different gene-targeting real-time RT-PCR assays for the clinical diagnosis of influenza.

  15. Detection of Tumor Cell-Specific mRNA in the Peripheral Blood of Patients with Breast Cancer — Evaluation of Several Markers with Real-Time Reverse Transcription-PCR

    Directory of Open Access Journals (Sweden)

    Ulrich Andergassen

    2013-01-01

    Full Text Available It is widely known that cells from epithelial tumors, e.g., breast cancer, detach from their primary tissue and enter blood circulation. We show that the presence of circulating tumor cells (CTCs in samples of patients with primary and metastatic breast cancer can be detected with an array of selected tumor-marker-genes by reverse transcription real-time PCR. The focus of the presented work is on detecting differences in gene expression between healthy individuals and adjuvant and metastatic breast cancer patients, not an accurate quantification of these differences. Therefore, total RNA was isolated from blood samples of healthy donors and patients with primary or metastatic breast cancer after enrichment of mononuclear cells by density gradient centrifugation. After reverse transcription real-time PCR was carried out with a set of marker genes (BCSP, CK8, Her2, MGL, CK18, CK19. B2M and GAPDH were used as reference genes. Blood samples from patients with metastatic disease revealed increased cytokine gene levels in comparison to normal blood samples. Detection of a single gene was not sufficient to detect CTCs by reverse transcription real-time PCR. Markers used here were selected based on a recent study detecting cancer cells on different protein levels. The combination of such a marker array leads to higher and more specific discovery rates, predominantly in metastatic patients. Identification of CTCs by PCR methods may lead to better diagnosis and prognosis and could help to choose an adequate therapy.

  16. SYBR green-based real-time reverse transcription-PCR for typing and subtyping of all hemagglutinin and neuraminidase genes of avian influenza viruses and comparison to standard serological subtyping tests

    Science.gov (United States)

    Tsukamoto, K.; Javier, P.C.; Shishido, M.; Noguchi, D.; Pearce, J.; Kang, H.-M.; Jeong, O.M.; Lee, Y.-J.; Nakanishi, K.; Ashizawa, T.

    2012-01-01

    Continuing outbreaks of H5N1 highly pathogenic (HP) avian influenza virus (AIV) infections of wild birds and poultry worldwide emphasize the need for global surveillance of wild birds. To support the future surveillance activities, we developed a SYBR green-based, real-time reverse transcriptase PCR (rRT-PCR) for detecting nucleoprotein (NP) genes and subtyping 16 hemagglutinin (HA) and 9 neuraminidase (NA) genes simultaneously. Primers were improved by focusing on Eurasian or North American lineage genes; the number of mixed-base positions per primer was set to five or fewer, and the concentration of each primer set was optimized empirically. Also, 30 cycles of amplification of 1:10 dilutions of cDNAs from cultured viruses effectively reduced minor cross- or nonspecific reactions. Under these conditions, 346 HA and 345 NA genes of 349 AIVs were detected, with average sensitivities of NP, HA, and NA genes of 10 1.5, 10 2.3, and 10 3.1 50% egg infective doses, respectively. Utility of rRT-PCR for subtyping AIVs was compared with that of current standard serological tests by using 104 recent migratory duck virus isolates. As a result, all HA genes and 99% of the NA genes were genetically subtyped, while only 45% of HA genes and 74% of NA genes were serologically subtyped. Additionally, direct subtyping of AIVs in fecal samples was possible by 40 cycles of amplification: approximately 70% of HA and NA genes of NP gene-positive samples were successfully subtyped. This validation study indicates that rRT-PCR with optimized primers and reaction conditions is a powerful tool for subtyping varied AIVs in clinical and cultured samples. Copyright ?? 2012, American Society for Microbiology. All Rights Reserved.

  17. Nested quantization index modulation for reversible watermarking and its application to healthcare information management systems.

    Science.gov (United States)

    Ko, Lu-Ting; Chen, Jwu-E; Shieh, Yaw-Shih; Hsin, Hsi-Chin; Sung, Tze-Yun

    2012-01-01

    Digital watermarking has attracted lots of researches to healthcare information management systems for access control, patients' data protection, and information retrieval. The well-known quantization index modulation-(QIM-) based watermarking has its limitations as the host image will be destroyed; however, the recovery of medical images is essential to avoid misdiagnosis. In this paper, we propose the nested QIM-based watermarking, which is preferable to the QIM-based watermarking for the medical image applications. As the host image can be exactly reconstructed by the nested QIM-based watermarking. The capacity of the embedded watermark can be increased by taking advantage of the proposed nest structure. The algorithm and mathematical model of the nested QIM-based watermarking including forward and inverse model is presented. Due to algorithms and architectures of forward and inverse nested QIM, the concurrent programs and special processors for the nested QIM-based watermarking are easily implemented.

  18. In Situ Reverse Transcriptase-Nested Polymerase Chain Reaction to Identify Intracellular Nucleic Acids without the Necessity of Dnase Pretreatment and Hybridisation

    OpenAIRE

    Mario Menschikowski; Margot Vogel; Rolf Eckey; Gerd Dinnebier; Werner Jaross

    2001-01-01

    In the present study a protocol of in situ reverse transcriptase‐nested polymerase chain reaction (in situ RT‐nested PCR) was examined based on the following modifications. (i) To exclude false positive signals caused by “DNA repair mechanisms” and “endogenous priming”, a two‐step PCR was applied after reverse transcription. The first step was performed in the presence of extrinsic primers and unlabeled nucleotides with a maximum of PCR cycles possible without destroying the cell morphology. ...

  19. Subtyping of new Brazilian avian metapneumovirus isolates from chickens and turkeys by reverse transcriptase-nested-polymerase chain reaction.

    Science.gov (United States)

    D'Arce, Regina C F; Coswig, Lia T; Almeida, Renata S; Trevisol, Iara M; Monteiro, Maria C B; Rossini, Lavínia I; Di Fabio, José; Hafez, Hafez M; Arns, Clarice W

    2005-04-01

    The aim of this study was to improve a reverse transcriptase (RT)-nested-polymerase chain reaction (PCR) able to differentiate avian pneumovirus (APV) subtypes A and B, and to characterize new Brazilian isolates. Representative APV strains and clinical field samples from chickens and turkey flocks were amplified in the chicken embryo-related cell line. Viral RNA was extracted from harvested cells, and submitted to cDNA synthesis. The primers utilized for RT-PCR were compatible with the G gene of both the A and B subtypes of APV, while the nested primers were subtype specific. This approach showed that three new APVs from chickens and one from turkeys were subtype A, confirmed by sequencing. This is the first report of APV isolation from turkeys in Brazil. Four other APVs were detected and classified as subtype A by RT-nested-PCR. These optimized techniques could be useful for differentiation of APV subtypes A and B, proving to be a valuable molecular epidemiological tool.

  20. Selective control of primer usage in multiplex one-step reverse transcription PCR

    Directory of Open Access Journals (Sweden)

    Paul Natasha

    2009-12-01

    Full Text Available Abstract Background Multiplex RT-PCR is a valuable technique used for pathogen identification, disease detection and relative quantification of gene expression. The simplification of this protocol into a one-step procedure saves time and reagents. However, intensive PCR optimization is often required to overcome competing undesired PCR primer extension during the RT step. Results Herein, we report multiplex one-step RT-PCR experiments in which the PCR primers contain thermolabile phosphotriester modification groups. The presence of these groups minimizes PCR primer extension during the RT step and allows for control of PCR primer extension until the more stringent, elevated temperatures of PCR are reached. Results reveal that the use of primers whose extension can be controlled in a temperature-mediated way provides improved one-step RT-PCR specificity in both singleplex and multiplex reaction formats. Conclusions The need for an accurate and sensitive technique to quantify mRNA expression levels makes the described modified primer technology a promising tool for use in multiplex one-step RT-PCR. A more accurate representation of the abundances in initial template sample is feasible with modified primers, as artifacts of biased PCR are reduced because of greater improvements in reaction specificity.

  1. Propidium monoazide reverse transcription PCR and RT-qPCR for detecting infectious enterovirus and norovirus

    Science.gov (United States)

    Presently there is no established cell line or small animal model that allows for the detection of infectious human norovirus. Current methods based on RT-PCR and RT-qPCR detect both infectious and non-infectious virus and thus the conclusions that may be drawn regarding the publ...

  2. Design and evaluation of reverse transcription nested PCR primers for the detection of betanodavirus in finfish.

    Science.gov (United States)

    Rajan, J Joseph Sahaya; Praveena, P Ezhil; Bhuvaneswari, T; Jithendran, K P

    2016-06-01

    Viral encephalopathy and retinopathy otherwise known as viral nervous necrosis (VNN) is a neuropathological condition affecting more than 50 fish species worldwide, mostly marine. Different PCR protocols with specific primers were reported from many countries for confirmation of VNN in fishes. In the present study, two pairs of primers were designed and evaluated for the diagnosis of clinical and subclinical cases of infections from field. These primers designated as BARL-F1/BARL-R1 amplified a 902 bp product in the variable region (T4) of the coat protein gene by first step PCR. Nested PCR primers BARL-F2/BARL-R2 amplified a fragment of 313 bp. The results were comparable with other commonly used primer sets such as F2/R3 and RG668f/RG919r primers. These new primers could detect betanodavirus in standard reference samples containing low, moderate and high viral load. Known positive and negative control samples of fish also revealed a predictive value of 100 % by RT-PCR diagnosis.

  3. In situ reverse transcriptase-nested polymerase chain reaction to identify intracellular nucleic acids without the necessity of DNAse pretreatment and hybridisation.

    Science.gov (United States)

    Menschikowski, M; Vogel, M; Eckey, R; Dinnebier, G; Jaross, W

    2001-01-01

    In the present study a protocol of in situ reverse transcriptase-nested polymerase chain reaction (in situ RT-nested PCR) was examined based on the following modifications. (i) To exclude false positive signals caused by "DNA repair mechanisms" and "endogenous priming", a two-step PCR was applied after reverse transcription. The first step was performed in the presence of extrinsic primers and unlabeled nucleotides with a maximum of PCR cycles possible without destroying the cell morphology. The second step consisted of only one annealing/elongation reaction, the target sequence marked by addition of digoxigenin-labeled nucleotides and intrinsic primers. (ii) In order to prevent amplifications of genomic DNA nested primer pairs were applied crossing intron sequences. (iii) To minimize the diffusion of PCR products in cells, the extrinsic primers were extended with complementary 5(prime, variant)-tails. This approach results in the generation of high molecular weight concatamers during PCR cycles. By applying this protocol, immunostainings specific for phospholipase A2 of type IIA mRNA were exclusively detectable in the cytoplasm of HepG2 hepatoma cells, which were used as a model system, whereas the nuclei were unstained. Multiple control experiments yielded completely negative results. These data suggest that the in situ RT-nested PCR, which in comparison to the method of in situ RT-PCR-in situ-hybridisation is simpler and less time-consuming, can be used as an alternative approach to identify intracellular nucleic acids.

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

    Directory of Open Access Journals (Sweden)

    Cui Shang-jin

    2010-05-01

    Full Text Available Abstract 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.

  5. In Situ Reverse Transcriptase-Nested Polymerase Chain Reaction to Identify Intracellular Nucleic Acids without the Necessity of Dnase Pretreatment and Hybridisation

    Directory of Open Access Journals (Sweden)

    Mario Menschikowski

    2001-01-01

    Full Text Available In the present study a protocol of in situ reverse transcriptase‐nested polymerase chain reaction (in situ RT‐nested PCR was examined based on the following modifications. (i To exclude false positive signals caused by “DNA repair mechanisms” and “endogenous priming”, a two‐step PCR was applied after reverse transcription. The first step was performed in the presence of extrinsic primers and unlabeled nucleotides with a maximum of PCR cycles possible without destroying the cell morphology. The second step consisted of only one annealing/elongation reaction, the target sequence marked by addition of digoxigenin‐labeled nucleotides and intrinsic primers. (ii In order to prevent amplifications of genomic DNA nested primer pairs were applied crossing intron sequences. (iii To minimize the diffusion of PCR products in cells, the extrinsic primers were extended with complementary 5′‐tails. This approach results in the generation of high molecular weight concatamers during PCR cycles. By applying this protocol, immunostainings specific for phospholipase A2 of type IIA mRNA were exclusively detectable in the cytoplasm of HepG2 hepatoma cells, which were used as a model system, whereas the nuclei were unstained. Multiple control experiments yielded completely negative results. These data suggest that the in situ RT‐nested PCR, which in comparison to the method of in situ RT‐PCR‐in situ‐hybridisation is simpler and less time‐consuming, can be used as an alternative approach to identify intracellular nucleic acids.

  6. Foraging Habitat Quality Constrains Effectiveness of Artificial Nest-Site Provisioning in Reversing Population Declines in a Colonial Cavity Nester

    Science.gov (United States)

    Catry, Inês; Franco, Aldina M. A.; Rocha, Pedro; Alcazar, Rita; Reis, Susana; Cordeiro, Ana; Ventim, Rita; Teodósio, Joaquim; Moreira, Francisco

    2013-01-01

    Among birds, breeding numbers are mainly limited by two resources of major importance: food supply and nest-site availability. Here, we investigated how differences in land-use and nest-site availability affected the foraging behaviour, breeding success and population trends of the colonial cavity-dependent lesser kestrel Falco naumanni inhabiting two protected areas. Both areas were provided with artificial nests to increase nest-site availability. The first area is a pseudo-steppe characterized by traditional extensive cereal cultivation, whereas the second area is a previous agricultural zone now abandoned or replaced by forested areas. In both areas, lesser kestrels selected extensive agricultural habitats, such as fallows and cereal fields, and avoided scrubland and forests. In the second area, tracked birds from one colony travelled significantly farther distances (6.2 km ±1.7 vs. 1.8 km ±0.4 and 1.9 km ±0.6) and had significant larger foraging-ranges (144 km2 vs. 18.8 and 14.8 km2) when compared to the birds of two colonies in the extensive agricultural area. Longer foraging trips were reflected in lower chick feeding rates, lower fledging success and reduced chick fitness. Availability and occupation of artificial nests was high in both areas but population followed opposite trends, with a positive increment recorded exclusively in the first area with a large proportion of agricultural areas. Progressive habitat loss around the studied colony in the second area (suitable habitat decreased from 32% in 1990 to only 7% in 2002) is likely the main driver of the recorded population decline and suggests that the effectiveness of bird species conservation based on nest-site provisioning is highly constrained by habitat quality in the surrounding areas. Therefore, the conservation of cavity-dependent species may be enhanced firstly by finding the best areas of remaining habitat and secondly by increasing the carrying capacity of high-quality habitat areas

  7. Detection of EWS-FLI1 fusion transcripts in paraffin embedded tissues of peripheral primitive neuroectodermal tumors by nested reverse transcription polymerase chain reaction

    Institute of Scientific and Technical Information of China (English)

    Qixing Gong; Qinhe Fan; Zhihong Zhang; Weiming Zhang

    2005-01-01

    Objective: To assess the feasibility and significance of detecting EWS-FLIlfusion transcripts in paraffin embedded tissues of peripheral primitive neuroectodermal tumors (PNETs) by nested reverse transcription polymerase chain reaction (RT-PCR).Methods: Twelve formalin-fixed and paraffin-embedded (FFPE) samples of PNET were retrieved from archive and consultation materials,together with eight cases of controlled tumor. EWS-FLI1 fusion transcripts were detected by nested RT-PCR. Home-keeping gene β-actin was used to detect the quality of mRNA. Results: β-actin mRNA was detected in 9 of the 12 tumor cases. EWS-FLI1 fusion transcripts were detected in 6 cases, among which 4 had a "type 1" fusion transcript and 2 had a "type 2" fusion transcript. None of the controlled tumor was detected the fusion gene. Conclusion: RT-PCR is a feasible method for the detection of EWS-FLI1 fusion transcripts in FFPE tissues in PNET and the result is meaningful in differential diagnosis and prognostic evaluation.

  8. A Two-Tube Multiplex Reverse Transcription PCR Assay for Simultaneous Detection of Viral and Bacterial Pathogens of Infectious Diarrhea

    Directory of Open Access Journals (Sweden)

    Ji Wang

    2014-01-01

    Full Text Available Diarrhea caused by viral and bacterial infections is a major health problem in developing countries. The purpose of this study is to develop a two-tube multiplex PCR assay using automatic electrophoresis for simultaneous detection of 13 diarrhea-causative viruses or bacteria, with an intended application in provincial Centers for Diseases Control and Prevention, China. The assay was designed to detect rotavirus A, norovirus genogroups GI and GII, human astrovirus, enteric adenoviruses, and human bocavirus (tube 1, and Salmonella, Vibrio parahaemolyticus, diarrheagenic Escherichia coli, Campylobacter jejuni, Shigella, Yersinia, and Vibrio cholera (tube 2. The analytical specificity was examined with positive controls for each pathogen. The analytical sensitivity was evaluated by performing the assay on serial tenfold dilutions of in vitro transcribed RNA, recombinant plasmids, or bacterial culture. A total of 122 stool samples were tested by this two-tube assay and the results were compared with those obtained from reference methods. The two-tube assay achieved a sensitivity of 20–200 copies for a single virus and 102-103 CFU/mL for bacteria. The clinical performance demonstrated that the two-tube assay had comparable sensitivity and specificity to those of reference methods. In conclusion, the two-tube assay is a rapid, cost-effective, sensitive, specific, and high throughput method for the simultaneous detection of enteric bacteria and virus.

  9. Real-Time Reverse Transcription PCR Assay for Detection of Senecavirus A in Swine Vesicular Diagnostic Specimens.

    Directory of Open Access Journals (Sweden)

    Alexa J Bracht

    Full Text Available Senecavirus A (SV-A, formerly, Seneca Valley virus (SVV, has been detected in swine with vesicular lesions and is thought to be associated with swine idiopathic vesicular disease (SIVD, a vesicular disease syndrome that lacks a defined causative agent. The clinical presentation of SIVD resembles that of other more contagious and economically devastating vesicular diseases, such as foot-and-mouth disease (FMD, swine vesicular disease (SVD, and vesicular stomatitis (VS, that typically require immediate rule out diagnostics to lift restrictions on animal quarantine, movement, and trade. This study presents the development of a sensitive, SYBR Green RT-qPCR assay suitable for detection of SV-A in diagnostic swine specimens. After testing 50 pigs with clinical signs consistent with vesicular disease, 44 (88% were found to be positive for SV-A by RT-qPCR as compared to none from a negative cohort of 35 animals without vesicular disease, indicating that the assay is able to successfully detect the virus in an endemic population. SV-A RNA was also detectable at a low level in sera from a subset of pigs that presented with (18% or without (6% vesicular signs. In 2015, there has been an increase in the occurrence of SV-A in the US, and over 200 specimens submitted to our laboratory for vesicular investigation have tested positive for the virus using this method. SV-A RNA was detectable in all common types of vesicular specimens including swabs and tissue from hoof lesions, oral and snout epithelium, oral swabs, scabs, and internal organ tissues such as liver and lymph node. Genome sequencing analysis from recent virus isolates was performed to confirm target amplicon specificity and was aligned to previous isolates.

  10. Verification of reference genes for relative quantification of gene expression by real-time reverse transcription PCR in the pig.

    Science.gov (United States)

    Svobodová, Katerina; Bílek, Karel; Knoll, Ales

    2008-01-01

    The aim of this study was to develop a set of reliable reference genes for quantification of mRNA expression in the pig. The mRNA expression stability in pig tissues was studied for 4 genes: EEF1A1, GAPDH, HPRT1 and TOP2B. The level of expression was characterized by Ct values for each gene and each tissue. By using the geNorm algorithm, the stability of the reference genes was determined in the diaphragm, heart, kidney, liver, lungs, longissimus muscle, and spleen. On the basis of this information, suitable reference genes can be selected for mRNA expression studies in relevant pig tissues.

  11. Sample type is vital for diagnosing infection with peste des petits ruminants virus by reverse transcription PCR.

    Science.gov (United States)

    Luka, Pam Dachung; Ayebazibwe, Chrisostom; Shamaki, David; Mwiine, Frank Norbert; Erume, Joseph

    2012-09-01

    Peste des petits ruminants (PPR) diagnosis from suspected samples from sheep and goats was carried out. Buffy coat, tissues, and oculo-nasal swabs were analyzed using nucleoprotein (NP3/NP4) and fusion protein (F1/F2) gene primers, respectively. Analysis of the sample types and primer set revealed that buffy coat are the best type of samples for PPR diagnosis and the use of two set of primers will increase the number of positives.

  12. Stimulation of nodulation in Medicago truncatula by low concentrations of ammonium: quantitative reverse transcription PCR analysis of selected genes.

    Science.gov (United States)

    Fei, Houman; Vessey, J Kevin

    2009-03-01

    Although mineral nitrogen generally has negative effects on nodulation in legume-rhizobia symbioses, low concentrations of ammonium stimulate nodulation in some legumes. In this study, the effects of ammonium and nitrate on growth, nodulation and expression of 2 nitrogen transport and 12 putative nodulation-related genes of the model symbiosis of Medicago truncatula - Sinorhizobium meliloti are investigated. After 3 weeks of hydroponic growth, whole-plant nodulation was enhanced in all the ammonium treatments and up to three-fold in the 0.5 mM treatment compared with the zero-nitrogen control. Specific nodulation (nodules g(-1) root dry weight) was greatly stimulated in the 0.1 and 0.5 mM NH4+ treatments, to a lower extent in the 0.1 mM NO3- treatment, and inhibited in all other treatments. Expression of the 14 selected genes was observed at 0, 6, 12 and 24 h after exposure to rhizobia and nitrogen. Expression of nitrogen transporter genes increased significantly, but responses of the three genes putatively associated with symbiosis signaling/nodule initiation were mixed. There were infrequent responses of genes coding for an ABA-activated protein kinase or a gibberellin-regulated protein, but an ethylene-responsive element-binding factor showed increased expression in various treatments and sampling times. Three auxin-responsive genes and three cytokinin-responsive genes showed varied responses to ammonium and nitrate. This study indicates that low concentrations of ammonium stimulate nodulation in M. truncatula, but the data were inconclusive in verifying the hypothesis that a relatively high ratio of cytokinin to auxin in roots may be an underlying mechanism in this stimulation of nodulation.

  13. Combining Multiplex Reverse Transcription-PCR and a Diagnostic Microarray To Detect and Differentiate Enterovirus 71 and Coxsackievirus A16

    OpenAIRE

    Chen, Tsan-Chi; Chen, Guang-Wu; Hsiung, Chao Agnes; Yang, Jyh-Yuan; Shih, Shin-Ru; Lai, Yiu-Kay; Juang, Jyh-Lyh

    2006-01-01

    Cluster A enteroviruses, including enterovirus 71 (EV71) and coxsackievirus A16 (CA16), are known to cause hand-foot-and-mouth disease (HFMD). Despite the close genetic relationship between these two viruses, EV71 is generally known to be a more perpetuating pathogen involved in severe clinical manifestations and deaths. While the serotyping of enteroviruses is mostly done by conventional immunological methods, many clinical isolates remain unclassifiable due to the limited number of antibodi...

  14. 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.

    Science.gov (United States)

    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.

  15. Detection of feline coronavirus in cheetah (Acinonyx jubatus) feces by reverse transcription-nested polymerase chain reaction in cheetahs with variable frequency of viral shedding.

    Science.gov (United States)

    Gaffney, Patricia M; Kennedy, Melissa; Terio, Karen; Gardner, Ian; Lothamer, Chad; Coleman, Kathleen; Munson, Linda

    2012-12-01

    Cheetahs (Acinonyx jubatus) are a highly threatened species because of habitat loss, human conflict, and high prevalence of disease in captivity. An epidemic of feline infectious peritonitis and concern for spread of infectious disease resulted in decreased movement of cheetahs between U.S. zoological facilities for managed captive breeding. Identifying the true feline coronavirus (FCoV) infection status of cheetahs is challenging because of inconsistent correlation between seropositivity and fecal viral shedding. Because the pattern of fecal shedding of FCoV is unknown in cheetahs, this study aimed to assess the frequency of detectable fecal viral shedding in a 30-day period and to determine the most efficient fecal sampling strategy to identify cheetahs shedding FCoV. Fecal samples were collected from 16 cheetahs housed at seven zoological facilities for 30 to 46 consecutive days; the samples were evaluated for the presence of FCoV by reverse transcription-nested polymerase chain reaction (RT-nPCR). Forty-four percent (7/16) of cheetahs had detectable FCoV in feces, and the proportion of positive samples for individual animals ranged from 13 to 93%. Cheetahs shed virus persistently, intermittently, or rarely over 30-46 days. Fecal RT-nPCR results were used to calculate the probability of correctly identifying a cheetah known to shed virus given multiple hypothetical fecal collection schedules. The most efficient hypothetical fecal sample collection schedule was evaluation of five individual consecutive fecal samples, resulting in a 90% probability of identifying a known shedder. Demographic and management risk factors were not significantly associated (P cheetahs shed virus intermittently to rarely, fecal sampling schedules meant to identify all known shedders would be impractical with current tests and eradication of virus from the population unreasonable. Managing the captive population as endemically infected with FCoV may be a more feasible approach.

  16. Detection and differentiation of field and vaccine strains of canine distemper virus using reverse transcription followed by nested real time PCR (RT-nqPCR) and RFLP analysis.

    Science.gov (United States)

    Fischer, Cristine Dossin Bastos; Ikuta, Nilo; Canal, Cláudio Wageck; Makiejczuk, Aline; Allgayer, Mariangela da Costa; Cardoso, Cristine Hoffmeister; Lehmann, Fernanda Kieling; Fonseca, André Salvador Kazantzi; Lunge, Vagner Ricardo

    2013-12-01

    Canine distemper virus (CDV) is the cause of a severe and highly contagious disease in dogs. Practical diagnosis of canine distemper based on clinical signs and laboratory tests are required to confirm CDV infection. The present study aimed to develop a molecular assay to detect and differentiate field and vaccine CDV strains. Reverse transcription followed by nested real time polymerase chain reaction (RT-nqPCR) was developed, which exhibited analytical specificity (all the samples from healthy dogs and other canine infectious agents were not incorrectly detected) and sensitivity (all replicates of a vaccine strain were positive up to the 3125-fold dilution - 10(0.7) TCID50). RT-nqPCR was validated for CDV detection on different clinical samples (blood, urine, rectal and conjunctival swabs) of 103 animals suspected to have distemper. A total of 53 animals were found to be positive based on RT-nqPCR in at least one clinical sample. Blood resulted in more positive samples (50 out of 53, 94.3%), followed by urine (44/53, 83.0%), rectal (38/53, 71%) and conjunctival (27/53, 50.9%) swabs. A commercial immunochromatography (IC) assay had detected CDV in only 30 conjunctival samples of these positive dogs. Nucleoprotein (NC) gene sequencing of 25 samples demonstrated that 23 of them were closer to other Brazilian field strains and the remaining two to vaccine strains. A single nucleotide sequences difference, which creates an Msp I restriction enzyme digestion, was used to differentiate between field and vaccine CDV strains by restriction fragment length polymorphism (RFLP) analysis. The complete assay was more sensitive than was IC for the detection of CDV. Blood was the more frequently positive specimen and the addition of a restriction enzyme step allowed the differentiation of vaccine and Brazilian field strains.

  17. Gastroenteritis outbreaks associated with Norwalk-like viruses and their investigation by nested RT-PCR

    Directory of Open Access Journals (Sweden)

    Mitchell Frederick

    2001-08-01

    Full Text Available Abstract Background Norwalk-like viruses are the most common cause of gastroenteritis outbreaks and sporadic cases of vomiting and diarrhoea. In healthy individuals infection is often mild and short-lived but in debilitated patients infection can be severe. It is essential that the virus laboratory can offer a sensitive and specific test, delivered in a timely manner. Methods We have developed a nested reverse transcriptase PCR based on published primers against the RNA polymerase gene and after comparison with electronmicroscopy used the assay to investigate 31 outbreaks of gastroenteritis. These were in diverse situations including nursing homes, small district hospitals, large general hospitals, a ferry ship, hotels, restaurants and staff canteens. Results A positive diagnosis was made in 30/31 outbreaks investigated giving an overall outbreak positive detection rate of 97%. At an individual patient level there was a positive diagnostic rate of 11.5% in a large hospital environment to 100% in smaller outbreak situations. The average patient positive rate was 34%. In addition we investigated 532 control faecal specimens from adults. Of these 530 were negative and 2 were repeatedly positive. Conclusions It is essential that insensitive electronmicroscopy is replaced with the more sensitive reverse transcription PCR assays. These tests should be made available "on call" at weekends and public holidays. It is also important that outbreaks of NLV infection are monitored using sensitive RT-PCR assays so that the laboratory information can be used in ascertaining the spread and duration of the outbreak

  18. Triangular Nests!

    Science.gov (United States)

    Powell, R. I.

    2002-01-01

    Shows how integer-sided triangles can be nested, each nest having a single enclosing isosceles triangle. Brings to light what can be seen as a relatively simple generalization of Pythagoras' theorem, a result that should be readily accessible to many secondary school pupils. (Author/KHR)

  19. Hawaii ESI: NESTS (Nest Points)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for seabird nesting colonies in coastal Hawaii. Vector points in this data set represent locations of...

  20. Louisiana ESI: NESTS (Nest Points)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for seabird and wading bird nesting colonies in coastal Louisiana. Vector points in this data set represent...

  1. Reverse transcription - 3' rapid amplification of cDNA ends-nested PCR of ACT1 and SAP2 mRNA as a means of detecting viable Candida albicans in an in vitro cutaneous candidiasis model.

    Science.gov (United States)

    Okeke, C N; Tsuboi, R; Kawai, M; Yamazaki, M; Reangchainam, S; Ogawa, H

    2000-01-01

    The presence of viable cells of Candida albicans, in broth or in a reconstructed living skin equivalent, was determined by the detection of amplicons of partial mRNA sequences of the genes encoding fungal actin (ACT1) and secreted aspartyl proteinase 2 (SAP2). The mRNA of both genes were amplified by reverse transcription-3' rapid amplification of cDNA ends-nested polymerase chain reaction. Single bands of ACT1 (315 bp) and SAP2 (162 bp) mRNA were amplified from total RNA extracts of C. albicans grown in yeast carbon base-albumin broth or in living skin equivalent tissue; only the former was amplified from Sabouraud broth-grown organisms. Primer pairs targeted for ACT1 and SAP2 were Candida genus-specific and C. albicans-specific, respectively. The sensitivity limits of the assay were 100 fg of total RNA or 10 cells of C. albicans, by ethidium bromide staining. When C. albicans-infected living skin equivalent was exposed to amorolfine, amplicons of ACT1 and SAP2 mRNA were not detected in total RNA extracts. Non-amplification of the mRNA correlated with the absence of C. albicans growth in Sabouraud agar cultures of living skin equivalent samples. Reverse transcription-3' rapid amplification of cDNA ends-nested polymerase chain reaction of the mRNA encoding specific proteins of an organism has potential application in determining the viability of the organism in tissue, thus monitoring the efficacy of an antimicrobial therapy, and in detecting mRNA expressed in very little amounts in tissue.

  2. The development of a GeXP-based multiplex reverse transcription-PCR assay for simultaneous detection of sixteen human respiratory virus types/subtypes

    Directory of Open Access Journals (Sweden)

    Li Jin

    2012-08-01

    Full Text Available Abstract Background Existing standard non-molecular diagnostic methods such as viral culture and immunofluorescent (DFA are time-consuming, labor intensive or limited sensitivity. Several multiplex molecular assays are costly. Therefore, there is a need for the development of a rapid and sensitive diagnosis of respiratory viral pathogens. Methods A GeXP-based multiplex RT-PCR assay (GeXP assay was developed to detect simultaneously sixteen different respiratory virus types/subtypes. Seventeen sets of chimeric primers were used to initiate the RT-PCR, and one pair of universal primers was used for the subsequent cycles of the RT-PCR. The specificity of the GeXP assay was examined with positive controls for each virus type/subtype. The sensitivity was evaluated by performing the assay on serial ten-fold dilutions of in vitro-transcribed RNA of all RNA viruses and the plasmids containing the Adv and HBoV target sequence. GeXP assay was further evaluated using 126 clinical specimens and compared with Luminex xTAG RVP Fast assay. Results The GeXP assay achieved a sensitivity of 20–200 copies for a single virus and 1000 copies when all of the 16 pre-mixed viral targets were present. Analyses of 126 clinical specimens using the GeXP assay demonstrated that GeXP assay and the RVP Fast assay were in complete agreement for 109/126 (88.51% of the specimens. GeXP assay was more sensitive than the RVP Fast assay for the detection of HRV and PIV3, and slightly less sensitive for the detection of HMPV, Adv, RSVB and HBoV. The whole process of the GeXP assay for the detection of 12 samples was completed within 2.5 hours. Conclusions In conclusion, the GeXP assay is a rapid, cost-effective, sensitive, specific and high throughput method for the detection of respiratory virus infections.

  3. A Novel Duplex Real-Time Reverse-Transcription PCR Assay for the Detection of Influenza A and the Novel Influenza A(H1N1 Strain

    Directory of Open Access Journals (Sweden)

    Theo P. Sloots

    2009-12-01

    Full Text Available Timely implementation of antiviral treatment and other public health based responses are dependent on accurate and rapid diagnosis of the novel pandemic influenza A(H1N1 strain. In this study we developed a duplex real-time PCR (RT-PCR (dFLU-TM assay for the simultaneous detection of a broad range of influenza A subtypes and specific detection of the novel H1N1 2009 pandemic strain. The assay was compared to the combined results of two previously described monoplex RT-PCR assays using 183 clinical samples and 10 seasonal influenza A isolates. Overall, the results showed that the dFLU-TM RT-PCR method is suitable for detection of influenza A, including the novel H1N1 pandemic strain, in clinical samples.

  4. Real-time quantitative reverse transcription-PCR analysis of expression stability of Actinobacillus pleuropneumoniae housekeeping genes during in vitro growth under iron-depleted conditions

    DEFF Research Database (Denmark)

    Nielsen, K. K.; Boye, Mette

    2005-01-01

    control genes was used to correct five genes of interest. These genes were three genes involved in iron acquisition (tbpA, exbB, and fhuD), the heat shock protein gene groEL, and a putative quorum-sensing gene (luxS). The level of tbpA, exbB, and fhuD expression in A. pleuropneumoniae showed significant...

  5. A broad spectrum, one-step reverse-transcription PCR amplification of the neuraminidase gene from multiple subtypes of influenza A virus

    Directory of Open Access Journals (Sweden)

    Chen Wenbin

    2008-07-01

    Full Text Available Abstract Background The emergence of high pathogenicity strains of Influenza A virus in a variety of human and animal hosts, with wide geographic distribution, has highlighted the importance of rapid identification and subtyping of the virus for outbreak management and treatment. Type A virus can be classified into subtypes according to the viral envelope glycoproteins, hemagglutinin and neuraminidase. Here we review the existing specificity and amplification of published primers to subtype neuraminidase genes and describe a new broad spectrum primer pair that can detect all 9 neuraminidase subtypes. Results Bioinformatic analysis of 3,337 full-length influenza A neuraminidase segments in the NCBI database revealed semi-conserved regions not previously targeted by primers. Two degenerate primers with M13 tags, NA8F-M13 and NA10R-M13 were designed from these regions and used to generate a 253 bp cDNA product. One-step RT-PCR testing was successful in 31/32 (97% cases using a touchdown protocol with RNA from over 32 different cultured influenza A virus strains representing the 9 neuraminidase subtypes. Frozen blinded clinical nasopharyngeal aspirates were also assayed and were mostly of subtype N2. The region amplified was direct sequenced and then used in database searches to confirm the identity of the template RNA. The RT-PCR fragment generated includes one of the mutation sites related to oseltamivir resistance, H274Y. Conclusion Our one-step RT-PCR assay followed by sequencing is a rapid, accurate, and specific method for detection and subtyping of different neuraminidase subtypes from a range of host species and from different geographical locations.

  6. Clearance of human-pathogenic viruses from sludge: study of four stabilization processes by real-time reverse transcription-PCR and cell culture.

    Science.gov (United States)

    Monpoeho, S; Maul, A; Bonnin, C; Patria, L; Ranarijaona, S; Billaudel, S; Ferré, V

    2004-09-01

    Sludges derived from wastewater treatment are foul-smelling, biologically unstable substances. As well as containing numerous pathogenic microorganisms, they also consist of organic matter that can be used as agricultural fertilizer. Legislation nevertheless requires sludges to be virologically tested prior to spreading by the counting of infectious enterovirus particles. This method, based on culture of enterovirus on BGM cells, is lengthy and not very sensitive. The aim of this study was to propose an alternative method of genome quantification for all enteroviruses that is applicable to verifying the elimination of viruses in complex samples such as sludges. Our complete protocol was compared to the official method, consisting of enterovirus enumeration with the most probable number of cythopathic unit (MPNCU) assay through the study of four stabilization procedures: liming, composting, heat treatment, and mesophile anaerobic digestion. Enterovirus quantities at the start of the stabilization procedures were between 37 and 288 MPNCU/g on the one scale and between 4 and 5 log genome copies/g on the other. It was shown that all procedures except mesophile anaerobic digestion were highly effective in the elimination of enterovirus particles and genomes in wastewater sludges. Reduction of viruses by mesophile anaerobic digestion was by only 1 log (infectious particles and genomes). In conclusion, stabilization processes can indeed be checked by virological quality control of sludges with gene amplification. However, the infectivity of genomes needs to be confirmed with cell culture or a correlation model if the virological risk inherent in the agricultural use of such sludges is to be fully addressed.

  7. Quantitative assessment of the effect of uracil-DNA glycosylase on amplicon DNA degradation and RNA amplification in reverse transcription-PCR

    Directory of Open Access Journals (Sweden)

    Kleiboeker Steven B

    2005-04-01

    Full Text Available Abstract Although PCR and RT-PCR provided a valuable approach for detection of pathogens, the high level of sensitivity of these assays also makes them prone to false positive results. In addition to cross-contamination with true positive samples, false positive results are also possible due to "carry-over" contamination of samples with amplicon DNA generated by previous reactions. To reduce this source of false positives, amplicon generated by reactions in which dUTP was substituted for dTTP can be degraded by uracil DNA glycosylase (UNG. UNG does not degrade RNA but will cleave contaminating uracil-containing DNA while leaving thymine-containing DNA intact. The availability of heat-labile UNG makes use of this approach feasible for RT-PCR. In this study, real-time RT-PCR was used to quantify UNG degradation of amplicon DNA and the effect of UNG on RNA detection. Using the manufacturers' recommended conditions, complete degradation of DNA was not observed for samples containing 250 copies of amplicon DNA. Doubling the UNG concentration resulted in degradation of the two lowest concentrations of DNA tested, but also resulted in an increase of 1.94 cycles in the CT for RNA detection. To improve DNA degradation while minimizing the effect on RNA detection, a series of time, temperature and enzyme concentrations were evaluated. Optimal conditions were found to be 0.25 U UNG per 25 μl reaction with a 20 min, 30°C incubation prior to RT-PCR. Under these conditions, high concentrations of amplicon DNA could be degraded while the CT for RNA detection was increased by 1.2 cycles.

  8. Quantitative Real-Time Reverse Transcription-PCR Assay for the Expression of Tob mRNA in Human Colorectal Cancer

    Institute of Scientific and Technical Information of China (English)

    Dian-chao WU

    2010-01-01

    OBJECTIVE Tob is a member of Tob/BTG antiproliferative family. To date, Tob expression in human carcinoma using clinical specimens has not been studied in depth except for lung carcinoma and thyroid carcinoma. This study is the first to investigate the expression levels of Tob gene in human colorectal cancer tissues,and their corresponding para-cancerous tissues. The correlation of expression of the Tob gene with clinicopathological characteristics of colorectal cancer was also analyzed.METHODS Quantitative real time RT-PCR was used to detect the expression of Tob mRNA in 31 colorectal cancers.RESULTS Compared with normal tissues, up-regulation of Tob mRNA was observed in 31 colorectal cancer tissues (P = 0.020).The expression level of Tob at Dukes C + D phase was higher than Dukes A + B phase, and the difference was signifi cant (P < 0.05).However, in this study, it was found that the expression of Tob mRNA was not related with age, gender, and pathological type of colorectal cancer.CONCLUSION The up-regulation of Tob may be closely associated with tumorigenesis of colorectal carcinoma.

  9. Expression analysis of ETS1 gene in peripheral blood mononuclear cells with systemic lupus erythematosus by real-time reverse transcription PCR

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    @@ To the editor: Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease with complex genetic inheritance.l In recent years, genome-wide association studies (GWAS) had further provided novel insights into the genetics background of SLE by identifying multiple susceptibility genes in different ethnic populations.

  10. American Samoa ESI: NESTS (Nest Points)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for nesting birds in American Samoa. Vector points in this data set represent locations of nesting...

  11. Florida harvester ant nest architecture, nest relocation and soil carbon dioxide gradients.

    Science.gov (United States)

    Tschinkel, Walter R

    2013-01-01

    Colonies of the Florida harvester ant, Pogonomyrmex badius, excavate species-typical subterranean nests up the 3 m deep with characteristic vertical distribution of chamber area/shape, spacing between levels and vertical arrangement of the ants by age and brood stage. Colonies excavate and occupy a new nest about once a year, and doing so requires that they have information about the depth below ground. Careful excavation and mapping of vacated and new nests revealed that there was no significant difference between the old and new nests in any measure of nest size, shape or arrangement. Colonies essentially built a replicate of the just-vacated nest (although details differed), and they did so in less than a week. The reason for nest relocation is not apparent. Tschinkel noted that the vertical distribution of chamber area, worker age and brood type was strongly correlated to the soil carbon dioxide gradient, and proposed that this gradient serves as a template for nest excavation and vertical distribution. To test this hypothesis, the carbon dioxide gradient of colonies that were just beginning to excavate a new nest was eliminated by boring 6 vent holes around the forming nest, allowing the soil CO2 to diffuse into the atmosphere and eliminating the gradient. Sadly, neither the nest architecture nor the vertical ant distribution of vented nests differed from either unvented control or from their own vacated nest. In a stronger test, workers excavated a new nest under a reversed carbon dioxide gradient (high concentration near the surface, low below). Even under these conditions, the new and old nests did not differ significantly, showing that the soil carbon dioxide gradient does not serve as a template for nest construction or vertical worker distribution. The possible importance of soil CO2 gradients for soil-dwelling animals is discussed.

  12. Recruitment study nest card

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is a survey on waterfowl nests in Stillwater Wildlife Management Area. Visits were made to each nest on an approximately weekly basis, and the stage of the eggs...

  13. Simulated nest study guide

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The instructions outlined here will provide uniform methods for measuring total predator activity in blocks of nesting cover or at special kinds of nest sites. The...

  14. Columbia River ESI: NESTS (Nest Points)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for bird nesting sites in the Columbia River area. Vector points in this data set represent locations of...

  15. PyMultiNest: Python interface for MultiNest

    Science.gov (United States)

    Buchner, Johannes

    2016-06-01

    PyMultiNest provides programmatic access to MultiNest (ascl:1109.006) and PyCuba, integration existing Python code (numpy, scipy), and enables writing Prior & LogLikelihood functions in Python. PyMultiNest can plot and visualize MultiNest's progress and allows easy plotting, visualization and summarization of MultiNest results. The plotting can be run on existing MultiNest output, and when not using PyMultiNest for running MultiNest.

  16. Morphology of nested fullerenes

    Energy Technology Data Exchange (ETDEWEB)

    Srolovitz, D.J.; Safran, S.A.; Homyonfer, M.; Tenne, R. (Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100 (Israel))

    1995-03-06

    We introduce a continuum model which shows that dislocations and/or grain boundaries are intrinsic features of nested fullerenes whose thickness exceeds a critical value to relieve the large inherent strains in these structures. The ratio of the thickness to the radius of the nested fullerenes is determined by the ratio of the surface to curvature and dislocation (or grain boundary) energies. Confirming experimental evidence is presented for nested fullerenes with small thicknesses and with spherosymmetric shapes.

  17. 逆转录-套式PCR检测汉坦病毒感染的实验研究%Detection of hantavirus infection using reverse transcriptional - nested polymerase chain reaction

    Institute of Scientific and Technical Information of China (English)

    朱子犁; 刘建军; 阳帆; 汪洪富; 何建凡

    2007-01-01

    目的:探讨逆转录-套式聚合酶链反应(RT-nested-PCR)检测汉坦病毒(Hantavirus,HV)感染的准确性和敏感性.方法:用RT-nested-PCR和直接免疫荧光法(direct immunofluorescence,FA)分别检测深圳市2005年肾综合征出血热宿主动物监测中捕获的鼠类中HV的感染情况.结果:在76份特异性总抗体阳性的鼠肺标本中,用RT-nested-PCR检出61份抗原阳性,而FA仅检出47份阳性.结论:RT-nested-PCR是一种比较准确的检测汉坦病毒感染的方法,其敏感性高于FA.

  18. Superposition Enhanced Nested Sampling

    Directory of Open Access Journals (Sweden)

    Stefano Martiniani

    2014-08-01

    Full Text Available The theoretical analysis of many problems in physics, astronomy, and applied mathematics requires an efficient numerical exploration of multimodal parameter spaces that exhibit broken ergodicity. Monte Carlo methods are widely used to deal with these classes of problems, but such simulations suffer from a ubiquitous sampling problem: The probability of sampling a particular state is proportional to its entropic weight. Devising an algorithm capable of sampling efficiently the full phase space is a long-standing problem. Here, we report a new hybrid method for the exploration of multimodal parameter spaces exhibiting broken ergodicity. Superposition enhanced nested sampling combines the strengths of global optimization with the unbiased or athermal sampling of nested sampling, greatly enhancing its efficiency with no additional parameters. We report extensive tests of this new approach for atomic clusters that are known to have energy landscapes for which conventional sampling schemes suffer from broken ergodicity. We also introduce a novel parallelization algorithm for nested sampling.

  19. Multistate nested canalizing functions

    CERN Document Server

    Adeyeye, J O; Laubenbacher, R; Li, Y

    2013-01-01

    The concept of a nested canalizing Boolean function has been studied over the course of the last decade in the context of understanding the regulatory logic of molecular interaction networks, such as gene regulatory networks. Such functions appear preferentially in published models of such networks. Recently, this concept has been generalized to include multi-state functions, and a recursive formula has been derived for their number, as a function of the number of variables. This paper carries out a detailed analysis of the class of nested canalizing functions over an arbitrary finite field. Furthermore, the paper generalizes the concept further, and derives a closed formula for the number of such generalized functions. The paper also derives a closed formula for the number of equivalence classes under permutation of variables. This is motivated by the fact that two nested canalizing functions that differ by a permutation of the variables share many important properties with each other. The paper contributes ...

  20. Serenbe Nest Cottages

    Energy Technology Data Exchange (ETDEWEB)

    Butler, T.; Curtis, O.; Kim, E.; Roberts, S.; Stephenson, R.

    2012-12-01

    As part of the NAHB Research Center Industry Partnership, Southface partnered with Martin Dodson Builders and the Serenbe community on the construction of a new test home in the suburbs of Atlanta, GA in the mixed humid climate zone. The most recent subdivision within the Serenbe community, the Nest, will contain 15 small footprint cottage style homes, and Southface has selected Lot Nine, as the test home for this study. This Nest subdivision serves as a project showcase for both the builder partner and the Serenbe community as a whole. The planning and design incorporated into the Nest cottages will be implemented in each home within the subdivision. These homes addresses Building America Savings targets and serve as a basis of design for other homes Martin Dodson plans to build within the Serenbe community.

  1. Density-dependent nest predation in waterfowl: the relative importance of nest density versus nest dispersion

    Science.gov (United States)

    Ackerman, Joshua T.; Ringelman, Kevin M.; Eadie, J.M.

    2012-01-01

    When nest predation levels are very high or very low, the absolute range of observable nest success is constrained (a floor/ceiling effect), and it may be more difficult to detect density-dependent nest predation. Density-dependent nest predation may be more detectable in years with moderate predation rates, simply because there can be a greater absolute difference in nest success between sites. To test this, we replicated a predation experiment 10 years after the original study, using both natural and artificial nests, comparing a year when overall rates of nest predation were high (2000) to a year with moderate nest predation (2010). We found no evidence for density-dependent predation on artificial nests in either year, indicating that nest predation is not density-dependent at the spatial scale of our experimental replicates (1-ha patches). Using nearest-neighbor distances as a measure of nest dispersion, we also found little evidence for “dispersion-dependent” predation on artificial nests. However, when we tested for dispersion-dependent predation using natural nests, we found that nest survival increased with shorter nearest-neighbor distances, and that neighboring nests were more likely to share the same nest fate than non-adjacent nests. Thus, at small spatial scales, density-dependence appears to operate in the opposite direction as predicted: closer nearest neighbors are more likely to be successful. We suggest that local nest dispersion, rather than larger-scale measures of nest density per se, may play a more important role in density-dependent nest predation.

  2. Feathering Your Nest

    Science.gov (United States)

    Nabors, Martha L.; Edwards, Linda Carol; Decker, Suzanne

    2010-01-01

    The first-grade classroom was like a natural history museum. Bird nests of every shape and size lay on top of bookshelves that lined two walls. Methods students, who were visiting the classroom in preparation for the science lessons they would teach there, were immediately inspired by the collection. They used the collection as a springboard for…

  3. Simulated nests in wildlife management

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Many of us have studied game bird nests. Usually we hoped to learn something about nesting cover, cover management and the birds and animals which seemed to eat the...

  4. Nest and nest site characterisitcs of some ground-nesting, non-passerine birds of northern grasslands

    Science.gov (United States)

    Kantrud, H.A.; Higgins, K.F.

    1992-01-01

    We summarized biological and ecologic characteristics of 2490 nests of 16 species of upland-nesting, non-passerine birds of northern grasslands found during 1963 through 1991. Nest initiation and hatch dates, clutch sizes, nest fates, causes of failure, success rates of nests among major habitat types and land uses, and vegetation measurements at nest sites are analyzed.

  5. Studies on Reverse Transcription PCR Method for Infectious Pancreatic Necrosis Virus%传染性胰脏坏死病毒逆转录聚合酶链式反应法(RT-PCR)的研究

    Institute of Scientific and Technical Information of China (English)

    吴斌; 肇慧君; 李叶; 胡晓利

    2012-01-01

      本文针对 IPNV A 片段 VP5基因和 VP3基因分别设计了两对特异性引物,同时优化了反应体系和反应条件,建立了检测 IPNV 逆转录聚合酶链式反应法。并用优化好的反应条件对从人工感染的斑马病鱼中提取的核酸进行扩增,分别扩增出了224 bp 和206 bp 的目的条带。%  Two pairs of specific primers were designed based on VP5 and VP3 gene of IPNV fragment A,and the reaction system and conditions were optimized to establish a RT-PCR assay for detection of IPNV. And the optimized reaction system was used to amplify the nucleic acid extracted from the artificially infected Zebra diseased fish,gaining the target bands of 224 bp and 206 bp. The detection sensitivity was 1pg.

  6. Significance of detecting circulating hepatocellular carcinoma cells in peripheral blood of hepatocellular carcinoma patients by nested reverse transcription-polymerase chain reaction and its clinical value: a retrospective study.

    Science.gov (United States)

    Liu, Yang; Wang, Yue-ru; Wang, Long; Song, Rui-mei; Zhou, Bo; Song, Zhen-shun

    2014-01-01

    Circulating hepatocellular carcinoma cells may be detected by reverse transcription-polymerase chain reaction. We investigated the relationship between circulating hepatocellular carcinoma cells and hepatoma patient survival after different managements and survival periods. Peripheral vein blood (5 ml) samples were obtained from 113 patients with hepatocellular carcinoma and from 33 control subjects (9 with liver cirrhosis after hepatitis B, 14 with chronic hepatitis B, 10 healthy individuals) between January 1, 2009, and December 31, 2013. To detect circulating hepatocellular carcinoma cells in peripheral blood, alpha-fetoprotein messenger RNA was amplified from total RNA extracted from whole blood by reverse transcription-polymerase chain reaction. Alpha-fetoprotein messenger RNA was detected in 59 blood samples from the hepatocellular carcinoma patients (59/113, 52.2%). In contrast, there were no clinical control subjects whose samples showed detectable alpha-fetoprotein messenger RNA. The presence of alpha-fetoprotein messenger RNA in blood seemed to be correlated with the stage (by TNM classification) of hepatocellular carcinoma, serum alpha-fetoprotein value, and the presence of intrahepatic metastasis, portal vein thrombosis, tumor diameter and/or distant metastasis. In addition, alpha-fetoprotein messenger RNA was detected in the blood of 25 patients showing distant metastasis at extrahepatic organs (100%), in contrast to 32 of 88 cases without metastasis (36.4%). All the patients with hepatocellular carcinoma were followed. Seventeen patients with resection of a T 2 stage hepatocellular carcinoma had a survival of 3.2 years after surgical management, 38 cases with resection of a T3 stage hepatocellular carcinoma had a 1.3-year survival, and only 37 cases with T4 stage disease after different treatments except surgery survived for 0.6 years (P <0.01). The presence of alpha-fetoprotein messenger RNA in peripheral blood may be an indicator of circulating

  7. Intelligent nesting system

    Directory of Open Access Journals (Sweden)

    Đuričić Zoran

    2003-01-01

    Full Text Available The economy of the process for the manufacture of parts from sheet metal plates depends on successful solution of the process of cutting various parts from sheet metal plates. Essentially, the problem is to arrange contours within a defined space so that they take up minimal surface. When taken in this way, the considered problem assumes a more general nature; it refers to the utilization of a flat surface, and it can represent a general principle of arranging 2D contours on a certain surface. The paper presents a conceptual solution and a prototypal intelligent nesting system for optimal cutting. The problem of nesting can generally be divided into two intellectual phases: recognition and classification of shapes, and arrangement of recognized shapes on a given surface. In solving these problems, methods of artificial intelligence are applied. In the paper, trained neural network is used for recognition of shapes; on the basis of raster record of a part's drawing, it recognizes the part's shape and which class it belongs to. By means of the expert system, based on rules defined on the basis of acquisition of knowledge from manufacturing sections, as well as on the basis of certain mathematical algorithms, parts are arranged on the arrangement surface. Both systems can also work independently, having been built on the modular principle. The system uses various product models as elements of integration for the entire system. .

  8. PyNEST: a convenient interface to the NEST simulator

    Directory of Open Access Journals (Sweden)

    Jochen M Eppler

    2009-01-01

    Full Text Available The neural simulation tool NEST (http://www.nest-initiative.org is a simulator for heterogeneous networks of point neurons or neurons with a small number of compartments. It aims at simulations of large neural systems with more than 10^4 neurons and 10^7 to 10^9 synapses. NEST is implemented in C++ and can be used on a large range of architectures from single-core laptops over multi-core desktop computers to super-computers with thousands of processor cores. Python (http://www.python.org is a modern programming language that has recently received considerable attention in Computational Neuroscience. Python is easy to learn and has many extension modules for scientific computing (e.g. http://www.scipy.org. In this contribution we describe PyNEST, the new user interface to NEST. PyNEST combines NEST’s efficient simulation kernel with the simplicity and flexibility of Python. Compared to NEST’s native simulation language SLI, PyNEST makes it easier to set up simulations, generate stimuli, and analyze simulation results. We describe how PyNEST connects NEST and Python and how it is implemented. With a number of examples, we illustrate how it is used.

  9. Diagnosis of hepatitis C virus in Brazilian blood donors using a reverse transcriptase nested polymerase chain reaction: comparison with enzyme immunoassay and recombinant protein immunoblot assay Diagnóstico da hepatite por vírus C em doadores de sangue brasileiros, usando a reação de transcrição reversa e a reação em cadeia da polimerase "nested": comparação com os ensaios imunoenzimáticos e imunoblot recombinante

    Directory of Open Access Journals (Sweden)

    Neiva S. L. GONÇALES

    2000-10-01

    Full Text Available Screening blood donations for anti-HCV antibodies and alanine aminotransferase (ALT serum levels generally prevents the transmission of hepatitis C virus (HCV by transfusion. The aim of the present study was to evaluate the efficiency of the enzyme immunoassay (EIA screening policy in identifying potentially infectious blood donors capable to transmit hepatitis C through blood transfusion. We have used a reverse transcriptase (RT-nested polymerase chain reaction (PCR to investigate the presence of HCV-RNA in blood donors. The prevalence of HCV-RNA positive individuals was compared with the recombinant immunoblot assay (RIBA-2 results in order to assess the usefulness of both tests as confirmatory assays. Both tests results were also compared with the EIA-2 OD/C ratio (optical densities of the samples divided by the cut off value. ALT results were expressed as the ALT quotient (qALT, calculated dividing the ALT value of the samples by the maximum normal value (53UI/l for the method. Donors (n=178 were divided into five groups according to their EIA anti-HCV status and qALT: group A (EIA > or = 3, ALT or = 3, ALT>1, group C (11 and group E (EIA or = 3 and detectable HCV-RNA by RT-nested PCR. We have also noted that blood donors with RIBA-2 indeterminate presented a high degree of detectable HCV-RNA using RT-nested PCR (75%, especially when the c22.3 band was detected.Na prevenção da transmissão de Hepatite por Vírus C (HCV em transfusões de hemocomponentes, utiliza-se rotineiramente, como testes de triagem de doadores de sangue, ensaios que detectam anticorpos anti-HCV e dosagens da enzima alanina-aminotransferase (ALT. O presente estudo tem como objetivo principal avaliar a eficiência do ensaio imunoenzimático de segunda geração (EIA-2 como teste de triagem, na identificação de doadores de sangue potencialmente infectados, e portanto, capazes de transmitir hepatite C pelos hemocomponentes. Nós utilizamos o ensaio de transcri

  10. The Nest Home

    Energy Technology Data Exchange (ETDEWEB)

    Pickerill, Heath [Missouri Univ. of Science and Technology, Rolla, MO (United States)

    2016-07-11

    The purpose of the project was to build a competitive solar-powered house for the U.S. Department of Energy Solar Decathlon 2015 held in Irvine, California. The house, named the Nest Home, was an innovative design that works with the environment to meet the needs of the occupants, identified as a growing family. Reused materials were instrumental in the design. Three refurbished shipping containers composed the primary structure of the house, creating an open floor plan that defies common architecture for container homes. The exterior siding was made of deconstructed shipping pallets collected locally. Other recycled products included carpet composed of discarded fishing nets, denim batting made of recycled blue jeans that outperform traditional fiberglass insulation in sound proofing and thermal resistance, and kitchen cabinets that were purchased used and refinished. Collectively these elements formed a well-balanced blend of modern design, comfort, and sustainability. The house was Missouri University of Science and Technology’s sixth entry in the DOE Solar Decathlon. Missouri S&T has been invited to compete in six of the seven decathlons held, more than any other university worldwide. The house was brought back to Rolla after the Decathlon in California where it has been placed in its permanent location on the S&T campus.

  11. Nested subgraphs of complex networks

    Energy Technology Data Exchange (ETDEWEB)

    Corominas-Murtra, Bernat; Sole, Ricard V [ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 80, 08003 Barcelona (Spain); Mendes, Jose F F [Departamento de Fisica da Universidade de Aveiro, 3810-193 Aveiro (Portugal)], E-mail: bernat.corominas@upf.edu

    2008-09-26

    We analytically explore the scaling properties of a general class of nested subgraphs in complex networks, which includes the K-core and the K-scaffold, among others. We name such a class of subgraphs K-nested subgraphs since they generate families of subgraphs such that ...S{sub K+1}(G) subset or equal S{sub K}(G) subset or equal S{sub K-1}(G).... Using the so-called configuration model it is shown that any family of nested subgraphs over a network with diverging second moment and finite first moment has infinite elements (i.e. lacking a percolation threshold). Moreover, for a scale-free network with the above properties, we show that any nested family of subgraphs is self-similar by looking at the degree distribution. Both numerical simulations and real data are analyzed and display good agreement with our theoretical predictions.

  12. Factors influencing depredation of artificial duck nests

    Science.gov (United States)

    Esler, Daniel N.; Grand, James B.

    1993-01-01

    Because artificial nests can facilitate controlled experiments of nest success, we used them to assess whether human visitation, nest density, vegetation structure, and proximity to habitat edge could affect depredation of duck nests on Yukon Flats National Wildlife Refuge, Alaska. More (P depredated than those in plots visited at intervals of 7 (40%), 14 (35%), or 28 days (45%). More (P depredated in a plot with 10 nests/ha (95%) than nests in a plot of a lower density (2/ha; 40%). Vegetation height, vegetation density, distance to a wetland, distance to forest edge, or distance to the nearest ecotone did not differ (P > 0.05) between depredated and undisturbed nests. We suggest that daily visitation of duck nests increases depredation, but longer intervals, typical of most nest studies, do not. High nesting densities, which could occur when flooding limits nesting habitat, may result in higher depredation rates.

  13. Are nest sites actively chosen? Testing a common assumption for three non-resource limited birds

    Science.gov (United States)

    Goodenough, A. E.; Elliot, S. L.; Hart, A. G.

    2009-09-01

    Many widely-accepted ecological concepts are simplified assumptions about complex situations that remain largely untested. One example is the assumption that nest-building species choose nest sites actively when they are not resource limited. This assumption has seen little direct empirical testing: most studies on nest-site selection simply assume that sites are chosen actively (and seek explanations for such behaviour) without considering that sites may be selected randomly. We used 15 years of data from a nestbox scheme in the UK to test the assumption of active nest-site choice in three cavity-nesting bird species that differ in breeding and migratory strategy: blue tit ( Cyanistes caeruleus), great tit ( Parus major) and pied flycatcher ( Ficedula hypoleuca). Nest-site selection was non-random (implying active nest-site choice) for blue and great tits, but not for pied flycatchers. We also considered the relative importance of year-specific and site-specific factors in determining occupation of nest sites. Site-specific factors were more important than year-specific factors for the tit species, while the reverse was true for pied flycatchers. Our results show that nest-site selection, in birds at least, is not always the result of active choice, such that choice should not be assumed automatically in studies of nesting behaviour. We use this example to highlight the need to test key ecological assumptions empirically, and the importance of doing so across taxa rather than for single "model" species.

  14. Nest poaching in Neotropical parrots

    Science.gov (United States)

    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.

  15. Reverse Logistics

    OpenAIRE

    Kulikova, Olga

    2016-01-01

    This thesis was focused on the analysis of the concept of reverse logistics and actual reverse processes which are implemented in mining industry and finding solutions for the optimization of reverse logistics in this sphere. The objective of this paper was the assessment of the development of reverse logistics in mining industry on the example of potash production. The theoretical part was based on reverse logistics and mining waste related literature and provided foundations for further...

  16. Reversible Communicating Processes

    Directory of Open Access Journals (Sweden)

    Geoffrey Brown

    2016-02-01

    Full Text Available Reversible distributed programs have the ability to abort unproductive computation paths and backtrack, while unwinding communication that occurred in the aborted paths. While it is natural to assume that reversibility implies full state recovery (as with traditional roll-back recovery protocols, an interesting alternative is to separate backtracking from local state recovery. For example, such a model could be used to create complex transactions out of nested compensable transactions where a programmer-supplied compensation defines the work required to "unwind" a transaction. Reversible distributed computing has received considerable theoretical attention, but little reduction to practice; the few published implementations of languages supporting reversibility depend upon a high degree of central control. The objective of this paper is to demonstrate that a practical reversible distributed language can be efficiently implemented in a fully distributed manner. We discuss such a language, supporting CSP-style synchronous communication, embedded in Scala. While this language provided the motivation for the work described in this paper, our focus is upon the distributed implementation. In particular, we demonstrate that a "high-level" semantic model can be implemented using a simple point-to-point protocol.

  17. Successful nesting behavior of Puerto Rican parrots

    Science.gov (United States)

    Wilson, K.A.; Field, R.; Wilson, M.H.

    1995-01-01

    We analyzed nesting behavior of five pairs of the endangered Puerto Rican Parrot (Amazona vittata) during eight successful nesting attempts. Each stage of the nesting cycle (egg laying, incubation, early chick rearing, and late chick rearing) was characterized by distinct trends or levels of behavior. During egg laying, female attentiveness to tile nest increased, and male attentiveness decreased. Throughout incubation and the first several days of early chick rearing, females were highly attentive to their nests, whereas males rarely entered the nest cavities. Female attentiveness then began to decline. Male attentiveness to the nest was sporadic until chicks were 10-12 days old. when all males began to enter their nests at least once each day. During late chick rearing, both male and female attentiveness were erratic and highly variable. Biologists may be able to use these results to identify nest problems and the need for management intervention when patterns of nest attentiveness deviate from the limits described in this study..

  18. A new method for screening splice variants using gene-specific primer for reverse transcription followed by nested PCR approaches%利用GSP逆转录结合巢式PCR技术鉴定剪接变体的新方法及其在小鼠TrkC基因变体发现中的应用

    Institute of Scientific and Technical Information of China (English)

    张艳春; 严瑞芬; 吴永红; 张成岗

    2011-01-01

    Objective To develop a new method for screening splice variants using gene-specific reverse primer ( GSP ) to specifically reverse transcribe ( RT ) the target genes followed by nested PCR( nPCR ) approaches. Methods The reverse primer for transcription and nPCR primers of the known splicing variant No. I and variant No. 2 of the mouse TrlcC gene were used to obtain the GSP-transcribed cDNA products, followed by two or three rounds of nPCR. The PCR products were separated and extracted by 1. 5% agarase gel electrophoresis and subcloned into the pMD19-T vector for direct sequencing and similarity analysis with the known cDNA sequence of the TrkC gene in the RefSeq database. Results Not only was the known variant ( splicing variant No. I ) of the TrlcC gene obtained, but the new splicing variant was found. The 1669 bp from 520 to 2188 of the sequence of splicing variant No. 1 of the TrkC gene was spliced in the newly identified variant No. 3 , indicating a splicing pattern of cassette exon. Conclusion This method of screening gene splice variants using RT-GSPs and nPCR is a simple and valuable approach to screening novel splice variants, which is important for the function studies of eukaryotic genes and for understanding the mechanism of aberrant splicing-related diseases.%目的 利用基因特异性引物(gene specific primer,GSP)逆转录结合巢式PCR(nPCR)技术,建立鉴定剪接变体的新方法.方法 以小鼠TrkC基因为例,参考其已知变体1和变体2的序列分别设计GSP和nPCR引物,以逆转录产物为模板进行nPCR反应,扩增产物采用1.5%琼脂糖凝胶分离并回收具有递减趋势的DNA片段,利用T/A克隆技术亚克隆到载体pMD19-T进行直接测序,并与小鼠RefSeq数据库进行比对.结果 利用GSP逆转录结合nPCR技术不仅可鉴定出TrkC基因的已知剪接变体,而且还能够筛选到TrkC基因的新剪接变体并命名为变体3,与变体1相比属于盒式外显子剪接模式,缺失了变体1的520

  19. Can selection on nest size from nest predation explain the latitudinal gradient in clutch size?

    Science.gov (United States)

    Biancucci, L.; Martin, T.E.

    2010-01-01

    1. Latitudinal variation in clutch sizes of birds is a well described, but poorly understood pattern. Many hypotheses have been proposed, but few have been experimentally tested, and none have been universally accepted by researchers. 2. The nest size hypothesis posits that higher nest predation in the tropics favours selection for smaller nests and thereby constrains clutch size by shrinking available space for eggs and/or nestlings in the nest. We tested this hypothesis with an experiment in a tropical forest and a comparative study between temperate and tropical field sites. 3. Specifically, we tested if: (i) predation increased with nest size; (ii) tropical birds had smaller nests controlled for body size; and (iii) clutch size was explained by nest size controlled for body size. 4. Experimental swapping of nests of different sizes showed that nest predation increased with nest size in the tropical site. Moreover, nest predation rates were higher in species with larger nests in both sites. However, nest size, corrected for body mass and phylogeny, did not differ between sites and was not related to clutch size between sites. 5. Hence, nest predation can exert selection on nest size as predicted by the hypothesis. Nest size increased with adult body mass, such that adult size might indirectly influence reproductive success through effects on nest size and nest predation risk. Ultimately, however, selection from nest predation on nest size does not explain the smaller clutch sizes typical of the tropics.

  20. Nested Dynamic Condition Response Graphs

    DEFF Research Database (Denmark)

    Hildebrandt, Thomas; Mukkamala, Raghava Rao; Slaats, Tijs

    2012-01-01

    We present an extension of the recently introduced declarative process model Dynamic Condition Response Graphs ( DCR Graphs) to allow nested subgraphs and a new milestone relation between events. The extension was developed during a case study carried out jointly with our industrial partner...... Exformatics, a danish provider of case and workflow management systems. We formalize the semantics by giving first a map from Nested to (flat) DCR Graphs with milestones, and then extending the previously given mapping from DCR Graphs to Buchi-automata to include the milestone relation....

  1. Patterns of magpie nest utilization by a nesting raptor community in a secondary forest

    Institute of Scientific and Technical Information of China (English)

    Tong Zhou; Haitao Wang; Yu Liu; Fumin Lei; Wei Gao

    2009-01-01

    For a total of 9 years, we examined the patterns of a nesting raptor community that utilized European Magpie (Pica pica) nests in the Zuojia Natural Reserve, northeast China. Eight raptor species and two other bird species were recorded nesting in magpie nests. The reuse rate of abandoned magpie nests was 51.6%, and the number of reused nests was positively correlated with their availability. Raptors utilized 83.3% of the reused abandoned magpie nests. Nests followed for more than 1 year were reused by raptors an average of 1.13 times. Inter-specific nest usurpation was common, with 17.3% of new magpie nests being usurped by raptors, and four cases of usurpation occurred among different raptor species. At the community level, 8 of 11 raptor species took over magpie nests to breed in the study area, and 91.9% of their nests came from magpie nests. European Magpies represent the core species in the nest web of the local raptor community that utilizes magpie nests. At the forest stand level, closer proximity to forest edges and greater distances from occupied raptor nests were the best predictors of nest reuse. At the nest-site level, arbor density and canopy coverage were the best predictors of nest reuse.

  2. Unusual raptor nests around the world

    Science.gov (United States)

    Ellis, D.H.; Craig, T.; Craig, E.; Postupalsky, S.; LaRue, C.T.; Nelson, R.W.; Anderson, D.W.; Henny, C.J.; Watson, J.; Millsap, B.A.; Dawson, J.W.; Cole, K.L.; Martin, E.M.; Margalida, A.; Kung, P.

    2009-01-01

    From surveys in many countries, we report raptors using unusual nesting materials (e.g., paper money, rags, metal, antlers, and large bones) and unusual nesting situations. For example, we documented nests of Steppe Eagles Aquila nipalensis and Upland Buzzards Buteo hemilasius on the ground beside well-traveled roads, Saker Falcon Falco cherrug eyries in attics and a cistern, and Osprey Pandion haliaetus nests on the masts of boats and on a suspended automobile. Other records include a Golden Eagle A. chrysaetos nest 7.0 m in height, believed to be the tallest nest ever described, and, for the same species, we report nesting in rudimentary nests. Some nest sites are within a few meters of known predators or competitors. These unusual observations may be important in revealing the plasticity of a species' behavioral repertoire. ?? 2009 The Raptor Research Foundation, Inc.

  3. Instantiation Schemes for Nested Theories

    CERN Document Server

    Echenim, Mnacho

    2011-01-01

    This paper investigates under which conditions instantiation-based proof procedures can be combined in a nested way, in order to mechanically construct new instantiation procedures for richer theories. Interesting applications in the field of verification are emphasized, particularly for handling extensions of the theory of arrays.

  4. Development with age of nest box use and gregarious nesting in laying hens

    DEFF Research Database (Denmark)

    Riber, Anja Brinch

    2010-01-01

    Use of nest boxes is an important part of the behavioural repertoire of laying hens kept under commercial conditions. A special form of nest box use is gregarious nesting, which occurs when a hen given the choice between an occupied and an unoccupied nest site chooses the occupied nest site...... experiences in selection of nest locations, causing the found decrease in frequency of gregarious nesting after age 20 weeks. A general preference for corner and end nest boxes is suggested to have triggered the initial use of the left nest box by the first hens coming into lay and to have maintained...... risk of broken or dirty eggs. The main objectives were to investigate the use of nest boxes according to their position and the occurrence of gregarious nesting with age. Twelve groups of 15 Isa Warren hens were housed in pens each containing three adjacent roll-out nest boxes only differing...

  5. Influence of Habitat Types on Prairie Nesting Waterfowl Nest Density and Nest Success in Northeastern North Dakota, 2010 – 2013

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Nest density and nest success of ducks in native and non-native grasslands within the Devils Lake WMD, Northeastern North Dakota. Waterfowl representing 8 species of...

  6. Importance Nested Sampling and the MultiNest Algorithm

    CERN Document Server

    Feroz, F; Cameron, E; Pettitt, A N

    2013-01-01

    Bayesian inference involves two main computational challenges. First, in estimating the parameters of some model for the data, the posterior distribution may well be highly multi-modal: a regime in which the convergence to stationarity of traditional Markov Chain Monte Carlo (MCMC) techniques becomes incredibly slow. Second, in selecting between a set of competing models the necessary estimation of the Bayesian evidence for each is, by definition, a (possibly high-dimensional) integration over the entire parameter space; again this can be a daunting computational task, although new Monte Carlo (MC) integration algorithms offer solutions of ever increasing efficiency. Nested sampling (NS) is one such contemporary MC strategy targeted at calculation of the Bayesian evidence, but which also enables posterior inference as a by-product, thereby allowing simultaneous parameter estimation and model selection. The widely-used MultiNest algorithm presents a particularly efficient implementation of the NS technique for...

  7. Ouray National Wildlife Refuge : Duck nesting survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Summary report of the 1991 duck nest survey at Ouray National Wildlife Refuge. Key areas of the refuge were nest searched during the period between May 25th and July...

  8. Sorting it out: bedding particle size and nesting material processing method affect nest complexity.

    Science.gov (United States)

    Robinson-Junker, Amy; Morin, Amelia; Pritchett-Corning, Kathleen; Gaskill, Brianna N

    2017-04-01

    As part of routine husbandry, an increasing number of laboratory mice receive nesting material in addition to standard bedding material in their cages. Nesting material improves health outcomes and physiological performance in mice that receive it. Providing usable nesting material uniformly and efficiently to various strains of mice remains a challenge. The aim of this study was to determine how bedding particle size, method of nesting material delivery, and processing of the nesting material before delivery affected nest building in mice of strong (BALB/cAnNCrl) and weak (C3H/HeNCrl) gathering abilities. Our data suggest that processing nesting material through a grinder in conjunction with bedding material, although convenient for provision of bedding with nesting material 'built-in', negatively affects the integrity of the nesting material and subsequent nest-building outcomes. We also found that C3H mice, previously thought to be poor nest builders, built similarly scored nests to those of BALB/c mice when provided with unprocessed nesting material. This was true even when nesting material was mixed into the bedding substrate. We also observed that when nesting material was mixed into the bedding substrate, mice of both strains would sort their bedding by particle size more often than if it were not mixed in. Our findings support the utility of the practice of distributing nesting material mixed in with bedding substrate, but not that of processing the nesting material with the bedding in order to mix them.

  9. Nested Quantum Error Correction Codes

    CERN Document Server

    Wang, Zhuo; Fan, Hen; Vedral, Vlatko

    2009-01-01

    The theory of quantum error correction was established more than a decade ago as the primary tool for fighting decoherence in quantum information processing. Although great progress has already been made in this field, limited methods are available in constructing new quantum error correction codes from old codes. Here we exhibit a simple and general method to construct new quantum error correction codes by nesting certain quantum codes together. The problem of finding long quantum error correction codes is reduced to that of searching several short length quantum codes with certain properties. Our method works for all length and all distance codes, and is quite efficient to construct optimal or near optimal codes. Two main known methods in constructing new codes from old codes in quantum error-correction theory, the concatenating and pasting, can be understood in the framework of nested quantum error correction codes.

  10. An Undecidable Nested Recurrence Relation

    CERN Document Server

    Celaya, Marcel

    2012-01-01

    Roughly speaking, a recurrence relation is nested if it contains a subexpression of the form ... A(...A(...)...). Many nested recurrence relations occur in the literature, and determining their behavior seems to be quite difficult and highly dependent on their initial conditions. A nested recurrence relation A(n) is said to be undecidable if the following problem is undecidable: given a finite set of initial conditions for A(n), is the recurrence relation calculable? Here calculable means that for every n >= 0, either A(n) is an initial condition or the calculation of A(n) involves only invocations of A on arguments in {0,1,...,n-1}. We show that the recurrence relation A(n) = A(n-4-A(A(n-4)))+4A(A(n-4)) +A(2A(n-4-A(n-2))+A(n-2)). is undecidable by showing how it can be used, together with carefully chosen initial conditions, to simulate Post 2-tag systems, a known Turing complete problem.

  11. Supramolecular nesting of cyclic polymers.

    Science.gov (United States)

    Kondratuk, Dmitry V; Perdigão, Luís M A; Esmail, Ayad M S; O'Shea, James N; Beton, Peter H; Anderson, Harry L

    2015-04-01

    Advances in template-directed synthesis make it possible to create artificial molecules with protein-like dimensions, directly from simple components. These synthetic macromolecules have a proclivity for self-organization that is reminiscent of biopolymers. Here, we report the synthesis of monodisperse cyclic porphyrin polymers, with diameters of up to 21 nm (750 C–C bonds). The ratio of the intrinsic viscosities for cyclic and linear topologies is 0.72, indicating that these polymers behave as almost ideal flexible chains in solution. When deposited on gold surfaces, the cyclic polymers display a new mode of two-dimensional supramolecular organization, combining encapsulation and nesting; one nanoring adopts a near-circular conformation, thus allowing a second nanoring to be captured within its perimeter, in a tightly folded conformation. Scanning tunnelling microscopy reveals that nesting occurs in combination with stacking when nanorings are deposited under vacuum, whereas when they are deposited directly from solution under ambient conditions there is stacking or nesting, but not a combination of both.

  12. Nesting behavior of the poo-uli

    Science.gov (United States)

    Kepler, C.B.; Pratt, T.K.; Ecton, A.M.; Engilis, A.; Fluetsch, K.M.

    1996-01-01

    We describe two sequential nestings of a pair of Poo-uli (Melamprosops phaeosoma), a Hawaiian honeycreeper nearing extinction. Similarities to nesting of most other honeycreepers included: nest site in ohia lehua (Metrosideros polymorpha Gaud.) canopy; breeding in March through June; monogamous breeding system with the putative male helping build the nest, feeding the putative female throughout each nesting event, and feeding the chicks, but not incubating or brooding; and complete nest sanitation. Notable differences were the paucity of songs and calls by the parents and inclusion of snails in the diet of nestlings. Clutch size was probably two eggs for both nests. High winds, rain, or both influenced parental behavior: the female stayed longer on the nest and took shorter recesses in poor weather. Weather did not affect rates at which the male fed the female on the nest; however, the feeding rate increased from the egg to the chick stage probably because food was passed on to the chicks. At nest #2, parents fed young chicks (<14 days old) more often in good than in poor weather; data were insufficient for old chicks. Weather is usually poor throughout the year in the relictual range of the Poo-uli and is likely to impact nesting success. The first nest failed in poor weather. The second fledged a single young 21 days old. Diet of nestlings appeared to consist of a higher proportion of insect larvae than that of older birds, which are reported to eat mostly snails.

  13. On the Denesting of Nested Square Roots

    Science.gov (United States)

    Gkioulekas, Eleftherios

    2017-01-01

    We present the basic theory of denesting nested square roots, from an elementary point of view, suitable for lower level coursework. Necessary and sufficient conditions are given for direct denesting, where the nested expression is rewritten as a sum of square roots of rational numbers, and for indirect denesting, where the nested expression is…

  14. Nest Material Shapes Eggs Bacterial Environment.

    Directory of Open Access Journals (Sweden)

    Cristina Ruiz-Castellano

    Full Text Available Selective pressures imposed by pathogenic microorganisms to embryos have selected in hosts for a battery of antimicrobial lines of defenses that includes physical and chemical barriers. Due to the antimicrobial properties of volatile compounds of green plants and of chemicals of feather degrading bacteria, the use of aromatic plants and feathers for nest building has been suggested as one of these barriers. However, experimental evidence suggesting such effects is scarce in the literature. During two consecutive years, we explored experimentally the effects of these nest materials on loads of different groups of bacteria (mesophilic bacteria, Enterobacteriaceae, Staphylococcus and Enterococcus of eggshells in nests of spotless starlings (Sturnus unicolor at the beginning and at the end of the incubation period. This was also explored in artificial nests without incubation activity. We also experimentally increased bacterial density of eggs in natural and artificial nests and explored the effects of nest lining treatments on eggshell bacterial load. Support for the hypothetical antimicrobial function of nest materials was mainly detected for the year and location with larger average values of eggshell bacterial density. The beneficial effects of feathers and plants were more easily detected in artificial nests with no incubation activity, suggesting an active role of incubation against bacterial colonization of eggshells. Pigmented and unpigmented feathers reduced eggshell bacterial load in starling nests and artificial nest boxes. Results from artificial nests allowed us to discuss and discard alternative scenarios explaining the detected association, particularly those related to the possible sexual role of feathers and aromatic plants in starling nests. All these results considered together confirm the antimicrobial functionality mainly of feathers but also of plants used as nest materials, and highlight the importance of temporally and

  15. Effect of heterogeneity of nest boxes on occurrence of gregarious nesting in laying hens

    DEFF Research Database (Denmark)

    Clausen, Tina; Riber, Anja Brinch

    2012-01-01

    Gregarious nesting, where hens select already occupied nest boxes even when other nest boxes are unoccupied, is an unwanted behaviour in laying hens that may reduce animal welfare and pose a financial cost to the producer. It has been suggested that gregarious nesting is caused by the difficulties...... experienced by hens in distinguishing between nest boxes in long rows of identical boxes. Heterogeneity of nest boxes has therefore been suggested as a method to reduce gregarious nesting. To test this hypothesis two experiments were performed. Twelve groups of 13–15 ISA Warren hens 27 weeks of age were...... nesting was higher in experimental groups compared to control groups (P laying period did not differ between the experimental and control groups (P = 0.41). Numbers of visits to and eggs laid in nest boxes positioned either left or right were higher compared to nest boxes positioned...

  16. Reverse logistics

    NARCIS (Netherlands)

    M.P. de Brito (Marisa); S.D.P. Flapper; R. Dekker (Rommert)

    2002-01-01

    textabstractThis paper gives an overview of scientific literature that describes and discusses cases of reverse logistics activities in practice. Over sixty case studies are considered. Based on these studies we are able to indicate critical factors for the practice of reverse logistics. In addi

  17. Nest predation increases with parental activity: separating nest site and parental activity effects.

    OpenAIRE

    Martin, T E; Scott, J; Menge, C

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators h...

  18. Nest Predation Deviates from Nest Predator Abundance in an Ecologically Trapped Bird.

    Science.gov (United States)

    Hollander, Franck A; Van Dyck, Hans; San Martin, Gilles; Titeux, Nicolas

    2015-01-01

    In human-modified environments, ecological traps may result from a preference for low-quality habitat where survival or reproductive success is lower than in high-quality habitat. It has often been shown that low reproductive success for birds in preferred habitat types was due to higher nest predator abundance. However, between-habitat differences in nest predation may only weakly correlate with differences in nest predator abundance. An ecological trap is at work in a farmland bird (Lanius collurio) that recently expanded its breeding habitat into open areas in plantation forests. This passerine bird shows a strong preference for forest habitat, but it has a higher nest success in farmland. We tested whether higher abundance of nest predators in the preferred habitat or, alternatively, a decoupling of nest predator abundance and nest predation explained this observed pattern of maladaptive habitat selection. More than 90% of brood failures were attributed to nest predation. Nest predator abundance was more than 50% higher in farmland, but nest predation was 17% higher in forest. Differences between nest predation on actual shrike nests and on artificial nests suggested that parent shrikes may facilitate nest disclosure for predators in forest more than they do in farmland. The level of caution by parent shrikes when visiting their nest during a simulated nest predator intrusion was the same in the two habitats, but nest concealment was considerably lower in forest, which contributes to explaining the higher nest predation in this habitat. We conclude that a decoupling of nest predator abundance and nest predation may create ecological traps in human-modified environments.

  19. Reversible arithmetic logic unit for quantum arithmetic

    DEFF Research Database (Denmark)

    Thomsen, Michael Kirkedal; Glück, Robert; Axelsen, Holger Bock

    2010-01-01

    -bit operands and does not use ancillae. This remarkable low resource consumption was achieved by generalizing the V-shape design first introduced for quantum ripple-carry adders and nesting multiple V-shapes in a novel integrated design. This communication shows that the realization of an efficient reversible...

  20. DNest3: Diffusive Nested Sampling

    Science.gov (United States)

    Brewer, Brendon

    2016-04-01

    DNest3 is a C++ implementation of Diffusive Nested Sampling (ascl:1010.029), a Markov Chain Monte Carlo (MCMC) algorithm for Bayesian Inference and Statistical Mechanics. Relative to older DNest versions, DNest3 has improved performance (in terms of the sampling overhead, likelihood evaluations still dominate in general) and is cleaner code: implementing new models should be easier than it was before. In addition, DNest3 is multi-threaded, so one can run multiple MCMC walkers at the same time, and the results will be combined together.

  1. Nested-cone transformer antenna

    Science.gov (United States)

    Ekdahl, Carl A.

    1991-01-01

    A plurality of conical transmission lines are concentrically nested to form n output antenna for pulsed-power, radio-frequency, and microwave sources. The diverging conical conductors enable a high power input density across a bulk dielectric to be reduced below a breakdown power density at the antenna interface with the transmitting medium. The plurality of cones maintain a spacing between conductors which minimizes the generation of high order modes between the conductors. Further, the power input feeds are isolated at the input while enabling the output electromagnetic waves to add at the transmission interface. Thus, very large power signals from a pulse rf, or microwave source can be radiated.

  2. Polytypic Functions Over Nested Datatypes

    Directory of Open Access Journals (Sweden)

    Ralf Hinze

    1999-12-01

    Full Text Available The theory and practice of polytypic programming is intimately connected with the initial algebra semantics of datatypes. This is both a blessing and a curse. It is a blessing because the underlying theory is beautiful and well developed. It is a curse because the initial algebra semantics is restricted to so-called regular datatypes. Recent work by R. Bird and L. Meertens [3] on the semantics of non-regular or nested datatypes suggests that an extension to general datatypes is not entirely straightforward. Here we propose an alternative that extends polytypism to arbitrary datatypes, including nested datatypes and mutually recursive datatypes. The central idea is to use rational trees over a suitable set of functor symbols as type arguments for polytypic functions. Besides covering a wider range of types the approach is also simpler and technically less involving than previous ones. We present several examples of polytypic functions, among others polytypic reduction and polytypic equality. The presentation assumes some background in functional and in polytypic programming. A basic knowledge of monads is required for some of the examples.

  3. Eggs in the Freezer: Energetic Consequences of Nest Site and Nest Design in Arctic Breeding Shorebirds

    Science.gov (United States)

    Tulp, Ingrid; Schekkerman, Hans; de Leeuw, Joep

    2012-01-01

    Birds construct nests for several reasons. For species that breed in the Arctic, the insulative properties of nests are very important. Incubation is costly there and due to an increasing surface to volume ratio, more so in smaller species. Small species are therefore more likely to place their nests in thermally favourable microhabitats and/or to invest more in nest insulation than large species. To test this hypothesis, we examined characteristics of nests of six Arctic breeding shorebird species. All species chose thermally favourable nesting sites in a higher proportion than expected on the basis of habitat availability. Site choice did not differ between species. Depth to frozen ground, measured near the nests, decreased in the course of the season at similar non-species-specific speeds, but this depth increased with species size. Nest cup depth and nest scrape depth (nest cup without the lining) were unrelated to body mass (we applied an exponent of 0.73, to account for metabolic activity of the differently sized species). Cup depth divided by diameter2 was used as a measure of nest cup shape. Small species had narrow and deep nests, while large species had wide shallow nests. The thickness of nest lining varied between 0.1 cm and 7.6 cm, and decreased significantly with body mass. We reconstruct the combined effect of different nest properties on the egg cooling coefficient using previously published quantitative relationships. The predicted effect of nest cup depth and lining depth on heat loss to the frozen ground did not correlate with body mass, but the sheltering effect of nest cup diameter against wind and the effects of lining material on the cooling coefficient increased with body mass. Our results suggest that small arctic shorebirds invest more in the insulation of their nests than large species. PMID:22701596

  4. Nested Canalizing Functions and Their Networks

    CERN Document Server

    Kadelka, Claus; Adeyeye, John O; Laubenbacher, Reinhard

    2014-01-01

    The concept of a nested canalizing Boolean function has been studied over the last decade in the context of understanding the regulatory logic of molecular interaction networks, such as gene regulatory networks. Such networks are predominantly governed by nested canalizing functions. Derrida values are frequently used to analyze the robustness of a Boolean network to perturbations. This paper introduces closed formulas for the calculation of Derrida values of networks governed by Boolean nested canalizing functions, which previously required extensive simulations. Recently, the concept of nested canalizing functions has been generalized to include multistate functions, and a recursive formula has been derived for their number, as a function of the number of variables. This paper contains a detailed analysis of the class of nested canalizing functions over an arbitrary finite field. In addition, the concept of nested canalization is further generalized and closed formulas for the number of such generalized fun...

  5. Sparrow nest survival in relation to prescribed fire and woody plant invasion in a northern mixed-grass prairie

    Science.gov (United States)

    Murphy, Robert K.; Shaffer, Terry L.; Grant, Todd A.; Derrig, James L.; Rubin, Cory S.; Kerns, Courtney K.

    2017-01-01

    Prescribed fire is used to reverse invasion by woody vegetation on grasslands, but managers often are uncertain whether influences of shrub and tree reduction outweigh potential effects of fire on nest survival of grassland birds. During the 2001–2003 breeding seasons, we examined relationships of prescribed fire and woody vegetation to nest survival of clay-colored sparrow (Spizella pallida) and Savannah sparrow (Passerculus sandwichensis) in mixed-grass prairie at Des Lacs National Wildlife Refuge in northwestern North Dakota, USA. We assessed relationships of nest survival to 1) recent fire history, in terms of number of breeding seasons (2, 3, or 4–5) since the last prescribed fire, and 2) prevalence of trees and tall (>1.5 m) shrubs in the landscape and of low (≤1.5 m) shrubs within 5 m of nests. Nest survival of both species exhibited distinct patterns related to age of the nest and day of year, but bore no relationship to fire history. Survival of clay-colored sparrow nests declined as the amount of trees and tall shrubs within 100 m increased, but we found no relationship to suggest nest parasitism by brown-headed cowbirds (Molothrus ater) as an underlying mechanism. We found little evidence linking nest survival of Savannah sparrow to woody vegetation. Our results suggest that fire can be used to restore northern mixed-grass prairies without adversely affecting nest survival of ≥2 widespread passerine species. Survival of nests of clay-colored sparrow may increase when tall woody cover is reduced by fire. Our data lend support to the use of fire for reducing scattered patches of tall woody cover to enhance survival of nests of ≥1 grassland bird species in northern mixed-grass prairies, but further study is needed that incorporates experimental approaches and assessments of shorter term effects of fire on survival of nests of grassland passerines.

  6. The design and function of birds' nests.

    Science.gov (United States)

    Mainwaring, Mark C; Hartley, Ian R; Lambrechts, Marcel M; Deeming, D Charles

    2014-10-01

    All birds construct nests in which to lay eggs and/or raise offspring. Traditionally, it was thought that natural selection and the requirement to minimize the risk of predation determined the design of completed nests. However, it is becoming increasingly apparent that sexual selection also influences nest design. This is an important development as while species such as bowerbirds build structures that are extended phenotypic signals whose sole purpose is to attract a mate, nests contain eggs and/or offspring, thereby suggesting a direct trade-off between the conflicting requirements of natural and sexual selection. Nest design also varies adaptively in order to both minimize the detrimental effects of parasites and to create a suitable microclimate for parents and developing offspring in relation to predictable variation in environmental conditions. Our understanding of the design and function of birds' nests has increased considerably in recent years, and the evidence suggests that nests have four nonmutually exclusive functions. Consequently, we conclude that the design of birds' nests is far more sophisticated than previously realized and that nests are multifunctional structures that have important fitness consequences for the builder/s.

  7. Optimal Nesting for Continuous Shape Stamping Processes

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    This paper discusses the optimal nesting problem for minimizing the scrap in continuous shape stamping processes. The shape sliding technique is used to propose a new approach, OVERLAP-and-ESCAPE, to solve the problem of continuously nesting shapes onto a metal coil of fixed or selectable width. The approach is used to construct the objective function of the mathematical model of the problem using the Simulated Annealing Algorithm to determine the globally minimal configurations for the nesting problems. Some representative cases are studied and the results are encouraging. An automatic nesting software package for manufacturing bicycle chain link blanks is also described.

  8. Nest distribution and nest habitat of the Tibetan Partridge (Perdix hodgsoniae) near Lhasa, Tibet

    Institute of Scientific and Technical Information of China (English)

    Tsering; Dorge; G?ran; H?gstedt; Terje; Lislevand

    2014-01-01

    Background: Little is hitherto known about the breeding ecology of the Tibetan Partridge(Perdix hodgsoniae)which is endemic to the Tibetan plateau. Here we describe nest densities, inter-nest distances and general nest site characteristics in this gallinaceous bird species and explore the possibilities that certain shrub and plant types are preferred as nest surroundings.Method: A total of 56 nests were found over three breeding seasons near Lhasa, Tibet. Nest site characteristics were compared with random control plots and the proportions of specific plant species covering nests were compared with their estimated general occurrence in the study area.Results: Nest density in the two years with highest search effort was estimated at 1.43/km2 and 1.04/km2 but was clearly higher in the part of the study area facing north(1.86–2.35/km2) than that facing south(0.11–0.34/ km2). The average nearest neighbour distance of nests was about 300 m. Nests were situated in relatively lush vegetation and covered by a total of eight shrub species and three herbs. In contrast to previous reports, Caragana shrub did not constitute an important part of the nest habitat. The flowering, non-thorny bush Potentilla fruticosa was significantly over-represented as nest cover, while Rhododendron nivale was similarly under-represented. Nest bush foliage covered a larger area of ground, and the shrub surrounding nests was generally denser, than in control samples. Also, nests were placed closer to paths and in areas with lower densities of Yak(Bos grunniens) dung than in control samples.Except that soil temperatures were lower on nest sites than on control sites, micro-climate variables measured in this study did not differ between nest sites and control plots.Conclusions: Opportunity for nest concealment is probably an important quality of the nest habitat in Tibetan Partridges, yet it is unclear why the species should prefer P. fruticosa as nest cover. It is possible that nest sites are

  9. Nest distribution and nest habitat of the Tibetan Partridge (Perdix hodgsoniae) near Lhasa, Tibet

    Institute of Scientific and Technical Information of China (English)

    Tsering Dorge; Gran Hgstedt; Terje Lislevand

    2014-01-01

    Background:Little is hitherto known about the breeding ecology of the Tibetan Partridge (Perdix hodgsoniae) which is endemic to the Tibetan plateau. Here we describe nest densities, inter-nest distances and general nest site characteristics in this gallinaceous bird species and explore the possibilities that certain shrub and plant types are preferred as nest surroundings. Method:A total of 56 nests were found over three breeding seasons near Lhasa, Tibet. Nest site characteristics were compared with random control plots and the proportions of specific plant species covering nests were compared with their estimated general occurrence in the study area. Results:Nest density in the two years with highest search effort was estimated at 1.43/km2 and 1.04/km2 but was clearly higher in the part of the study area facing north (1.86–2.35/km2) than that facing south (0.11–0.34/km2). The average nearest neighbour distance of nests was about 300 m. Nests were situated in relatively lush vegetation and covered by a total of eight shrub species and three herbs. In contrast to previous reports, Caragana shrub did not constitute an important part of the nest habitat. The flowering, non-thorny bush Potentil a fruticosa was significantly over-represented as nest cover, while Rhododendron nivale was similarly under-represented. Nest bush foliage covered a larger area of ground, and the shrub surrounding nests was generally denser, than in control samples. Also, nests were placed closer to paths and in areas with lower densities of Yak (Bos grunniens) dung than in control samples. Except that soil temperatures were lower on nest sites than on control sites, micro-climate variables measured in this study did not differ between nest sites and control plots. Conclusions:Opportunity for nest concealment is probably an important quality of the nest habitat in Tibetan Partridges, yet it is unclear why the species should prefer P. fruticosa as nest cover. It is possible that nest sites

  10. Nested Trampoline Resonators for Optomechanics

    CERN Document Server

    Weaver, Matthew J; Luna, Fernando; Buters, Frank M; Eerkens, Hedwig J; Welker, Gesa; Perock, Blaise; Heeck, Kier; de Man, Sven; Bouwmeester, Dirk

    2015-01-01

    Two major challenges in the development of optomechanical devices are achieving a low mechanical and optical loss rate and vibration isolation from the environment. We address both issues by fabricating novel trampoline resonators made from low pressure chemical vapor deposition (LPCVD) Si$_3$N$_4$ with a distributed bragg reflector (DBR) mirror. We construct a nested double resonator structure that generates approximately 80 dB of mechanical isolation from the mounting surface, eliminating the strong mounting dependence of the quality factor observed with single resonators. With the consistency provided by this isolation scheme we reliably fabricate devices with mechanical quality factors of around 400,000 at room temperature. In addition these devices were used to form optical cavities with finesse up to 181,000 $\\pm$ 1,000. These promising parameters will enable experiments in the quantum regime with macroscopic mechanical resonators.

  11. Nested trampoline resonators for optomechanics

    Energy Technology Data Exchange (ETDEWEB)

    Weaver, M. J., E-mail: mweaver@physics.ucsb.edu; Pepper, B.; Luna, F.; Perock, B. [Department of Physics, University of California, Santa Barbara, California 93106 (United States); Buters, F. M.; Eerkens, H. J.; Welker, G.; Heeck, K.; Man, S. de [Huygens-Kamerlingh Onnes Laboratorium, Universiteit Leiden, 2333 CA Leiden (Netherlands); Bouwmeester, D. [Department of Physics, University of California, Santa Barbara, California 93106 (United States); Huygens-Kamerlingh Onnes Laboratorium, Universiteit Leiden, 2333 CA Leiden (Netherlands)

    2016-01-18

    Two major challenges in the development of optomechanical devices are achieving a low mechanical and optical loss rate and vibration isolation from the environment. We address both issues by fabricating trampoline resonators made from low pressure chemical vapor deposition Si{sub 3}N{sub 4} with a distributed Bragg reflector mirror. We design a nested double resonator structure with 80 dB of mechanical isolation from the mounting surface at the inner resonator frequency, and we demonstrate up to 45 dB of isolation at lower frequencies in agreement with the design. We reliably fabricate devices with mechanical quality factors of around 400 000 at room temperature. In addition, these devices were used to form optical cavities with finesse up to 181 000 ± 1000. These promising parameters will enable experiments in the quantum regime with macroscopic mechanical resonators.

  12. 1989 Waterfowl Nesting Study and Nesting Summary 1984-1989 : Big Stone National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The 1989 nesting season marked the sixth consecutive and final year that Big Stone personnel have conducted waterfowl nesting research. In addition, an experimental...

  13. Frog Foam Nest Protein Diversity and Synthesis.

    Science.gov (United States)

    Hissa, Denise Cavalcante; Bezerra, Walderly Melgaço; Freitas, Cléverson Diniz Teixeira De; Ramos, Márcio Viana; Lopes, José Luiz De Souza; Beltramini, Leila Maria; Roberto, Igor Joventino; Cascon, Paulo; Melo, Vânia Maria Maciel

    2016-08-01

    Some amphibian species have developed a breeding strategy in which they deposit their eggs in stable foam nests to protect their eggs and larvae. The frog foam nests are rich in proteins (ranaspumin), especially surfactant proteins, involved in the production of the foam nest. Despite the ecological importance of the foam nests for evolution and species conservation, the biochemical composition, the long-term stability and even the origin of the components are still not completely understood. Recently we showed that Lv-RSN-1, a 23.5-kDa surfactant protein isolated from the nest of the frog Leptodacylus vastus, presents a structural conformation distinct from any protein structures yet reported. So, in the current study we aimed to reveal the protein composition of the foam nest of L. vastus and further characterize the Lv-RSN-1. Proteomic analysis showed the foam nest contains more than 100 of proteins, and that Lv-RSN-1 comprises 45% of the total proteins, suggesting a key role in the nest construction and stability. We demonstrated by Western blotting that Lv-RSN-1 is mainly produced only by the female in the pars convoluta dilata, which highlights the importance of the female preservation for conservation of species that depend on the production of foam nests in the early stages of development. Overall, our results showed the foam nest of L. vastus is composed of a great diversity of proteins and that besides Lv-RSN-1, the main protein in the foam, other proteins must have a coadjuvant role in building and stability of the nest.

  14. Aromatic Plants in Eurasian Blue Tit Nests: The ‘Nest

    OpenAIRE

    Pires, Bárbara A.; Anabela F. Belo; Rabaça, João E.

    2012-01-01

    The ‘Nest Protection Hypothesis’ suggests that some birds add aromatic plants to their nests to repel or kill ectoparasites. This behavior has been described for several species, including the Eurasian Blue Tit (Cyanistes caeruleus). We studied the reproductive performance, based on 26 nests (in nest boxes), of this species in mixed forested areas of Quercus spp. and Pinus pinea in the Parque Florestal de Monsanto, the largest park of Lisbon, Portugal. The frequency of aromatic plant...

  15. Chapter 6: Characteristics of Marbled Murrelet Nest Trees and Nesting Stands

    Science.gov (United States)

    Thomas E. Hamer; S. Kim Nelson

    1995-01-01

    We summarize the characteristics of 61 tree nests and nesting stands of the Marbled Murrelet ( Brachyramphus marmoratus ) located from 1974 to 1993 in Alaska, British Columbia, Washington, Oregon, and California. Evidence of breeding 30-60 km inland was common in California, Oregon, and Washington. Nesting greater distances from the coast may have...

  16. Landscape forest cover and edge effects on songbird nest predation vary by nest predator

    Science.gov (United States)

    W. Andrew Cox; Frank R. III Thompson; John. Faaborg

    2012-01-01

    Rates of nest predation for birds vary between and within species across multiple spatial scales, but we have a poor understanding of which predators drive such patterns. We video-monitored nests and identified predators at 120 nests of the Acadian Flycatcher (Empidonax virescens) and the Indigo Bunting (Passerina cyanea) at eight...

  17. Waterbird nest-site selection is influenced by neighboring nests and island topography

    Science.gov (United States)

    Hartman, Christopher; Ackerman, Josh; Takekawa, John Y.; Herzog, Mark

    2016-01-01

    Avian nest-site selection is influenced by factors operating across multiple spatial scales. Identifying preferred physical characteristics (e.g., topography, vegetation structure) can inform managers to improve nesting habitat suitability. However, social factors (e.g., attraction, territoriality, competition) can complicate understanding physical characteristics preferred by nesting birds. We simultaneously evaluated the physical characteristics and social factors influencing selection of island nest sites by colonial-nesting American avocets (Recurvirostra americana) and Forster's terns (Sterna forsteri) at 2 spatial scales in San Francisco Bay, 2011–2012. At the larger island plot (1 m2) scale, we used real-time kinematics to produce detailed topographies of nesting islands and map the distribution of nests. Nesting probability was greatest in island plots between 0.5 m and 1.5 m above the water surface, at distances less likely to nest in plots adjacent to plots with nesting avocets, suggesting an influence of intra-specific territoriality. At the smaller microhabitat scale, or the area immediately surrounding the nest, we compared topography, vegetation, and distance to nearest nest between nest sites and paired random sites. Topography had little influence on selection of the nest microhabitat. Instead, nest sites were more likely to have vegetation present, and greater cover, than random sites. Finally, avocet, and to a lesser extent tern, nest sites were closer to other active conspecific or heterospecific nests than random sites, indicating that social attraction played a role in selection of nest microhabitat. Our results demonstrate key differences in nest-site selection between co-occurring avocets and terns, and indicate the effects of physical characteristics and social factors on selection of nesting habitat are dependent on the spatial scale examined. Moreover, these results indicate that islands with abundant area between 0.5 m and 1.5

  18. Conservation significance of alternative nests of golden eagles

    Directory of Open Access Journals (Sweden)

    Brian A. Millsap

    2015-01-01

    Full Text Available Golden eagles (Aquila chrysaetos are long-lived raptors that maintain nesting territories that may be occupied for a century or longer. Within occupied nesting territories there is one nest in which eagles lay their eggs in a given year (i.e., the used nest, but there are usually other nests (i.e., alternative nests. Conservation plans often protect used nests, but not alternative nests or nesting territories that appear vacant. Our objective is to review literature on golden eagle use of alternative nests and occupancy of nesting territories to determine if alternative nests are biologically significant and warrant greater conservation consideration. Our review shows that: (1 alternative nests or their associated habitat are most often in core areas of golden eagle nesting territories; (2 alternative nests likely will become used in the future; (3 probability of an alternative nest becoming used is greatest where prey availability is high and alternative nest sites are limited; (4 likelihood of annual occupancy or reoccupancy of golden eagle nesting territories is high; and (5 prey availability is the most important determinant of nesting territory occupancy and breeding activity. We recommend alternative nests be treated with the same deference as used nests in land use planning.

  19. 7 CFR 29.6027 - Nested.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Nested. 29.6027 Section 29.6027 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... INSPECTION Standards Definitions § 29.6027 Nested. Any tobacco which has been loaded, packed, or arranged...

  20. Dune vegetation fertilization by nesting sea turtles.

    Science.gov (United States)

    Hannan, Laura B; Roth, James D; Ehrhart, Llewellyn M; Weishampel, John F

    2007-04-01

    Sea turtle nesting presents a potential pathway to subsidize nutrient-poor dune ecosystems, which provide the nesting habitat for sea turtles. To assess whether this positive feedback between dune plants and turtle nests exists, we measured N concentration and delta15N values in dune soils, leaves from a common dune plant (sea oats [Uniola paniculata]), and addled eggs of loggerhead (Caretta caretta) and green turtles (Chelonia mydas) across a nesting gradient (200-1050 nests/km) along a 40.5-km stretch of beach in east central Florida, USA. The delta15N levels were higher in loggerhead than green turtle eggs, denoting the higher trophic level of loggerhead turtles. Soil N concentration and delta15N values were both positively correlated to turtle nest density. Sea oat leaf tissue delta15N was also positively correlated to nest density, indicating an increased use of augmented marine-based nutrient sources. Foliar N concentration was correlated with delta15N, suggesting that increased nutrient availability from this biogenic vector may enhance the vigor of dune vegetation, promoting dune stabilization and preserving sea turtle nesting habitat.

  1. Reversible Computing

    Science.gov (United States)

    1980-02-01

    will have been introduced. 9. Reversible celular autemata We shall assume the reader to have some familiarity with the concept of cel- lular...10003 Mr. Kin B. Thcmpson 1 copy Technical Director Information Systems Divisia.i Naval Research Laboratory (OP-91T) Technical Information Division

  2. Dinosaurs nesting on a red beach?

    Science.gov (United States)

    Sander, P. Martin; Peitz, Christian; Gallemi, Jaume; Cousin, Rémi

    1998-07-01

    The Upper Cretaceous Basturs locality (Tremp Basin, northern Spain) preserves numerous dinosaur eggs ( Megaloolithus cf. M. mammilare Vianey-Liaud, 1994). The locality was recently studied by Sanz et al. (1995) as well as by us. However, we have to disagree with several conclusions by Sanz et al. and suggest alternative interpretations incorporating data from other localities (Coll de Nargó). The dinosaurs at Basturs did not nest at the beach, nor is there evidence for colonial nesting and territorial behaviour. However, the locality superbly documents nesting site fidelity with an estimated occupation time of over 10 000 years.

  3. Emperor penguins nesting on Inaccessible Island

    Science.gov (United States)

    Jonkel, G.M.; Llano, G.A.

    1975-01-01

    Emperor penguins were observed nesting on Inaccessible I. during the 1973 winter. This is the southernmost nesting of emperor penguins thus far recorded; it also could be the first record of emperors attempting to start a new rookery. This site, however, may have been used by emperors in the past. The closest reported nesting of these penguins to Inaccessible I. is on the Ross Ice Shelf east of Cape Crozier. With the exception of the Inaccessible I. record, there is little evidence that emperor penguins breed in McMurdo Sound proper.

  4. 1988 Duck nesting study: Stillwater Wildlife Management Area

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — During the summer, 1988, we conducted a duck nesting study to determine nest success for ducks at Stillwater Wildlife Management Area (WMA). We calculated nest...

  5. Nest site characteristics and nesting success of the Western Burrowing Owl in the eastern Mojave Desert

    Science.gov (United States)

    Longshore, Kathleen M.; Crowe, Dorothy E.

    2013-01-01

    We evaluated nest site selection at two spatial scales (microsite, territory) and reproductive success of Western Burrowing Owls (Athene cunicularia hypugaea) at three spatial scales (microsite, territory, landscape) in the eastern Mojave Desert. We used binary logistic regression within an information-theoretic approach to assess factors influencing nest site choice and nesting success. Microsite-scale variables favored by owls included burrows excavated by desert tortoise (Gopherus agassizii), burrows with a large mound of excavated soil at the entrance, and a greater number of satellite burrows within 5 m of the nest burrow. At the territory scale, owls preferred patches with greater cover of creosote bush (Larrea tridentata) within 50 m of the nest burrow. An interaction between the presence or absence of a calcic soil horizon layer over the top of the burrow (microsite) and the number of burrows within 50 m (territory) influenced nest site choice. Nesting success was influenced by a greater number of burrows within 5 m of the nest burrow. Total cool season precipitation was a predictor of nesting success at the landscape scale. Conservation strategies can rely on management of habitat for favored and productive nesting sites for this declining species.

  6. The nest as fortress: Defensive behavior of Polybia emaciata, a mud-nesting eusocial wasp

    Directory of Open Access Journals (Sweden)

    Sean O'Donnell

    2002-02-01

    Full Text Available The swarm-founding wasp Polybia emaciata is unusual among eusocial Vespidae because it uses mud, rather than wood pulp, as its primary nest construction material. Polybia emaciata nests are more durable than similarly sized paper nests. We tested the hypothesis that the defensive behavior of this wasp may have been modified to take advantage of their strong nests in defense against vertebrate attacks. We simulated vertebrate disturbances by tapping on, and breathing in, P. emaciata. nests and similarly sized P. occidentalis paper nests in the same location at the same time. Polybia emaciata. responses to disturbance were qualitatively different from those of P. occidentalis. The latter exit the nest and attack, while P. emaciata. workers typically fled or entered the nest, attacking only after repeated and extended disturbances. We conclude that durable nest material may permit predator avoidance behavior in P. emaciata.. We compare the defensive responses of P. emaciata. workers with those of other swarm-founding Vespidae, and discuss several selective forces that could cause the evolution of species variation in nest defense behavior.

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

    Science.gov (United States)

    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.

  8. Spatial dynamics of nesting behavior: lizards shift microhabitats to construct nests with beneficial thermal properties.

    Science.gov (United States)

    Angilletta, Michael J; Sears, Michael W; Pringle, Robert M

    2009-10-01

    Because temperature affects the growth, development, and survival of embryos, oviparous mothers should discriminate carefully among available nesting sites. We combined a radiotelemetric study of animal movements with a spatial mapping of environmental temperatures to test predictions about the nesting behavior of the eastern fence lizard (Sceloporus undulatus). Females made large excursions from their typical home ranges to construct nests in exposed substrates. These excursions appeared to be related solely to nesting because all females returned to forested habitat immediately afterward. On average, <1% (range = 0-8%, n = 19) of the area used by a female during nesting was contained within the area used before and after nesting. The selection of nesting sites matched predictions based on laboratory studies of embryonic performance; specifically, females nested in extremely open habitat at a mean of 6 cm depth. Spatial mapping of soil temperatures revealed that temperatures of nesting areas exceeded those of areas typically used by females, indicating that females preferred to construct warm nests that speed embryonic growth and development. However, this behavior could reduce the survivorship of females because of the need to rapidly navigate unfamiliar and exposed terrain.

  9. Construction patterns of birds’ nests provide insight into nest-building behaviours

    Science.gov (United States)

    Goodman, Adrian M.

    2017-01-01

    Previous studies have suggested that birds and mammals select materials needed for nest building based on their thermal or structural properties, although the amounts or properties of the materials used have been recorded for only a very small number of species. Some of the behaviours underlying the construction of nests can be indirectly determined by careful deconstruction of the structure and measurement of the biomechanical properties of the materials used. Here we examined this idea in an investigation of Bullfinch (Pyrrhula pyrrhula) nests as a model for open-nesting songbird species that construct a “twig” nest, and tested the hypothesis that materials in different parts of nests serve different functions. The quantities of materials present in the nest base, sides and cup were recorded before structural analysis. Structural analysis showed that the base of the outer nests were composed of significantly thicker, stronger and more rigid materials compared to the side walls, which in turn were significantly thicker, stronger and more rigid than materials used in the cup. These results suggest that the placement of particular materials in nests may not be random, but further work is required to determine if the final structure of a nest accurately reflects the construction process. PMID:28265501

  10. Construction patterns of birds’ nests provide insight into nest-building behaviours

    Directory of Open Access Journals (Sweden)

    Lucia Biddle

    2017-02-01

    Full Text Available Previous studies have suggested that birds and mammals select materials needed for nest building based on their thermal or structural properties, although the amounts or properties of the materials used have been recorded for only a very small number of species. Some of the behaviours underlying the construction of nests can be indirectly determined by careful deconstruction of the structure and measurement of the biomechanical properties of the materials used. Here we examined this idea in an investigation of Bullfinch (Pyrrhula pyrrhula nests as a model for open-nesting songbird species that construct a “twig” nest, and tested the hypothesis that materials in different parts of nests serve different functions. The quantities of materials present in the nest base, sides and cup were recorded before structural analysis. Structural analysis showed that the base of the outer nests were composed of significantly thicker, stronger and more rigid materials compared to the side walls, which in turn were significantly thicker, stronger and more rigid than materials used in the cup. These results suggest that the placement of particular materials in nests may not be random, but further work is required to determine if the final structure of a nest accurately reflects the construction process.

  11. Alcid Nesting Habitat on the Maine Coast

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Maine supports an extensive seabird population because of the abundance of relatively inaccessible rocky coastal islands which are ideal nesting grounds for many...

  12. Adult Health: Worried About Empty Nest Syndrome?

    Science.gov (United States)

    ... clinical diagnosis. Instead, empty nest syndrome is a phenomenon in which parents experience feelings of sadness and loss when the last child leaves home. Although you might actively encourage your ...

  13. Annual survival of Florida nesting loggerheads

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — 30 PAT tags were deployed on nesting loggerhead turtles at Juno Beach, FL in June 2012. There have been three premature pop-offs, one of which appeared to be a...

  14. Cackling Canada goose nesting populations, Yukon Delta

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Number of potential territories, number of cackling Canada Goose nests, and percent occupancy of available territories from CCG plots on the Yukon Delta National...

  15. Starling nest box monitoring [Rocky Mountain Arsenal

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This document described the standard operating procedures for observing and recording data collected from starling nest box monitoring at the Rocky Mountain Arsenal....

  16. Chesapeake Bay Bald Eagle Nesting Survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The Chesapeake Bay population of breeding bald eagles increased dramatically in 1981 in not only the number of breeding pairs but in the number of nests hatching...

  17. Island's terns nest again after unsuccessful start

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — For five consecutive summers the Trustees of Reservations have directed a program on Nantucket for the protection of the terns which nest in several colonies around...

  18. Duck-nesting Studies: Lower Souris Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — In this report an attempt has been made to summarize some of the notes made during the nesting studies at the Lower Souris Refuge in 1937. While assisting Mr....

  19. Nesting Loggerhead Sea Turtle Activity Report 2001

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This paper presents results from the 9th Annual Study (using Army Corp of Engineers funds) of nesting by the Atlantic loggerhead sea turtle (Caretta caretta) along...

  20. Nesting Loggerhead Sea Turtle Activity Report 1998

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This paper presents results from the sixth annual study of nesting along the Atlantic Oceanfront by the loggerhead sea turtle (Caretta carettd) in Virginia Beach,...

  1. Nesting Loggerhead Sea Turtle Activity Report 1999

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This paper presents results from the seventh annual study (using Army Corp of Engineers funds;) of nesting along the Atlantic Ocean coastline by the loggerhead sea...

  2. Linear Maps Preserving Idempotence on Nest Algebras

    Institute of Scientific and Technical Information of China (English)

    Jian Lian CUI; Jin Chuan HOU

    2004-01-01

    In this paper, we discuss the rank-1-preserving linear maps on nest algebras of Hilbertspace operators. We obtain several characterizations of such linear maps and apply them to show that a weakly continuous linear bijection on an atomic nest algebra is idempotent preserving if and only if it is a Jordan homomorphism, and in turn, if and only if it is an automorphism or an anti-automorphism.

  3. Sand and nest temperatures and an estimate of hatchling sex ratio from the Heron Island green turtle ( Chelonia mydas) rookery, Southern Great Barrier Reef

    Science.gov (United States)

    Booth, David T.; Freeman, Candida

    2006-11-01

    Sand and nest temperatures were monitored during the 2002-2003 nesting season of the green turtle, Chelonia mydas, at Heron Island, Great Barrier Reef, Australia. Sand temperatures increased from ˜ 24°C early in the season to 27-29°C in the middle, before decreasing again. Beach orientation affected sand temperature at nest depth throughout the season; the north facing beach remained 0.7°C warmer than the east, which was 0.9°C warmer than the south, but monitored nest temperatures were similar across all beaches. Sand temperature at 100 cm depth was cooler than at 40 cm early in the season, but this reversed at the end. Nest temperatures increased 2-4°C above sand temperatures during the later half of incubation due to metabolic heating. Hatchling sex ratio inferred from nest temperature profiles indicated a strong female bias.

  4. A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching

    Science.gov (United States)

    Romero, José R.; Carballido, Jessica A.; Garbus, Ingrid; Echenique, Viviana C.; Ponzoni, Ignacio

    2016-01-01

    The identification of nested motifs in genomic sequences is a complex computational problem. The detection of these patterns is important to allow the discovery of transposable element (TE) insertions, incomplete reverse transcripts, deletions, and/or mutations. In this study, a de novo strategy for detecting patterns that represent nested motifs was designed based on exhaustive searches for pairs of motifs and combinatorial pattern analysis. These patterns can be grouped into three categories, motifs within other motifs, motifs flanked by other motifs, and motifs of large size. The methodology used in this study, applied to genomic sequences from the plant species Aegilops tauschii and Oryza sativa, revealed that it is possible to identify putative nested TEs by detecting these three types of patterns. The results were validated through BLAST alignments, which revealed the efficacy and usefulness of the new method, which is called Mamushka. PMID:27812277

  5. Gregarious nesting - An anti-predator response in laying hens

    DEFF Research Database (Denmark)

    Riber, Anja Brinch

    2012-01-01

    Gregarious nesting can be defined as a behaviour that occurs when a laying hen (Gallus gallus domesticus) given the choice between an occupied and an unoccupied nest site chooses the occupied nest site. It occurs frequently in flocks of laying hens kept under commercial conditions, contrasting...... the behaviour displayed by feral hens that isolate themselves from the flock during nesting activities. What motivates laying hens to perform gregarious nesting is unknown. One possibility is that gregarious nesting is an anti-predator response to the risk of nest predation emerging from behavioural flexibility...... in nesting strategy. The aim of the present experiment was to investigate whether gregarious nesting due to behavioural flexibility in nesting strategy is an anti-predator response. Twelve groups of 14–15 Isa Warren hens age 44 weeks were housed in pens each containing three adjacent roll-out nest boxes...

  6. Reversible Statistics

    DEFF Research Database (Denmark)

    Tryggestad, Kjell

    2004-01-01

    The study aims is to describe how the inclusion and exclusion of materials and calculative devices construct the boundaries and distinctions between statistical facts and artifacts in economics. My methodological approach is inspired by John Graunt's (1667) Political arithmetic and more recent work...... within constructivism and the field of Science and Technology Studies (STS). The result of this approach is here termed reversible statistics, reconstructing the findings of a statistical study within economics in three different ways. It is argued that all three accounts are quite normal, albeit...... in different ways. The presence and absence of diverse materials, both natural and political, is what distinguishes them from each other. Arguments are presented for a more symmetric relation between the scientific statistical text and the reader. I will argue that a more symmetric relation can be achieved...

  7. Decline of spectacled eiders nesting in western Alaska

    Science.gov (United States)

    Stehn, Robert A.; Dau, Christian P.; Conant, Bruce; Butler, William I.

    1993-01-01

    Spectacled eider (Somateria fischeri) populations in western Alaska are now less than 4% of the numbers estimated in the early 1970s. In 1992, an estimated 1721 nesting pairs remained on the Yukon-Kuskokwim Delta. Causes of this rapid and continuing decline of -14% per year are undocumented. Many aspects of spectacled eider biology remain unknown, including their marine foraging habitats, food items, migratory movements, and population ecology. A review of some biological characteristics and possible threats to the species suggests the importance of quantifying potential impacts from parasites and disease, subsistence harvest, predation during brood rearing, and alteration of Bering Sea food resources. Factors causing the population decline of spectacled eiders must be determined and appropriate actions taken to reverse the trend.

  8. Discriminating the drivers of edge effects on nest predation: forest edges reduce capture rates of ship rats (Rattus rattus, a globally invasive nest predator, by altering vegetation structure.

    Directory of Open Access Journals (Sweden)

    Jay Ruffell

    Full Text Available Forest edges can strongly affect avian nest success by altering nest predation rates, but this relationship is inconsistent and context dependent. There is a need for researchers to improve the predictability of edge effects on nest predation rates by examining the mechanisms driving their occurrence and variability. In this study, we examined how the capture rates of ship rats, an invasive nest predator responsible for avian declines globally, varied with distance from the forest edge within forest fragments in a pastoral landscape in New Zealand. We hypothesised that forest edges would affect capture rates by altering vegetation structure within fragments, and that the strength of edge effects would depend on whether fragments were grazed by livestock. We measured vegetation structure and rat capture rates at 488 locations ranging from 0-212 m from the forest edge in 15 forest fragments, seven of which were grazed. Contrary to the vast majority of previous studies of edge effects on nest predation, ship rat capture rates increased with increasing distance from the forest edge. For grazed fragments, capture rates were estimated to be 78% lower at the forest edge than 118 m into the forest interior (the farthest distance for grazed fragments. This relationship was similar for ungrazed fragments, with capture rates estimated to be 51% lower at the forest edge than 118 m into the forest interior. A subsequent path analysis suggested that these 'reverse' edge effects were largely or entirely mediated by changes in vegetation structure, implying that edge effects on ship rats can be predicted from the response of vegetation structure to forest edges. We suggest the occurrence, strength, and direction of edge effects on nest predation rates may depend on edge-driven changes in local habitat when the dominant predator is primarily restricted to forest patches.

  9. Discriminating the drivers of edge effects on nest predation: forest edges reduce capture rates of ship rats (Rattus rattus), a globally invasive nest predator, by altering vegetation structure.

    Science.gov (United States)

    Ruffell, Jay; Didham, Raphael K; Barrett, Paul; Gorman, Nic; Pike, Rhonda; Hickey-Elliott, Andrée; Sievwright, Karin; Armstrong, Doug P

    2014-01-01

    Forest edges can strongly affect avian nest success by altering nest predation rates, but this relationship is inconsistent and context dependent. There is a need for researchers to improve the predictability of edge effects on nest predation rates by examining the mechanisms driving their occurrence and variability. In this study, we examined how the capture rates of ship rats, an invasive nest predator responsible for avian declines globally, varied with distance from the forest edge within forest fragments in a pastoral landscape in New Zealand. We hypothesised that forest edges would affect capture rates by altering vegetation structure within fragments, and that the strength of edge effects would depend on whether fragments were grazed by livestock. We measured vegetation structure and rat capture rates at 488 locations ranging from 0-212 m from the forest edge in 15 forest fragments, seven of which were grazed. Contrary to the vast majority of previous studies of edge effects on nest predation, ship rat capture rates increased with increasing distance from the forest edge. For grazed fragments, capture rates were estimated to be 78% lower at the forest edge than 118 m into the forest interior (the farthest distance for grazed fragments). This relationship was similar for ungrazed fragments, with capture rates estimated to be 51% lower at the forest edge than 118 m into the forest interior. A subsequent path analysis suggested that these 'reverse' edge effects were largely or entirely mediated by changes in vegetation structure, implying that edge effects on ship rats can be predicted from the response of vegetation structure to forest edges. We suggest the occurrence, strength, and direction of edge effects on nest predation rates may depend on edge-driven changes in local habitat when the dominant predator is primarily restricted to forest patches.

  10. Nest-site limitation and nesting resources of ants (Hymenoptera: Formicidae) in urban green spaces.

    Science.gov (United States)

    Friedrich, Russell; Philpott, Stacy M

    2009-06-01

    Urbanization impacts biodiversity, yet few studies examine general impacts of urbanization on insects. Furthermore, few studies examine availability and limitation of potential cavity nesting sites for ants, an important regulating factor in ant communities that may vary in different urban habitats. We compared three urban habitat types (gardens, vacant lots, and forests) in Toledo, OH, to examine availability and ant preferences for different cavity nesting resources (small and large hollow twigs and cavities). We added 72 artificial large hollow twigs (83 by 6 mm), small hollow twigs (140 by 2 mm), and spherical hollow cavities (6.52-31.1 cm(3) in volume, 1-mm opening) to six sites from May to August 2007 to determine whether nest-site limitation impacts ant communities. We collected natural nests to compare natural abundance and occupancy of cavity nests in different urban habitats. We opened artificial and natural nests to calculate the percentage occupied by cavity-nesting ants. Across all habitats, small twigs represented 81.1% of natural nests, spherical nests represented 10.1%, and large twigs 8.2%. Ants occupied 8.1% of natural large twigs, 14.6% of cavities, and 4.1% of small twigs. For artificial nests, 21.5% of large twigs, 1% of small twigs, and 1% of spheres were occupied. The high percentage of occupied artificial large twigs could imply this is a preferred and limiting resource in urban habitats. The results show that certain types of nesting resources may be an important factor mediating ant communities in urban green spaces.

  11. Nesting Activity of Loggerhead Turtles (Caretta caretta at Göksu Delta, Turkey during 2004 and 2008 nesting seasons

    Directory of Open Access Journals (Sweden)

    Salih H. Durmus

    2011-07-01

    Full Text Available Göksu Delta is one of the most important nesting beaches in Turkey for the endangered loggerhead turtle (Caretta caretta. This paper provides information on the nesting activities of loggerhead turtles, the spatial and temporal distribution of nesting, nesting success, nesting density, hatching success, incubation duration and clutch size over two nesting seasons. A total of 902 emergences occurred over two seasons, of which 239 (26.5% nests were deposited (137 nests in 2004 and 102 nests in 2008 and the overall mean nesting density was 3.4 nests/km. The peak of nesting emergences takes place mainly in June. Of the overall nests, 226 (94.6% were excavated and 16044 eggs were counted. Of these eggs, 3680 (22.9% hatchlings emerged and 2695 (73.2% of hatchlings of them were able to reach the sea. The mean number of eggs per clutch was 71 (range: 15 – 143. The shortest and longest incubation duration in these 2 seasons ranged from 46 to 62 days with a mean of 53 days. The main problems are negatively affecting loggerhead turtle population at Göksu Delta are dense jackal predation both adult and eggs and inundation in nests. The average nesting effort here (mean: 119.5 nests/season confirms that Göksu Delta is one of the most important nesting sites for loggerhead turtles in Turkey.

  12. The effects of large beach debris on nesting sea turtles

    Science.gov (United States)

    Fujisaki, Ikuko; Lamont, Margaret M.

    2016-01-01

    A field experiment was conducted to understand the effects of large beach debris on sea turtle nesting behavior as well as the effectiveness of large debris removal for habitat restoration. Large natural and anthropogenic debris were removed from one of three sections of a sea turtle nesting beach and distributions of nests and false crawls (non-nesting crawls) in pre- (2011–2012) and post- (2013–2014) removal years in the three sections were compared. The number of nests increased 200% and the number of false crawls increased 55% in the experimental section, whereas a corresponding increase in number of nests and false crawls was not observed in the other two sections where debris removal was not conducted. The proportion of nest and false crawl abundance in all three beach sections was significantly different between pre- and post-removal years. The nesting success, the percent of successful nests in total nesting attempts (number of nests + false crawls), also increased from 24% to 38%; however the magnitude of the increase was comparably small because both the number of nests and false crawls increased, and thus the proportion of the nesting success in the experimental beach in pre- and post-removal years was not significantly different. The substantial increase in sea turtle nesting activities after the removal of large debris indicates that large debris may have an adverse impact on sea turtle nesting behavior. Removal of large debris could be an effective restoration strategy to improve sea turtle nesting.

  13. 50 CFR 22.27 - Removal of eagle nests.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false Removal of eagle nests. 22.27 Section 22... WILDLIFE AND PLANTS (CONTINUED) EAGLE PERMITS Eagle Permits § 22.27 Removal of eagle nests. (a) Purpose and... active or inactive nest where necessary to alleviate a safety emergency; (ii) An inactive eagle nest...

  14. Nested Canalyzing, Unate Cascade, and Polynomial Functions.

    Science.gov (United States)

    Jarrah, Abdul Salam; Raposa, Blessilda; Laubenbacher, Reinhard

    2007-09-15

    This paper focuses on the study of certain classes of Boolean functions that have appeared in several different contexts. Nested canalyzing functions have been studied recently in the context of Boolean network models of gene regulatory networks. In the same context, polynomial functions over finite fields have been used to develop network inference methods for gene regulatory networks. Finally, unate cascade functions have been studied in the design of logic circuits and binary decision diagrams. This paper shows that the class of nested canalyzing functions is equal to that of unate cascade functions. Furthermore, it provides a description of nested canalyzing functions as a certain type of Boolean polynomial function. Using the polynomial framework one can show that the class of nested canalyzing functions, or, equivalently, the class of unate cascade functions, forms an algebraic variety which makes their analysis amenable to the use of techniques from algebraic geometry and computational algebra. As a corollary of the functional equivalence derived here, a formula in the literature for the number of unate cascade functions provides such a formula for the number of nested canalyzing functions.

  15. Nest survival patterns in Eurasian Bittern: effect of nest age, time and habitat variables

    Directory of Open Access Journals (Sweden)

    Marcin Polak

    2016-06-01

    Full Text Available Determining the key factors affecting the reproductive success of nesting birds is crucial in order to better understand the population dynamics of endangered species and to introduce effective conservation programmes for them. Inhabiting a variety of wetland habitats, aquatic birds actively select safe nesting sites so as to protect their nests against predators. The main aim of the present work was to assess the effect of temporal and habitat variables on the daily nest survival rate of Eurasian Bitterns colonizing semi–natural fishpond habitat in eastern Poland. MARK software was used for the modelling. Eurasian Bittern nests were most vulnerable to depredation at the beginning of the breeding season. This was probably because the reedbed vegetation at this time was not yet dense enough to effectively conceal the nests. There was a positive relationship between nest age and the daily survival rate. Two of the habitat variables analysed were of the greatest significance: water depth and vegetation density. In the Eurasian Bittern population studied here, nests built over deep water and in dense vegetation had the best chances of survival. The results of this work may be useful in the preparation of plans for the conservation and management of populations of this rare and endangered species. Conservation and restoration efforts that attempt to maintain high water levels will be especially beneficial to this avian species that is dependent on wetland ecosystems for breeding.

  16. The influence of regional hydrology on nesting behavior and nest fate of the American alligator

    Science.gov (United States)

    Ugarte, Cristina A.; Bass, Oron L.; Nuttle, William; Mazzotti, Frank J.; Rice, Kenneth G.; Fujisaki, Ikuko; Whelan, Kevin R.T.

    2013-01-01

    Hydrologic conditions are critical to the nesting behavior and reproductive success of crocodilians. In South Florida, USA, growing human settlement has led to extensive surface water management and modification of historical water flows in the wetlands, which have affected regional nesting of the American alligator (Alligator mississippiensis). Although both natural and anthropogenic factors are considered to determine hydrologic conditions, the aspects of hydrological patterns that affect alligator nest effort, flooding (partial and complete), and failure (no hatchling) are unclear. We deconstructed annual hydrological patterns using harmonic models that estimated hydrological matrices including mean, amplitude, timing of peak, and periodicity of surface water depth and discharge and examined their effects on alligator nesting using survey data from Shark Slough, Everglades National Park, from 1985 to 2005. Nest effort increased in years with higher mean and lesser periodicity of water depth. A greater proportion of nests were flooded and failed when peak discharge occurred earlier in the year. Also, nest flooding rates were greater in years with greater periodicity of water depth, and nest failure rate was greater when mean discharge was higher. This study guides future water management decisions to mitigate negative impacts on reproduction of alligators and provides wildlife managers with a tool for assessing and modifying annual water management plans to conserve crocodilians and other wetland species.

  17. Behavior of Puerto Rican parrots during failed nesting attempts

    Science.gov (United States)

    Wilson, K.A.; Wilson, M.H.; Field, R.

    1997-01-01

    We compared patterns of nesting behavior of four pairs of Puerto Rican Parrots (Amazona vittata) that experienced failed nesting attempts to behavior of four pairs of parrots that experienced no substantial nest problems and successfully fledged young without management intervention. Only changes in female parrots' behavior were clearly associated with nest failure. During incubation, decreases in nest attendance, increases in duration of recesses, and increases in frequency of nest entries by female parrots were associated with imminent abandonment of nests. During early chick rearing, similar behavior was associated with the loss of broods. Low nest attendance and long recesses by female parrots during incubation were also associated with successful hatching of eggs followed by death of young several days later. The behavior patterns and changes in Puerto Rican Parrot nesting behavior described in this paper may alert biologists to nest problems that might be mitigated by management intervention.

  18. Meadow birds on organic and conventional arable farms in the Netherlands: abundance and nest success

    OpenAIRE

    Kragten, Steven

    2010-01-01

    Intensification of agriculture is mentioned to be the key drive behind the decline of farmland birds on grassland and on arable land. This raises the question whether a less intensive system, such as organic, can stop or reverse these declines. The present study compares (1) the territory densities of meadow birds on organic and conventional arable farms, and (2) the nesting success of Lapwings (Vanellus vanellus) on both farm types. The study was carried out in Oostelijk Flevoland and Noordo...

  19. Buteo Nesting Ecology: Evaluating Nesting of Swainson’s Hawks in the Northern Great Plains

    Science.gov (United States)

    Inselman, Will M.; Datta, Shubham; Jenks, Jonathan A.; Jensen, Kent C.; Grovenburg, Troy W.

    2015-01-01

    Swainson’s hawks (Buteo swainsoni) are long-distance migratory raptors that nest primarily in isolated trees located in areas of high grassland density. In recent years, anthropogenic conversion of grassland habitat has raised concerns about the status of the breeding population in the northern Great Plains. In 2013, we initiated a study to investigate the influence of extrinsic factors influencing Swainson’s hawk nesting ecology in north-central South Dakota and south-central North Dakota. Using ground and aerial surveys, we located and monitored nesting Swainson’s hawk pairs: 73 in 2013 and 120 in 2014. We documented 98 successful breeding attempts that fledged 163 chicks; 1.52 and 1.72 fledglings per successful nest in 2013 and 2014, respectively. We used Program MARK to evaluate the influence of land cover on nest survival. The top model, SDist2Farm+%Hay, indicated that nest survival (fledging at least one chick) decreased as nests were located farther from farm sites and as the percent of hay cover increased within 1200-m of the nest site (34.4%; 95% CI = 27.6%–42.3%). We used logistic regression analysis to evaluate the influence of landscape variables on nest-site selection; Swainson’s hawks selected for nest sites located closer to roads. We suggest that tree belts associated with farm sites, whether occupied or not, provide critical breeding sites for Swainson’s hawks. Additionally, poor breeding success may be related to the late migratory behavior of this species which requires them to occupy marginal habitat due to other raptors occupying the most suitable habitat prior to Swainson’s hawks arriving to the breeding grounds. PMID:26327440

  20. Nest-site selection, nesting behaviour and spatial ecology of female Nile crocodiles (Crocodylus niloticus) in South Africa.

    Science.gov (United States)

    Combrink, Xander; Warner, Jonathan K; Downs, Colleen T

    2017-02-01

    Nesting biology and ecology have been investigated for Nile crocodiles (Crocodylus niloticus), but information on behaviour and movement patterns of nesting females during nest guarding is scant. Consequently, we investigated the home ranges, nest-site selection strategies, movement patterns, activity levels and nest fidelity of four nesting females using telemetry. Gravid females selected winter basking/breeding areas close (351±2m) to nest-sites. Mean home range and core-use areas of nesting females were 8539±4752m(2), and 4949±3302m(2) respectively. Mean home range (0.85ha) was significantly smaller than those of non-nesting females (108.4ha) during nesting season. Activity levels and mean daily movements while nesting were 8.1±2.5% and 213±64m, respectively, and increased to 47.9±11.7% and 2176±708m post-nesting. Overall levels of nest fidelity were 82.8±11.7%, (day 78.1±15.9%; night 87.3±7.8%). Highest nest fidelity recorded during incubation was 99.7% over 96days. Telemetry data from nesting females were helpful for elucidating spatial and behavioural patterns during the nest guarding period, and provided novel insights into this biologically important event.

  1. Boolean nested canalizing functions: a comprehensive analysis

    CERN Document Server

    Li, Yuan; Murrugarra, David; Aguilar, Boris; Laubenbacher, Reinhard

    2012-01-01

    Boolean network models of molecular regulatory networks have been used successfully in computational systems biology. The Boolean functions that appear in published models tend to have special properties, in particular the property of being nested canalizing, a property inspired by the concept of canalization in evolutionary biology. It has been shown that networks comprised of nested canalizing functions have dynamic properties that make them suitable for modeling molecular regulatory networks, namely a small number of (large) attractors, as well as relatively short limit cycles. This paper contains a detailed analysis of this class of functions, based on a novel normal form as polynomial functions over the Boolean field. The concept of layer is introduced that stratifies variables into different classes depending on their level of dominance. Using this layer concept a closed form formula is derived for the number of nested canalizing functions with a given number of variables. Additional metrics analyzed in...

  2. Managing American Oystercatcher (Haematopus palliatus) population qrowth by targeting nesting season vital rates

    Science.gov (United States)

    Felton, Shilo K.; Hostetter, Nathan J.; Pollock, Kenneth H.; Simons, Theodore R.

    2017-01-01

    In populations of long-lived species, adult survival typically has a relatively high influence on population growth. From a management perspective, however, adult survival can be difficult to increase in some instances, so other component rates must be considered to reverse population declines. In North Carolina, USA, management to conserve the American Oystercatcher (Haematopus palliatus) targets component vital rates related to fecundity, specifically nest and chick survival. The effectiveness of such a management approach in North Carolina was assessed by creating a three-stage female-based deterministic matrix model. Isoclines were produced from the matrix model to evaluate minimum nest and chick survival rates necessary to reverse population decline, assuming all other vital rates remained stable at mean values. Assuming accurate vital rates, breeding populations within North Carolina appear to be declining. To reverse this decline, combined nest and chick survival would need to increase from 0.14 to ≤ 0.27, a rate that appears to be attainable based on historical estimates. Results are heavily dependent on assumptions of other vital rates, most notably adult survival, revealing the need for accurate estimates of all vital rates to inform management actions. This approach provides valuable insights for evaluating conservation goals for species of concern.

  3. Ashtabula Breakwater Common Tern (Sterna Hirundo) Nesting

    Science.gov (United States)

    2016-05-01

    purchased from GG Telecom, Victoriaville, QC, Canada and connected to the solar panel system to help document activities at the site. Volunteers...blocks. Large 8’ x 8’ x 4’ blocks were used to form the base or toe of the structure, and smaller angled blocks were used to create the side slope...to nest. In addition to placing the blocks on top of the wall, lengths of angle iron were bolted down to attach the nesting blocks to those below

  4. PolyChord: nested sampling for cosmology

    CERN Document Server

    Handley, W J; Lasenby, A N

    2015-01-01

    PolyChord is a novel nested sampling algorithm tailored for high dimensional parameter spaces. In addition, it can fully exploit a hierarchy of parameter speeds such as is found in CosmoMC and CAMB. It utilises slice sampling at each iteration to sample within the hard likelihood constraint of nested sampling. It can identify and evolve separate modes of a posterior semi-independently and is parallelised using openMPI. PolyChord is available for download at: http://ccpforge.cse.rl.ac.uk/gf/project/polychord/

  5. Preliminary Evaluation of a Nest Usage Sensor to Detect Double Nest Occupations of Laying Hens

    Directory of Open Access Journals (Sweden)

    Mauro Zaninelli

    2015-01-01

    Full Text Available Conventional cage systems will be replaced by housing systems that allow hens to move freely. These systems may improve hens’ welfare, but they lead to some disadvantages: disease, bone fractures, cannibalism, piling and lower egg production. New selection criteria for existing commercial strains should be identified considering individual data about laying performance and the behavior of hens. Many recording systems have been developed to collect these data. However, the management of double nest occupations remains critical for the correct egg-to-hen assignment. To limit such events, most systems adopt specific trap devices and additional mechanical components. Others, instead, only prevent these occurrences by narrowing the nest, without any detection and management. The aim of this study was to develop and test a nest usage “sensor”, based on imaging analysis, that is able to automatically detect a double nest occupation. Results showed that the developed sensor correctly identified the double nest occupation occurrences. Therefore, the imaging analysis resulted in being a useful solution that could simplify the nest construction for this type of recording system, allowing the collection of more precise and accurate data, since double nest occupations would be managed and the normal laying behavior of hens would not be discouraged by the presence of the trap devices.

  6. Preliminary evaluation of a nest usage sensor to detect double nest occupations of laying hens.

    Science.gov (United States)

    Zaninelli, Mauro; Costa, Annamaria; Tangorra, Francesco Maria; Rossi, Luciana; Agazzi, Alessandro; Savoini, Giovanni

    2015-01-26

    Conventional cage systems will be replaced by housing systems that allow hens to move freely. These systems may improve hens' welfare, but they lead to some disadvantages: disease, bone fractures, cannibalism, piling and lower egg production. New selection criteria for existing commercial strains should be identified considering individual data about laying performance and the behavior of hens. Many recording systems have been developed to collect these data. However, the management of double nest occupations remains critical for the correct egg-to-hen assignment. To limit such events, most systems adopt specific trap devices and additional mechanical components. Others, instead, only prevent these occurrences by narrowing the nest, without any detection and management. The aim of this study was to develop and test a nest usage "sensor", based on imaging analysis, that is able to automatically detect a double nest occupation. Results showed that the developed sensor correctly identified the double nest occupation occurrences. Therefore, the imaging analysis resulted in being a useful solution that could simplify the nest construction for this type of recording system, allowing the collection of more precise and accurate data, since double nest occupations would be managed and the normal laying behavior of hens would not be discouraged by the presence of the trap devices.

  7. CyNEST: a maintainable Cython-based interface for the NEST simulator

    Directory of Open Access Journals (Sweden)

    Yury V. Zaytsev

    2014-03-01

    Full Text Available NEST is a simulator for large-scale networks of spiking point neuron models (Gewaltig and Diesmann, 2007. Originally, simulations were controlled via the Simulation Language Interpreter (SLI, a built-in scripting facility implementing a language derived from PostScript (Adobe Systems, 1999. The introduction of PyNEST (Eppler et al., 2008, the Python interface for NEST, enabled users to control simulations using Python. As the majority of NEST users found PyNEST easier to use and to combine with other applications, it immediately displaced SLI as the default NEST interface.However, developing and maintaining PyNEST has become increasingly difficult over time. This is partly because adding new features requires writing low-level C++ code intermixed with calls to the Python / C API, which is unrewarding. Moreover, the Python / C API evolves with each new version of Python, which results in a proliferation of version-dependent code branches.In this contribution we present the re-implementation of PyNEST in the Cython language, a superset of Python that additionally supports the declaration of C/C++ types for variables and class attributes, and provides a convenient foreign function interface (FFI for invoking C/C++ routines (Behnel et al., 2011. Code generation via Cython allows the production of smaller and more maintainable bindings, including increased compatibility with all supported Python releases without additional burden for NEST developers. Furthermore, this novel approach opens up the possibility to support alternative implementations of the Python language at no cost given a functional Cython back-end for the corresponding implementation, and also enables cross-compilation of Python bindings for embedded systems and supercomputers alike.

  8. Source Analysis of Bucaramanga Nest Intermediate-Depth Earthquakes

    Science.gov (United States)

    Prieto, G. A.; Pedraza, P.; Dionicio, V.; Levander, A.

    2016-12-01

    Intermediate-depth earthquakes are those that occur at depths of 50 to 300 km in subducting lithosphere and can occasionally be destructive. Despite their ubiquity in earthquake catalogs, their physical mechanism remains unclear because ambient temperatures and pressures at such depths are expected to lead to ductile flow, rather than brittle failure, as a response to stress. Intermediate-depth seismicity rates vary substantially worldwide, even within a single subduction zone having highly clustered seismicity in some cases (Vrancea, Hindu-Kush, etc.). One such places in known as the Bucaramanga Nest (BN), one of the highest concentration of intermediate-depth earthquakes in the world. Previous work on these earthquakes has shown 1) Focal mechanisms vary substantially within a very small volume. 2) Radiation efficiency is small for Mfamilies. For the larger events we will determine source parameters and radiation efficiencies. Preliminary results show that reverse polarity events are present and that two main focal mechanisms, with their corresponding reverse polarity events are dominant. Our results have significant implications in our understanding of intermedaite-depth earthquakes and the stress conditions that are responsible for this unusual cluster of seismicity.

  9. Ants' learning of nest entrance characteristics (Hymenoptera, Formicidae).

    Science.gov (United States)

    Cammaerts, M C

    2014-02-01

    Young workers, experimentally removed from their nest and set in front of it, are not very good at finding the nest entrance and entering the nest. I examined how young ants learn their nest entrance characteristics, dealing only with the entrance sensu stricto, not with its vicinity. I observed that young ants have the innate behavior of trying to exit and re-enter their nest. I found that they are imprinted with the nest entrance odor while they are still living inside their nest and that they learn the visual aspect of their nest entrances, thanks to operant conditioning, when they exit their nest and succeed in re-entering in the course of their first short trips outside.

  10. Nest sharing under semi-natural conditions in laying hens

    DEFF Research Database (Denmark)

    Riber, Anja Brinch

    2012-01-01

    problems to laying hens, and egg production may also be negatively affected. Understanding what causes this difference in nest location selection may provide solutions to the problems associated with simultaneous nest sharing. The aims were to investigate whether a commercial strain of laying hens normally...... daily of each nest with regard to number of eggs, position, and materials used. On five mornings nesting behaviour was observed. Nest sharing occurred on all but the first 5 days of egg-laying. The majority of hens (n = 14) chose to visit an occupied nest at least once, but no hens exclusively used......Under natural conditions, the feral hen (Gallus gallus domesticus) will choose a nest location away from the flock, whereas under commercial conditions, the domestic hen will often choose the same nest as other hens have used or are still using. Simultaneous nest sharing causes several welfare...

  11. Crossings and nestings in colored set partitions

    CERN Document Server

    Marberg, Eric

    2012-01-01

    Several years ago, Chen, Deng, Du, Stanley, and Yan introduced the notion of $k$-crossings and $k$-nestings for set partitions, and proved that the sizes of the largest $k$-crossings and $k$-nestings in the partitions of an $n$-set possess a symmetric joint distribution. The present work extends these results to $r$-colored set partitions, by which we mean set partitions whose arcs are labeled by an $r$-element set. A $k$-crossing or $k$-nesting in this context is a sequence or arcs, all with the same color, which form a $k$-crossing or $k$-nesting in the usual sense. To prove our extension, we produce a bijection from $r$-colored set partitions to certain sequences of $r$-partite partitions, which in the uncolored case specializes to a novel description of the map from set partitions to vacillating tableaux given by Chen et al. Among other applications, we explain how our construction implies recent results of Chen and Guo on colored matchings, and also an analogous symmetric joint distribution of crossings ...

  12. A Serialization Graph Construction for Nested Transactions

    Science.gov (United States)

    1990-02-01

    allowing replacement of entire subtrees of nested activity by single actions as well as the reordering of actions in a history . Also, they do not...systems. 28 [11] N. Lynch, M. Merritt, W. Weihl, and A. Fekete. A theory of atomic transactions. In International Conference on Database Theory, Bruges

  13. Collective fluid mechanics of honeybee nest ventilation

    Science.gov (United States)

    Gravish, Nick; Combes, Stacey; Wood, Robert J.; Peters, Jacob

    2014-11-01

    Honeybees thermoregulate their brood in the warm summer months by collectively fanning their wings and creating air flow through the nest. During nest ventilation workers flap their wings in close proximity in which wings continuously operate in unsteady oncoming flows (i.e. the wake of neighboring worker bees) and near the ground. The fluid mechanics of this collective aerodynamic phenomena are unstudied and may play an important role in the physiology of colony life. We have performed field and laboratory observations of the nest ventilation wing kinematics and air flow generated by individuals and groups of honeybee workers. Inspired from these field observations we describe here a robotic model system to study collective flapping wing aerodynamics. We microfabricate arrays of 1.4 cm long flapping wings and observe the air flow generated by arrays of two or more fanning robotic wings. We vary phase, frequency, and separation distance among wings and find that net output flow is enhanced when wings operate at the appropriate phase-distance relationship to catch shed vortices from neighboring wings. These results suggest that by varying position within the fanning array honeybee workers may benefit from collective aerodynamic interactions during nest ventilation.

  14. Activity patterns of nesting Mexican Spotted Owls

    Science.gov (United States)

    David K. Delaney; Teryl G. Grubb; Paul Beier

    1999-01-01

    We collected 2,665 hr of behavioral information using video surveillance on 19 Mexican Spotted Owl (Strix occidentalis lucida) pairs between 25 April and 26 July 1996. Prey deliveries per day increased as the nesting season progressed, with an average of 2.68 prey deliveries during incubation, 4.10 items during brooding, and 4.51 items during the...

  15. Field guide to red tree vole nests

    Science.gov (United States)

    Damon B. Lesmeister; James K. Swingle

    2017-01-01

    Surveys for red tree vole (Arborimus longicaudus) nests require tree climbing because the species is a highly specialized arboreal rodent that live in the tree canopy of coniferous forests in western Oregon and northwestern California. Tree voles are associated with old coniferous forest (≥80 years old) that are structurally complex, but are often...

  16. A catalog of Louisiana's nesting seabird colonies

    Science.gov (United States)

    Fontenot, William R.; Cardiff, Steve W.; DeMay, Richard A.; Dittmann, Donna L.; Hartley, Stephen B.; Jeske, Clinton W.; Lorenz, Nicole; Michot, Thomas C.; Purrington, Robert Dan; Seymour, Michael; Vermillion, William G.

    2012-01-01

    Summarizing his colonial nesting waterbird survey experiences along the northern coast of the Gulf of Mexico in a paper presented to the Colonial Waterbird Group of the Waterbird Society (Portnoy 1978), bird biologist John W. Portnoy stated, “This huge concentration of nesting waterbirds, restricted almost entirely to the wetlands and estuaries of southern Louisiana, is unmatched in all of North America; for example, a 1975 inventory of wading birds along the Atlantic Coast from Maine to Florida [Custer and Osborn, in press], tallied 250,000 breeding [waterbirds] of 14 species, in contrast with the 650,000 birds of 15 species just from Sabine Pass to Mobile Bay.” The “650,000 birds” to which Portnoy referred, were tallied by him in a 1976 survey of coastal Louisiana, Mississippi, and Alabama (see below, under “Major Surveys” section). According to the National Atlas of Coastal Waterbird Colonies in the Contiguous United States: 1976-82 (Spendelow and Patton 1988), the percentages of the total U.S. populations of Laughing Gull (11%), Forster's Tern (52%), Royal Tern (16%), Sandwich Tern (77%), and Black Skimmer (44%) which annually nest in Louisiana are significant – perhaps crucially so in the cases of Forster's Tern, Sandwich Tern, and Black Skimmer. Nearly three decades after Spendelow and Patton's determinations above, coastal Louisiana still stands out as the major center of colonial wading bird and seabird nesting in all of the United States. Within those three intervening decades, however, the

  17. Nested Dissection Interface Reconstruction in Pececillo

    Energy Technology Data Exchange (ETDEWEB)

    Jibben, Zechariah Joel [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-08-31

    A nested dissection method for interface reconstruction in a volume tracking framework has been implemented in Pececillo. This method provides a significant improvement over the traditional onion-skin method, which does not appropriately handle T-shaped multimaterial intersections and dynamic contact lines present in additive manufacturing simulations. The resulting implementation lays the groundwork for further re- search in numerical contact angle estimates.

  18. Establishment and assessment of real time reverse transcription PCR for rapid detection of viable mycobacterium tuberculosis based on Ag85B mRNA%基于Ag85B mRNA的荧光定量逆转录PCR快速检测活结核分枝杆菌方法的建立和评价

    Institute of Scientific and Technical Information of China (English)

    高文凤; 罗影殊; 黄偌颖; 徐园红; 钟晶; 刘衡川

    2013-01-01

    目的 建立评价荧光定量逆转录PCR快速检测活结核分枝杆菌的方法.方法 建立检测Ag85B mRNA的荧光定量逆转录PCR方法,评价其特异性、灵敏度、重复性、区分细菌存活状态及检测临床样本的能力.结果 该方法特异性强,仅扩增结核分枝杆菌.最低检出限是50 Copies/反应,菌落灵敏度为1.3×103cfu/ml,重复性好,可有效区分死菌和活菌.以培养法为“金标准”,PCR法的灵敏度为100.00%,特异度为84.38%,符合率为93.15%,Kappa值为0.86.结论 荧光定量逆转录PCR检测方法简便、快速、可靠,能有效区分结核分枝杆菌的存活状态,具有较高灵敏度和特异性,适用于临床样本的检测,为结核病的早期诊断、疗效评价及药敏情况分析提供了技术支持,有利于结核病的防控.

  19. 针对Asia-1型FMDV的qRT-PCR终点法中和试验的建立及初步研究%Establishment and preliminary study of a neutralization assay for Asia-1 type of FMDV using an end-point quantitative reverse transcription PCR

    Institute of Scientific and Technical Information of China (English)

    宋一鸣; 杨洋; 张志东

    2016-01-01

    为了缩短病毒中和试验(VNT)在口蹄疫病毒(FMDV)疫苗毒株选择以及病原检测中的时间,减少结果判断时人为因素的影响,试验采用qRT-PCR方法改进了传统的VNT,首先建立基于FMDV 3D序列的Taqman探针法qRT-PCR,之后使用FMDV Asia-1/JSL/06毒株感染IBRS-2细胞,提取不同时间收集的细胞病毒混合物的RNA进行qRT-PCR定量检测,获得FMDV Asia-1/JSL/06毒株在IBRS-2细胞中的病毒复制曲线,确定病毒复制的终点时间,即病毒中和试验中加入细胞维持液之后的第20小时,此时使用TRIzol裂解细胞并提取RNA进行qRT-PCR定量检测.以6作为拷贝浓度对数的临界值,拷贝浓度对数大于6的最低稀释度作为终点稀释度,建立了qRT-PCR-VNT方法的终点稀释度判断标准,并应用该方法对19份阴性血清以及4份阳性血清进行qRT-PCR-VNT检测.结果表明:该方法获得的阴性、阳性结果与传统VNT检测获得的结果完全相符.说明该方法具有快速、有效、重复性好等优点,具有代替传统VNT的潜能.

  20. Sensitivity of Coastal Environments and Wildlife to Spilled Oil: Northwest Arctic, Alaska: NESTS (Nest Points)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for nesting birds in Northwest Arctic, Alaska. Vector points in this data set represent locations of...

  1. Nesting Loggerhead Sea Turtle Activity Report 2000 and 1980-2000 Nesting Summary

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This paper presents results from the 8th Annual Study (using Army Corp of Engineers funds) of nesting by the Atlantic Loggerhead sea turtle (Caretta caretta) along...

  2. Rhode Island, Connecticut, New York, and New Jersey ESI: NESTS (Nest Points)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for nesting birds in coastal Rhode Island, Connecticut, New York, and New Jersey. Vector points in this...

  3. Exceptional sea turtle nest records in 2011 suggest an underestimated nesting potential in Sicily (Italy

    Directory of Open Access Journals (Sweden)

    Paolo Casale

    2012-07-01

    Full Text Available We report seven nesting events by loggerhead sea turtles in Sicily (Italy in 2011. In comparison to past records, this number is relatively high and may be at least in part due to an awareness campaign carried out in 2011 to solicit such reports. This suggests that Sicily may host a much higher nesting activity than previously thought and higher monitoring effort is recommended, especially in certain coastal tracts. Sand temperatures and incubation periods indicate that the beaches monitored so far in the southern coast are not optimal for development, resulting in low hatching success, and produce a majority of males. Five 2011 nests and two past nests from the same area had mtDNA haplotype CC-A2.1, the most common in the Mediterranean.

  4. Sensitivity of Coastal Environments and Wildlife to Spilled Oil: Southern California: NESTS (Nest Points)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for nesting and roosting gulls, terns, seabirds, shorebirds, and T/E species in Southern California....

  5. Timing of nest vegetation measurement may obscure adaptive significance of nest-site characteristics: A simulation study.

    Science.gov (United States)

    McConnell, Mark D; Monroe, Adrian P; Burger, Loren Wes; Martin, James A

    2017-02-01

    Advances in understanding avian nesting ecology are hindered by a prevalent lack of agreement between nest-site characteristics and fitness metrics such as nest success. We posit this is a result of inconsistent and improper timing of nest-site vegetation measurements. Therefore, we evaluated how the timing of nest vegetation measurement influences the estimated effects of vegetation structure on nest survival. We simulated phenological changes in nest-site vegetation growth over a typical nesting season and modeled how the timing of measuring that vegetation, relative to nest fate, creates bias in conclusions regarding its influence on nest survival. We modeled the bias associated with four methods of measuring nest-site vegetation: Method 1-measuring at nest initiation, Method 2-measuring at nest termination regardless of fate, Method 3-measuring at nest termination for successful nests and at estimated completion for unsuccessful nests, and Method 4-measuring at nest termination regardless of fate while also accounting for initiation date. We quantified and compared bias for each method for varying simulated effects, ranked models for each method using AIC, and calculated the proportion of simulations in which each model (measurement method) was selected as the best model. Our results indicate that the risk of drawing an erroneous or spurious conclusion was present in all methods but greater with Method 2 which is the most common method reported in the literature. Methods 1 and 3 were similarly less biased. Method 4 provided no additional value as bias was similar to Method 2 for all scenarios. While Method 1 is seldom practical to collect in the field, Method 3 is logistically practical and minimizes inherent bias. Implementation of Method 3 will facilitate estimating the effect of nest-site vegetation on survival, in the least biased way, and allow reliable conclusions to be drawn.

  6. Does nest site availability limit the density of hole nesting birds in small woodland patches?

    Directory of Open Access Journals (Sweden)

    J. Loman

    2006-11-01

    Full Text Available By providing nest boxes, previous studies have shown that nest sites are in short supply and limit the populations of several small passerines, including the Great Tit Parus major, the Blue Tit P. caeruleus, and the Pied Flycatcher Ficedula hypoleuca. Can this influence their distribution over a range of small woodland patch sizes in a heterogeneous landscape? To investigate this, a study was conducted in a heterogeneous agricultural landscape, with a mixture of wooded patches and cropped fields, in southern Sweden. The descriptive part of the study involved mapping territories of the three species in 135 patches. These species avoided small (<1 ha, Pied Flycatcher or very small (<0.2 ha, the two tit species forest patches in this landscape. In an experimental part, a subset of 34 patches, 0.01 to 24 ha in size was used. Territories were mapped in a first year as a control. In a second year, patches were matched by size and vegetation and nest-boxes were provided in one patch of each pair. Territories were again mapped. Providing nestboxes increased the density of breeding Great Tits in patches of all sizes and expanded their use of very small patches. The nest-boxes increased the density of Pied Flycatchers in large patches but not in small patches. So, is the lack of territories in small patches due to shortage of nest sites? The outcome of the experiment suggests nest site limitation as a cause of the observed Great Tit discrimination against very small habitat patches. The lack of Pied Flycatchers in small patches must however have another basis than lack of nest sites. The effect of providing nest-boxes on Blue Tit distribution was inconclusive.

  7. 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

    Science.gov (United States)

    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.

  8. Eggshell Porosity Provides Insight on Evolution of Nesting in Dinosaurs.

    Directory of Open Access Journals (Sweden)

    Kohei Tanaka

    Full Text Available Knowledge about the types of nests built by dinosaurs can provide insight into the evolution of nesting and reproductive behaviors among archosaurs. However, the low preservation potential of their nesting materials and nesting structures means that most information can only be gleaned indirectly through comparison with extant archosaurs. Two general nest types are recognized among living archosaurs: 1 covered nests, in which eggs are incubated while fully covered by nesting material (as in crocodylians and megapodes, and 2 open nests, in which eggs are exposed in the nest and brooded (as in most birds. Previously, dinosaur nest types had been inferred by estimating the water vapor conductance (i.e., diffusive capacity of their eggs, based on the premise that high conductance corresponds to covered nests and low conductance to open nests. However, a lack of statistical rigor and inconsistencies in this method render its application problematic and its validity questionable. As an alternative we propose a statistically rigorous approach to infer nest type based on large datasets of eggshell porosity and egg mass compiled for over 120 extant archosaur species and 29 archosaur extinct taxa/ootaxa. The presence of a strong correlation between eggshell porosity and nest type among extant archosaurs indicates that eggshell porosity can be used as a proxy for nest type, and thus discriminant analyses can help predict nest type in extinct taxa. Our results suggest that: 1 covered nests are likely the primitive condition for dinosaurs (and probably archosaurs, and 2 open nests first evolved among non-avian theropods more derived than Lourinhanosaurus and were likely widespread in non-avian maniraptorans, well before the appearance of birds. Although taphonomic evidence suggests that basal open nesters (i.e., oviraptorosaurs and troodontids were potentially the first dinosaurs to brood their clutches, they still partially buried their eggs in sediment

  9. Eggshell Porosity Provides Insight on Evolution of Nesting in Dinosaurs.

    Science.gov (United States)

    Tanaka, Kohei; Zelenitsky, Darla K; Therrien, François

    2015-01-01

    Knowledge about the types of nests built by dinosaurs can provide insight into the evolution of nesting and reproductive behaviors among archosaurs. However, the low preservation potential of their nesting materials and nesting structures means that most information can only be gleaned indirectly through comparison with extant archosaurs. Two general nest types are recognized among living archosaurs: 1) covered nests, in which eggs are incubated while fully covered by nesting material (as in crocodylians and megapodes), and 2) open nests, in which eggs are exposed in the nest and brooded (as in most birds). Previously, dinosaur nest types had been inferred by estimating the water vapor conductance (i.e., diffusive capacity) of their eggs, based on the premise that high conductance corresponds to covered nests and low conductance to open nests. However, a lack of statistical rigor and inconsistencies in this method render its application problematic and its validity questionable. As an alternative we propose a statistically rigorous approach to infer nest type based on large datasets of eggshell porosity and egg mass compiled for over 120 extant archosaur species and 29 archosaur extinct taxa/ootaxa. The presence of a strong correlation between eggshell porosity and nest type among extant archosaurs indicates that eggshell porosity can be used as a proxy for nest type, and thus discriminant analyses can help predict nest type in extinct taxa. Our results suggest that: 1) covered nests are likely the primitive condition for dinosaurs (and probably archosaurs), and 2) open nests first evolved among non-avian theropods more derived than Lourinhanosaurus and were likely widespread in non-avian maniraptorans, well before the appearance of birds. Although taphonomic evidence suggests that basal open nesters (i.e., oviraptorosaurs and troodontids) were potentially the first dinosaurs to brood their clutches, they still partially buried their eggs in sediment. Open nests

  10. Nest site preferences of the Woodlark (Lullula arborea) and its association with artificial nest predation

    Science.gov (United States)

    Buehler, Roman; Bosco, Laura; Arlettaz, Raphaël; Jacot, Alain

    2017-01-01

    The Woodlark is an insectivorous bird, which is listed as a priority species in Switzerland. In Valais, a stronghold of this species in the country, the birds breed in intensively managed vineyards and show a preference for parcels with ground vegetation during territory establishment. As a ground-breeder, the species is highly vulnerable to nest predation by avian and mammal predators. The aims of our study were firstly to investigate nest site preferences of the woodlark within vineyards and secondly to compare the predation risk of artificial nests dependent of ground vegetation structure. Our results point out that the Woodlark prefers patches of tall and dense ground cover within vegetated vineyard parcels and avoids parcels that have been treated with herbicides. In a follow-up experiment we conducted a study comparing the predation rate of artificial nests between bare parcels (40% vegetated area). Artificial nests equipped with one quail egg were distributed pairwise between two adjacent parcels that fulfilled the upper criteria and were monitored by trail cameras during 10-12 days. Predation rate was generally low (4 predation events) and only occurred in bare parcels. These data indicate that conspicuousness of avian nests may be decreased in vegetated parcels and that the amount of vegetation can lower the predation risk on ground breeding birds - another indication for the importance of ground vegetation for a successful conservation of the endangered Woodlark in Swiss vineyards.

  11. Nesting biology of Trypoxylon (Trypargilum) lactitarse Saussure (Hymenoptera, Crabronidae) in trap-nests in Southern Brazil.

    Science.gov (United States)

    Buschini, M L T; Niesing, F; Wolff, L L

    2006-08-01

    This study was carried in the Parque Municipal das Araucárias in the municipality of Guarapuava, state of Paraná, Southern Brazil. Three hundred and sixty five nests of T. lactitarse were obtained using trap-nests of 0.7, 1.0, and 1.3 cm in diameter. All of them had similar architecture, regardless of the diameter of the trap-nest. Completed nests consisted of a linear series of brood cells whose average number per nest was of 3.3, 4.0 and 3.6 for the nests with 0.7 cm, 1.0 cm and 1.3 cm in diameter, respectively. They were constructed more often during the summer. T. lactitarse had two types of life cycles: direct development (without diapause), and delayed development (with diapause during winter). Natural enemies included Chrysididae, Sarcophagidae, Dolichopodidae and Ichneumonidae. Out of 1,353 identified spider prey, 1,313 belonged to the Araneidae family.

  12. Nesting biology of Trypoxylon (Trypargilum lactitarse Saussure (Hymenoptera, Crabronidae in trap-nests in Southern Brazil

    Directory of Open Access Journals (Sweden)

    M. L. T. Buschini

    Full Text Available This study was carried in the Parque Municipal das Araucárias in the municipality of Guarapuava, state of Paraná, Southern Brazil. Three hundred and sixty five nests of T. lactitarse were obtained using trap-nests of 0.7, 1.0, and 1.3 cm in diameter. All of them had similar architecture, regardless of the diameter of the trap-nest. Completed nests consisted of a linear series of brood cells whose average number per nest was of 3.3, 4.0 and 3.6 for the nests with 0.7 cm, 1.0 cm and 1.3 cm in diameter, respectively. They were constructed more often during the summer. T. lactitarse had two types of life cycles: direct development (without diapause, and delayed development (with diapause during winter. Natural enemies included Chrysididae, Sarcophagidae, Dolichopodidae and Ichneumonidae. Out of 1,353 identified spider prey, 1,313 belonged to the Araneidae family.

  13. Nest predators, nest-site selection andnest success ofthe Emei Shan Liocichla (Liocichla omeiensis), a vulnerable babbler endemic tosouthwestern China

    Institute of Scientific and Technical Information of China (English)

    Yiqiang Fu; Benping Chen; Simon D Dowell; Zhengwang Zhang

    2016-01-01

    Background: The Emei Shan Liocichla (Liocichla omeiensis) is a globally vulnerable babbler, endemic to southwest-ern China. We investigated its nest predators, nest-site selection and nest success at the Laojunshan National Nature Reserve in Sichuan, China in order to identify the precise nesting-habitat requirements of the species, and to test whether the nest-site-selection cues, preferred by the Emei Shan Liocichla, are positively associated with nest success. Methods: We used infrared cameras to determine nest predators. We compared the microhabitat attributes between nest and random sites, as well as successful and failed nests. We used Binary Logistic Regression to determine the most important variables affecting nest-site selection of the Emei Shan Liocichla. We used the nest survival analysis in Program MARK to estimate daily nest survival rates (DSR). Nest success was calculated using the Mayifeld method. Results: In total 56 nests were found. The DSR for all nests that contained at least one egg was 0.9564± 0.0091 (95 % CI 0.9346–0.9711) (n= 40), while the total nest success was 27.5 %. We identiifed four categories of predators in 10 nest predation events, i.e. squirrels (n= 5), snakes (n= 3), raptors (n= 1) and wasps (n= 1). We found that: (1) nest predation was the primary reason for nest failure of the Emei Shan Liocichla, (2) tree cover, bamboo cover, liana abun-dance and distance to forest edge or gap were the most important variables affecting nest-site selection of this spe-cies, and (3) the nest-site-selection variables we measured appeared not to be positively associated with nest success. Conclusions: Our ifndings suggest that the Emei Shan Liocichla tended to select nest sites near forest edges or gaps with good concealment and that nest-site selection by this species was nonrandom but not necessarily adap-tive. Reducing forest-edge development and protecting bamboo stands should be effective for conservation of this species.

  14. Patterns of artificial nest depredation in a large floodplain forest

    Science.gov (United States)

    Knutson, Melinda G.; Gutreuter, Steven J.; Klaas, Erwin E.

    2000-01-01

    We used artificial bird nests to examine the relative effects of local habitat features and the surrounding landscape on the probability of songbird nest depredation in floodplain forests of the Upper Mississippi River. We found that the probability of depredation increased with size of floodplain forest plots. In small plots, the probability of depredation tended to increase away from the forest edge. Small patches of floodplain forest within a large river system can provide valuable nesting habitat for songbirds. We suggest that depredation pressure may be lower due to isolation effects. The probability of nest depredation increased with increasing canopy cover surrounding the nest tree and decreasing cover around the nest. Managers seeking to discourage nest predators in floodplain forests should consider managing for habitats that supply dense cover for nest concealment and an open tree canopy.

  15. 2012 waterfowl nesting study at Fish Springs National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Report on a 2012 duck nesting study at Fish Springs National Wildlife Refuge, where nest drag plots were surveyed within management units. Duck production estimates...

  16. 1972 American Eagle Nest Survey of the Chesapeake Bay Region.

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Data refers to the 1972 nesting season for the Bald Eagle in the Chesapeake area to include Virginia and Maryland. The 1972 nesting season for the Bald Eagle in the...

  17. 1971 American Eagle Nest Survey of the Chesapeake Bay Region.

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Data refers to the 1971 nesting season for the Bald Eagle in the Chesapeake area to include Virginia and Maryland. In general, the Chesapeake Bay region nesting...

  18. Potential Kittlitz's Murrelet Nesting Habitat in North America

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Using nest records and locations to identify landscape-scale parameters (distance to coast, elevation, slope, and land cover) that provide potential nesting habitat,...

  19. DISPERSAL OF SEEDS AS NEST MATERIAL BY THE CACTUS WREN

    Science.gov (United States)

    Cactus wren (Campylorhynchus brunneicapillus) nests from the southern Chihuahuan Desert contained viable seeds of grasses, forbs, and shrubs. The most common plants used as construction material in these nests were Muhlenbergia porteri, Boerhavia spicata, and the alien grass Era...

  20. Seedskadee National Wildlife Refuge : duck nesting success report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is a report summarizing the fourth consecutive year of data collection for duck nesting success at Seedskadee National Wildlife Refuge during the 1990 nesting...

  1. [Drug resistance reversal of HL-60/ADR cells by simultaneous suppression of XIAP and MRP].

    Science.gov (United States)

    Wang, Xiao-Fang; Wang, Chun; Qin, You-Wen; Yan, Shi-Ke; Gao, Yan-Rong

    2006-12-01

    This study was purposed to explore the mechanisms of drug resistance of HL-60/ADR cells and to compare the reversal drug-resistance effects of antisense oligonucleotides (AS ODN) of XIAP (X-linked inhibitor of apoptosis protein) and AS ODNs of MRP (multidrug resistance-associated protein) by use alone or in combination. Reverse transcription-PCR and Western blot were applied to detect the expression of XIAP, BCL-2, MRP and MDR1 in mRNA and protein levels of HL-60 cells and HL-60/ADR cells, respectively. Fully phosphorothioated AS ODN of XIAP and MRP was delivered into HL-60/ADR cells with Lipofectamine 2000 in the form of liposome-ODN complexes alone or in combination. CCK-8 cell viability assay was used to determine the effect of AS ODN of XIAP and MRP used alone or in combination on the chemotherapy sensitivity of HL-60/ADR cells to daunorubicin (DNR). Reverse transcription-PCR and Western blot were applied to examine the changes of XIAP, MRP in mRNA and protein levels respectively. The results showed that MRP and XIAP were both significantly higher in HL-60/ADR cells than those in HL-60 cells. AS ODN of XIAP and MRP down-regulated the expression of XIAP and MRP in HL-60/ADR cells and increased the sensitivity of HL-60/ADR cells to DNR, respectively. AS ODN of XIAP + MRP did not enhance the inhibition expression of XIAP in HL-60/ADR cells but increased the sensitivity of HL-60/ADR cells to DNR significantly as compared with AS ODN of XIAP (P MRP did not increase the concentration of DNR nor enhanced the inhibition expression of MRP in HL-60/ADR cells but increased the sensitivity of HL-60/ADR cells to DNR significantly (P MRP. It is concluded that both XIAP and MRP may be involved in the drug resistance mechanisms of HL-60/ADR cells. Drug-resistance of HL-60/ADR cells can be reversed significantly when antisense oligonucleotides of XIAP and MRP were used in combination.

  2. Nest sites selection by sympatric cavity-nesting birds in miombo woodlands

    Directory of Open Access Journals (Sweden)

    Vincent R. Nyirenda

    2016-03-01

    Full Text Available Deforestation and habitat fragmentation have long been known as drivers of wildlife depletion but information on their specific impacts on cavity-nesting birds in the miombo woodlands has been lacking. A comparative study of disturbed and undisturbed sites was conducted in miombo woodlands of Zambia to assess impacts of environmental stressors on birds. Foot patrols were employed to locate, identify and count host trees and cavities for cavity-nesting birds on twenty 200 m × 200 m sample plots. Undisturbed forests had three times more cavities (the nesting sites for birds, while there were 24.6% fewer abandoned cavities in undisturbed forests than in disturbed forests. The rate of cavity abandonment was about twice as high in human-dominated forests compared to undisturbed forests (61.3% c.f. 31.9%. Cavity-nesting birds preferred larger (> 36.0 cm diameter at breast height and taller (> 5.0 m trees for nest placement, especially in human-dominated forests. A number of cavity-nesting birds preferred Brachystegia spiciformis (zebrawood, Julbernadia paniculata (munsa, Parinari curatellifolia (mobola-plum and Uapaca kirkiana (mahobohobo as host trees to 14 other miombo tree species. Arnot’s Chat (Myrmecocichla arnoti had a wider selection of host trees for cavity-nesting than the other 40 cavity-nesting birds in the study areas. Anthropogenic activities such as uncontrolled firewood collection, wild fires, logging, and land clearing for agriculture negatively influenced wood abundance and diversity, with potential implications for persistence of cavity-nesting birds. The negative impacts of anthropogenic activities could be counteracted by conservation strategies such as implementation of sound forest policies, integrative land use practices, sustainable livelihood security and stakeholders’ awareness of the need to safeguard forest-dependent avifauna.Conservation implications: This comparative study unravels specific anthropogenic impacts on

  3. Nesting biology of four Tetrapedia species in trap-nests (Hymenoptera: Apidae: Tetrapediini).

    Science.gov (United States)

    Camillo, Evandro

    2005-01-01

    The nests used in this study were obtained from trap-nests (tubes of cardboard and cut bamboo stems) placed on Santa Carlota Farm (Itaoca Section-IS, Santana Section-SS and Cerrado-Ce), Cajuru, SP, Brazil. The number of nests and corresponding species obtained were as follows: 516 nests of T. curvitarsis, 104 of T. rugulosa, 399 of T. diversipes and 98 of T. gamfaloi. The most abundant species from SS and Ce was T. curvitarsis, and from IS it was T. diversipes. In general, most nests were collected during the hot and wet season (September to April). The nests were constructed with sand and an oily substance, and a single female established them. The cells were constructed in a linear series, sometimes followed by a vestibular cell. The number of brood cells ranged from 1 to 10 in T. curvitarsis (n=200), and in T. garofaloi (n-51), from 1 to 8 (n-30) in T. rugulosa, and from 1 to 6 (n=37) in T. diversipes. The pollen mass (pollen + oily substance) contained a hollow, sometimes divided by a transverse ridge, on the exposed face of the pollen mass. The egg was vertically positioned in the lower part of the hollow. At times, the closing of a cell was initiated before provisioning was completed, with a construction of a collar at the cell limit. In some nests the final cellular partition also acted as a closure plug. Females began activities at 6:18 a.m. and ended between 3:31 and 6:26 p.m. Some females (T. curvitarsis, T. rugiulosa and T. ganrfaloi) did not spend the nights at their nests, returning to them only the following morning with additional material. In general, the development period (for males and females) was greater in nests collected near the end of the hot and wet season than it was for nests collected in other months. Sex ratios for each species were as follows: T. curvitarsis. 1:1: T. rugulosa, 1.6:1 female; T. diversipes, 1.9:1: T. garofaloi, 2.8:1. Males and females of T. diversipes exhibited statistically similar sizes and in the other three species

  4. Comparing coefficients of nested nonlinear probability models

    DEFF Research Database (Denmark)

    Kohler, Ulrich; Karlson, Kristian Bernt; Holm, Anders

    2011-01-01

    In a series of recent articles, Karlson, Holm and Breen have developed a method for comparing the estimated coeffcients of two nested nonlinear probability models. This article describes this method and the user-written program khb that implements the method. The KHB-method is a general decomposi......In a series of recent articles, Karlson, Holm and Breen have developed a method for comparing the estimated coeffcients of two nested nonlinear probability models. This article describes this method and the user-written program khb that implements the method. The KHB-method is a general...... decomposition method that is unaffected by the rescaling or attenuation bias that arise in cross-model comparisons in nonlinear models. It recovers the degree to which a control variable, Z, mediates or explains the relationship between X and a latent outcome variable, Y*, underlying the nonlinear probability...

  5. Broadband DOA Estimation Based on Nested Arrays

    Directory of Open Access Journals (Sweden)

    Zhi-bo Shen

    2015-01-01

    Full Text Available Direction of arrival (DOA estimation is a crucial problem in electronic reconnaissance. A novel broadband DOA estimation method utilizing nested arrays is devised in this paper, which is capable of estimating the frequencies and DOAs of multiple narrowband signals in broadbands, even though they may have different carrier frequencies. The proposed method converts the DOA estimation of multiple signals with different frequencies into the spatial frequency estimation. Then, the DOAs and frequencies are pair matched by sparse recovery. It is possible to significantly increase the degrees of freedom (DOF with the nested arrays and the number of sources can be more than that of sensor array. In addition, the method can achieve high estimation precision without the two-dimensional search process in frequency and angle domain. The validity of the proposed method is verified by theoretic analysis and simulation results.

  6. Nested partitions method, theory and applications

    CERN Document Server

    Shi, Leyuan

    2009-01-01

    There is increasing need to solve large-scale complex optimization problems in a wide variety of science and engineering applications, including designing telecommunication networks for multimedia transmission, planning and scheduling problems in manufacturing and military operations, or designing nanoscale devices and systems. Advances in technology and information systems have made such optimization problems more and more complicated in terms of size and uncertainty. Nested Partitions Method, Theory and Applications provides a cutting-edge research tool to use for large-scale, complex systems optimization. The Nested Partitions (NP) framework is an innovative mix of traditional optimization methodology and probabilistic assumptions. An important feature of the NP framework is that it combines many well-known optimization techniques, including dynamic programming, mixed integer programming, genetic algorithms and tabu search, while also integrating many problem-specific local search heuristics. The book uses...

  7. Recursive Polynomial Remainder Sequence and the Nested Subresultants

    OpenAIRE

    Terui, Akira

    2008-01-01

    We give two new expressions of subresultants, nested subresultant and reduced nested subresultant, for the recursive polynomial remainder sequence (PRS) which has been introduced by the author. The reduced nested subresultant reduces the size of the subresultant matrix drastically compared with the recursive subresultant proposed by the authors before, hence it is much more useful for investigation of the recursive PRS. Finally, we discuss usage of the reduced nested subresultant in approxima...

  8. Imperfect nesting in unconventional density waves

    Science.gov (United States)

    Dóra, Balázs; Virosztek, Attila; Maki, Kazumi

    2002-03-01

    Recently, we have shown that unconventional charge density wave (UCDW) is the most likely candidate for the unidentified low-temperature phase (LTP) in α-(ET)2 salts. In particular, UCDW describes reasonably well the temperature dependence of the threshold electric field of LTP in α-(ET)2KHg(SCN)4. Here, we shall show that the imperfect nesting in UCDW is crucial to further improve the theoretical description of the threshold electric field.

  9. Structural relations between nested harmonic sums

    Energy Technology Data Exchange (ETDEWEB)

    Bluemlein, J.

    2008-07-15

    We describe the structural relations between nested harmonic sums emerging in the description of physical single scale quantities up to the 3-loop level in renormalizable gauge field theories. These are weight w=6 harmonic sums. We identify universal basic functions which allow to describe a large class of physical quantities and derive their complex analysis. For the 3-loop QCD Wilson coefficients 35 basic functions are required, whereas a subset of 15 describes the 3-loop anomalous dimensions. (orig.)

  10. Nested Dissection Interface Reconstruction in Pececillo

    Energy Technology Data Exchange (ETDEWEB)

    Jibben, Zechariah Joel [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Computer, Computational, and Statistical Sciences Division; Carlson, Neil N. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Computer, Computational, and Statistical Sciences Division; Francois, Marianne M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Computer, Computational, and Statistical Sciences Division

    2016-09-13

    A nested dissection method for interface reconstruction in a volume tracking framework has been implemented in Pececillo, a mini-app for Truchas, which is the ASC code for casting and additive manufacturing. This method provides a significant improvement over the traditional onion-skin method, which does not appropriately handle T-shaped multimaterial intersections and dynamic contact lines present in additive manufacturing simulations. The resulting implementation lays the groundwork for further research in contact angle estimates and surface tension calculations.

  11. DIAMONDS: a new Bayesian nested sampling tool*

    Directory of Open Access Journals (Sweden)

    Corsaro Enrico

    2015-01-01

    Full Text Available In the context of high-quality asteroseismic data provided by the NASA Kepler Mission, we developed a new code, termed DIAMONDS (high-DImensional And multi-MOdal NesteD Sampling, for fast Bayesian parameter estimation and model comparison by means of the Nested Sampling Monte Carlo (NSMC algorithm, an efficient and powerful method very suitable for high-dimensional problems (like the peak bagging analysis of solar-like oscillations and multi-modal problems (i.e. problems that show multiple solutions. We applied the code to the peak bagging analysis of solar-like oscillations observed in a challenging F-type star. By means of DIAMONDS one is able to detect the different backgrounds in the power spectrum of the star (e.g. stellar granulation and faculae activity and to understand whether one or two oscillation peaks can be identified or not. In addition, we demonstrate a novel approach to peak bagging based on multi-modality, which is able to reduce significantly the number of free parameters involved in the peak bagging model. This novel approach is therefore of great interest for possible future automatization of the entire analysis technique.

  12. Effects of prescribed burns on wintering cavity-nesting birds

    Science.gov (United States)

    Heather L. Bateman; Margaret A. O' Connell

    2006-01-01

    Primary cavity-nesting birds play a critical role in forest ecosystems by excavating cavities later used by other birds and mammals as nesting or roosting sites. Several species of cavity-nesting birds are non-migratory residents and consequently subject to winter conditions. We conducted winter bird counts from 1998 to 2000 to examine the abundance and habitat...

  13. Nest Success of Gunnison Sage-Grouse in Colorado, USA.

    Directory of Open Access Journals (Sweden)

    Amy J Davis

    Full Text Available Gunnison Sage-Grouse (Centrocercus minimus is a species of concern for which little demographic information exists. To help fill this information gap, we investigated factors affecting nest success in two populations of Gunnison Sage-Grouse. We assessed the relative effects of (1 vegetation characteristics (e.g., shrub height, shrub cover, grass cover, and grass height, (2 temporal factors (e.g., year, timing of incubation initiation, and nest age, (3 precipitation, and (4 age of the nesting female (yearling or adult on nest success rates. We found 177 nests in the Gunnison Basin population (that contains 85-90% of the species from 2005-2010 and 20 nests in the San Miguel population (that contains < 10% of the species from 2007-2010. Temporal factors had the greatest impact on nest success compared to vegetation characteristics, precipitation, and female age. Nest success varied considerably among years ranging from 4.0%-60.2% in Gunnison Basin and from 12.9%- 51.9% in San Miguel. Nests that were initiated earlier in the breeding season had higher nest success (at least one egg hatches. Daily nest survival rates decreased during the course of incubation. None of the vegetation characteristics we examined were strongly related to nest success.

  14. Ant colonies prefer infected over uninfected nest sites

    DEFF Research Database (Denmark)

    Pontieri, Luigi; Vojvodic, Svjetlana; Graham, Riley

    2014-01-01

    the high risk of epidemics in group-living animals. Choosing nest sites free of pathogens is hypothesized to be highly efficient in invasive ants as each of their introduced populations is often an open network of nests exchanging individuals (unicolonial) with frequent relocation into new nest sites...

  15. Communal nesting and kinship in degus (Octodon degus)

    Science.gov (United States)

    Ebensperger, Luis A.; Hurtado, María José; Soto-Gamboa, Mauricio; Lacey, Eileen A.; Chang, Ann T.

    Communal nesting is a fundamental component of many animal societies. Because the fitness consequences of this behavior vary with the relatedness among nest mates, understanding the kin structure of communally nesting groups is critical to understanding why such groups form. Observations of captive degus (Octodon degus) indicate that multiple females nest together, even when supplied with several nest boxes. To determine whether free-living degus also engage in communal nesting, we used radiotelemetry to monitor spatial relationships among adult females in a population of O. degus in central Chile. These analyses revealed that females formed stable associations of > 2-4 individuals, all of whom shared the same nest site at night. During the daytime, spatial overlap and frequency of social interactions were greatest among co-nesting females, suggesting that nesting associations represent distinct social units. To assess kinship among co-nesting females, we examined genotypic variation in our study animals at six microsatellite loci. These analyses indicated that mean pairwise relatedness among members of a nesting association (r=0.25) was significantly greater than that among randomly selected females (r=-0.03). Thus, communally nesting groups of degus are composed of female kin, making it possible for indirect as well as direct fitness benefits to contribute to sociality in this species.

  16. Trap-nests for stingless bees (Hymenoptera, Meliponini)

    NARCIS (Netherlands)

    Oliveira, Ricardo Caliari; Menezes, Cristiano; Egea Soares, Ademilson Espencer; Imperatriz Fonseca, Vera Lucia

    2013-01-01

    Most stingless bee species build their nests inside tree hollows. In this paper, we present trap-nest containers which simulate nesting cavities so as to attract swarms of stingless bees. Although regularly used by stingless bee beekeepers in Brazil, this technique to obtain new colonies has not yet

  17. Semantic Analysis of Virtual Classes and Nested Classes

    DEFF Research Database (Denmark)

    Madsen, Ole Lehrmann

    1999-01-01

    Virtual classes and nested classes are distinguishing features of BETA. Nested classes originated from Simula, but until recently they have not been part of main stream object- oriented languages. C++ has a restricted form of nested classes and they were included in Java 1.1. Virtual classes...... the central elements of the semantic analysis used in the Mjølner BETA compiler....

  18. A Local Characterization of Lie Homomorphisms of Nest Algebras

    Institute of Scientific and Technical Information of China (English)

    YANG Miao-xia; ZHANG Jian-hua

    2014-01-01

    In this paper, linear maps preserving Lie products at zero points on nest algebras are studied. It is proved that every linear map preserving Lie products at zero points on any finite nest algebra is a Lie homomorphism. As an application, the form of a linear bijection preserving Lie products at zero points between two finite nest algebras is obtained.

  19. An Architecture for Nested Transaction Support on Standard Database Systems

    NARCIS (Netherlands)

    Boertjes, E.M.; Grefen, P.W.P.J.; Vonk, J.; Apers, Peter M.G.

    Many applications dealing with complex processes require database support for nested transactions. Current commercial database systems lack this kind of support, offering flat, non-nested transactions only. This paper presents a three-layer architecture for implementing nested transaction support on

  20. Ground nesting in recultivated forest habitats - a study with artificial nests

    Energy Technology Data Exchange (ETDEWEB)

    Purger, J.J.; Meszaros, L.A.; Purger, D. [University of Pecs, Pecs (Hungary). Faculty of Science

    2004-01-01

    The study was carried out in the outskirts of the town of Pecs (southern Hungary) in a recultivated former coal mine. Bordered by Turkey Oak forests, this open area forms a wedge-shaped clearing in that woodland. Since trees and taller shrubs are rare in the area, it is mainly ground nesting bird species that occur in the clearing. In order to discover whether it is more advantageous to nest in the recultivated area (clearing) than in the nearby forest or at its edges, 150 artificial ground nests were constructed. On 7 May 2002, one quail egg and a plasticine egg of similar size were placed in each of the artificial nests. After a week it was found that 24% of nests in the clearing, 30% of those in the forest edge, and 44% of the ones inside the forest had suffered depredation. The proportions of damaged plasticine and quail eggs inside the forest and at the forest edge were similar, whereas the quail eggs in the clearings were significantly less damaged than plasticine eggs. Of all the experimental eggs, significantly more plasticine eggs (29%) were damaged than quail eggs (17%), which suggests that small-bodied predators are unable to break the quail eggs. 18% of the plasticine eggs attacked, and 72% of the quail eggs attacked were removed from the nest by the predator. Among the predators, small mammals were dominant in the clearing and inside the forest, and birds at the forest edge. Based on the predation of quail eggs, the survival chances of ground nests in the clearing are greater than at the forest edge or inside the forest.

  1. Changes in position and quality of preferred nest box: effects on nest box use by laying hens

    DEFF Research Database (Denmark)

    Riber, Anja Brinch; Nielsen, Birte L.

    2013-01-01

    Using laying hens, we investigated whether position of a nest box, both within the pen and relative to other nest boxes, influenced the preference for a nest box, and how a sudden and marked change to the preferred box influenced the use of nest boxes by the hens. Groups (n=12) of 15 Isa Warren...... revealed that some hens were location conservative, i.e. continued laying in a corner location (or as close to that as possible), whereas others were isolation conservative, i.e. continued laying in the most isolated nest box despite it being positioned in a different area of the pen....... hens were housed in pens, each with five identical nest boxes in different positions: Two single (in a corner or not) and a triplet of nest boxes (one of which in a corner). The use of nest boxes was determined by the number of eggs laid daily in each box. Three experiments, each lasting 10 days, were...

  2. Sharp-Tailed Grouse Nest Survival and Nest Predator Habitat Use in North Dakota’s Bakken Oil Field

    Science.gov (United States)

    2017-01-01

    Recent advancements in extraction technologies have resulted in rapid increases of gas and oil development across the United States and specifically in western North Dakota. This expansion of energy development has unknown influences on local wildlife populations and the ecological interactions within and among species. Our objectives for this study were to evaluate nest success and nest predator dynamics of sharp-tailed grouse (Tympanuchus phasianellus) in two study sites that represented areas of high and low energy development intensities in North Dakota. During the summers of 2012 and 2013, we monitored 163 grouse nests using radio telemetry. Of these, 90 nests also were monitored using miniature cameras to accurately determine nest fates and identify nest predators. We simultaneously conducted predator surveys using camera scent stations and occupancy modeling to estimate nest predator occurrence at each site. American badgers (Taxidea taxus) and striped skunks (Mephitis mephitis) were the primary nest predators, accounting for 56.7% of all video recorded nest depredations. Nests in our high intensity gas and oil area were 1.95 times more likely to succeed compared to our minimal intensity area. Camera monitored nests were 2.03 times more likely to succeed than non-camera monitored nests. Occupancy of mammalian nest predators was 6.9 times more likely in our study area of minimal gas and oil intensity compared to the high intensity area. Although only a correlative study, our results suggest energy development may alter the predator community, thereby increasing nest success for sharp-tailed grouse in areas of intense development, while adjacent areas may have increased predator occurrence and reduced nest success. Our study illustrates the potential influences of energy development on the nest predator—prey dynamics of sharp-tailed grouse in western North Dakota and the complexity of evaluating such impacts on wildlife. PMID:28081245

  3. Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman loops and other larger motifs within proteins.

    Science.gov (United States)

    Afzal, Avid M; Al-Shubailly, Fawzia; Leader, David P; Milner-White, E James

    2014-11-01

    The nest is a protein motif of three consecutive amino acid residues with dihedral angles 1,2-αR αL (RL nests) or 1,2-αL αR (LR nests). Many nests form a depression in which an anion or δ-negative acceptor atom is bound by hydrogen bonds from the main chain NH groups. We have determined the extent and nature of this bridging in a database of protein structures using a computer program written for the purpose. Acceptor anions are bound by a pair of bridging hydrogen bonds in 40% of RL nests and 20% of LR nests. Two thirds of the bridges are between the NH groups at Positions 1 and 3 of the motif (N1N3-bridging)-which confers a concavity to the nest; one third are of the N2N3 type-which does not. In bridged LR nests N2N3-bridging predominates (14% N1N3: 75% N2N3), whereas in bridged RL nests the reverse is true (69% N1N3: 25% N2N3). Most bridged nests occur within larger motifs: 45% in (hexapeptide) Schellman loops with an additional 4 → 0 hydrogen bond (N1N3), 11% in Schellman loops with an additional 5 → 1 hydrogen bond (N2N3), 12% in a composite structure including a type 1β-bulge loop and an asx- or ST- motif (N1N3)-remarkably homologous to the N1N3-bridged Schellman loop-and 3% in a composite structure including a type 2β-bulge loop and an asx-motif (N2N3). A third hydrogen bond is a previously unrecognized feature of Schellman loops as those lacking bridged nests have an additional 4 → 0 hydrogen bond.

  4. Nest-site competition between invasive and native cavity nesting birds and its implication for conservation.

    Science.gov (United States)

    Charter, Motti; Izhaki, Ido; Ben Mocha, Yitzchak; Kark, Salit

    2016-10-01

    Nesting cavities are often a limited resource that multiple species use. There is an ongoing discussion on whether invasive cavity nesting birds restrict the availability of this key limited resource. While the answer to this question has important conservation implications, little experimental work has been done to examine it. Here, we aimed to experimentally test whether alien cavity nesting birds affect the occupancy of cavities and the resulting breeding success of native cavity breeders in a large urban park located in Tel Aviv, Israel. Over three breeding seasons, we manipulated the entry size of nest boxes and compared the occupancy and breeding success of birds in nest boxes of two treatments. These included nest boxes with large-entrance and small-entrance holes. The large-entrance holes allowed access for both the native and invasive birds (the two main aliens in the park are the common mynas and rose-ringed parakeets). The smaller-entrance boxes, on the other hand, allowed only the smaller sized native cavity breeders (great tits and house sparrows) to enter the boxes but prevented the alien species from entering. We found that the large-entrance nest boxes were occupied by five different bird species, comprising three natives (great tit, house sparrow, Scops owl) and two invasive species (common myna, rose-ringed parakeet) while the small-entrance boxes were only occupied by the two native species. The alien common mynas and rose-ringed parakeets occupied 77.5% of the large-entrance nest boxes whereas native species, mainly great tits, occupied less than 9% of the large-entrance boxes and 36.5% of the small-entrance boxes. When examining the occupancy of those cavities that were not occupied by the aliens, natives occupied both the small and large-entrance nest boxes equally. Three quarters (78%) of the great tits breeding in the large-entrance boxes were usurped by common mynas during the breeding season and as a result breeding success was

  5. Effects of Nest Spacing on Nest Occupation, Mating Success and Mating Behaviour in the Two-spotted Goby (Gobiusculus flavescens)

    OpenAIRE

    2011-01-01

    I investigated hoe different spacing of breeding sited affects different aspects of mating behaviour in the two-spotted goby. I found that clumped nest spacing affects nest occupations and reproductive success negatively. Clumped nest spacing incresed male agonistic behaviour and led to a higher variance in reproductive success.

  6. EFL Students' and Teachers' Attitudes toward Foreign Language Speaking Anxiety: A Look at NESTs and Non-NESTs

    Science.gov (United States)

    Han, Turgay; Tanriöver, Ahmet Serkan; Sahan, Özgür

    2016-01-01

    Native English Speaking Teachers (NESTs) have been employed in various English language teaching (ELT) positions and departments at private and state universities in Turkey, particularly over the last three decades. However, undergraduate EFL students' attitudes toward NESTs and Non-Native English Speaking Teachers (Non-NESTs) remain seriously…

  7. Managing Reverse Logistics or Reversing Logistics Management?

    OpenAIRE

    Brito, Marisa

    2004-01-01

    textabstractIn the past, supply chains were busy fine-tuning the logistics from raw material to the end customer. Today an increasing flow of products is going back in the chain. Thus, companies have to manage reverse logistics as well.This thesis contributes to a better understanding of reverse logistics. The thesis brings insights on reverse logistics decision-making and it lays down theoretical principles for reverse logistics as a research field.In particular it puts together a framework ...

  8. Ant colonies prefer infected over uninfected nest sites

    DEFF Research Database (Denmark)

    Pontieri, Luigi; Vojvodic, Svjetlana; Graham, Riley;

    2014-01-01

    During colony relocation, the selection of a new nest involves exploration and assessment of potential sites followed by colony movement on the basis of a collective decision making process. Hygiene and pathogen load of the potential nest sites are factors worker scouts might evaluate, given...... and low genetic diversity, likely making these species particularly vulnerable to parasites and diseases. We investigated the nest site preference of the invasive pharaoh ant, Monomorium pharaonis, through binary choice tests between three nest types: nests containing dead nestmates overgrown...

  9. Estimating raptor nesting success: old and new approaches

    Science.gov (United States)

    Brown, Jessi L.; Steenhof, Karen; Kochert, Michael N.; Bond, Laura

    2013-01-01

    Studies of nesting success can be valuable in assessing the status of raptor populations, but differing monitoring protocols can present unique challenges when comparing populations of different species across time or geographic areas. We used large datasets from long-term studies of 3 raptor species to compare estimates of apparent nest success (ANS, the ratio of successful to total number of nesting attempts), Mayfield nesting success, and the logistic-exposure model of nest survival. Golden eagles (Aquila chrysaetos), prairie falcons (Falco mexicanus), and American kestrels (F. sparverius) differ in their breeding biology and the methods often used to monitor their reproduction. Mayfield and logistic-exposure models generated similar estimates of nesting success with similar levels of precision. Apparent nest success overestimated nesting success and was particularly sensitive to inclusion of nesting attempts discovered late in the nesting season. Thus, the ANS estimator is inappropriate when exact point estimates are required, especially when most raptor pairs cannot be located before or soon after laying eggs. However, ANS may be sufficient to assess long-term trends of species in which nesting attempts are highly detectable.

  10. Resource redistribution in polydomous ant nest networks: local or global?

    Science.gov (United States)

    Franks, Daniel W.; Robinson, Elva J.H.

    2014-01-01

    An important problem facing organisms in a heterogeneous environment is how to redistribute resources to where they are required. This is particularly complex in social insect societies as resources have to be moved both from the environment into the nest and between individuals within the nest. Polydomous ant colonies are split between multiple spatially separated, but socially connected, nests. Whether, and how, resources are redistributed between nests in polydomous colonies is unknown. We analyzed the nest networks of the facultatively polydomous wood ant Formica lugubris. Our results indicate that resource redistribution in polydomous F. lugubris colonies is organized at the local level between neighboring nests and not at the colony level. We found that internest trails connecting nests that differed more in their amount of foraging were stronger than trails between nests with more equal foraging activity. This indicates that resources are being exchanged directly from nests with a foraging excess to nests that require resources. In contrast, we found no significant relationships between nest properties, such as size and amount of foraging, and network measures such as centrality and connectedness. This indicates an absence of a colony-level resource exchange. This is a clear example of a complex behavior emerging as a result of local interactions between parts of a system. PMID:25214755

  11. Desmoplastic nested spindle cell tumours and nested stromal epithelial tumours of the liver.

    Science.gov (United States)

    Misra, Sunayana; Bihari, Chhagan

    2016-04-01

    Desmoplastic nested spindle cell tumour of liver (DNSTL), nested stromal-epithelial tumour (NSET) and calcifying nested stromal-epithelial tumour (CNSET) are recently described entities with similar morphology, immunohistochemistry and molecular genetics. These are rare entities with only three large case series described till date. These tumours commonly present in the paediatric age group. NSETs, in addition have been described to be associated with ectopic adrenocorticotropic hormone (ACTH) production and Cushingoid features. It is important to discuss this rare group of tumours with a low malignant potential as the most common radiological differential diagnosis is hepatoblastoma, which has a relatively poorer prognosis. Thus, a pathologist needs to keep this entity in mind, so as to offer a correct histological diagnosis.

  12. Grassland birds orient nests relative to nearby vegetation

    Science.gov (United States)

    Hoekman, S.T.; Ball, I.J.; Fondell, T.E.

    2002-01-01

    We studied orientation of nest sites relative to nearby vegetation for dabbling ducks (Cinnamon Teal, Anas cyanoptera; Blue-winged Teal, A. discors; Gadwall, A. strepera; Mallard, A. platyrhynchos; and Northern Shoveler, A. clypeata) and Short-eared Owls (Asio flammeus) in ungrazed grassland habitat during 1995-1997 in westcentral Montana. We estimated an index of vegetation height and density in intercardinal directions (NE, SE, SW, NW) immediately around nests. All species oriented nests with the least vegetation to the southeast and the most vegetation to either the southwest or northwest. Furthermore, maximum vegetation around nests shifted from the southwest to the northwest with increasing nest initiation date, apparently as a response of individuals tracking seasonal change in the afternoon solar path. Thus, nests were relatively exposed to solar insolation during cool morning hours but were shaded from intense insolation in the afternoon throughout the breeding season. We suggest that nest microhabitat was selected in part to moderate the thermal environment.

  13. Managing Reverse Logistics or Reversing Logistics Management?

    NARCIS (Netherlands)

    M.P. de Brito (Marisa)

    2004-01-01

    textabstractIn the past, supply chains were busy fine-tuning the logistics from raw material to the end customer. Today an increasing flow of products is going back in the chain. Thus, companies have to manage reverse logistics as well.This thesis contributes to a better understanding of reverse

  14. Managing Reverse Logistics or Reversing Logistics Management?

    NARCIS (Netherlands)

    M.P. de Brito (Marisa)

    2004-01-01

    textabstractIn the past, supply chains were busy fine-tuning the logistics from raw material to the end customer. Today an increasing flow of products is going back in the chain. Thus, companies have to manage reverse logistics as well.This thesis contributes to a better understanding of reverse log

  15. Blackbeard Island National Wildlife Refuge Loggerhead Sea Turtle Nest Monitoring: End of Season Report - 2013

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The 2013 Loggerhead sea turtle nesting season resulted in 284 nests with 17,915 emerged hatchlings. Of the 284 nests, 162 (57%) remained in situ with 122 (43%) nests...

  16. Specificity and transmission mosaic of ant nest-wall fungi.

    Science.gov (United States)

    Schlick-Steiner, Birgit C; Steiner, Florian M; Konrad, Heino; Seifert, Bernhard; Christian, Erhard; Moder, Karl; Stauffer, Christian; Crozier, Ross H

    2008-01-22

    Mutualism, whereby species interact to their mutual benefit, is extraordinary in a competitive world. To recognize general patterns of origin and maintenance from the plethora of mutualistic associations proves a persisting challenge. The simplest situation is believed to be that of a single mutualist specific to a single host, vertically transmitted from one host generation to the next. We characterized ascomycete fungal associates cultured for nest architecture by the ant subgenera Dendrolasius and Chthonolasius. The ants probably manage their fungal mutualists by protecting them against fungal competitors. The ant subgenera display different ant-to-fungus specificity patterns, one-to-two and many-to-one, and we infer vertical transmission, in the latter case overlaid by horizontal transmission. Possible evolutionary trajectories include a reversal from fungiculture by other Lasius subgenera and inheritance of fungi through life cycle interactions of the ant subgenera. The mosaic indicates how specificity patterns can be shaped by an interplay between host life-cycles and transmission adaptations.

  17. Synthesis of nanoparticles with frog foam nest proteins

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Hyo-Jick, E-mail: choihc@ucmail.uc.edu; Ebersbacher, Charles F. [University of Cincinnati, School of Energy, Environmental, Biological and Medical Engineering (United States); Myung, Nosang V. [University of California, Riverside, Department of Chemical and Environmental Engineering (United States); Montemagno, Carlo D., E-mail: montemcd@ucmail.uc.edu [University of Cincinnati, School of Energy, Environmental, Biological and Medical Engineering (United States)

    2012-09-15

    Microemulsions provide an efficient means of synthesizing monodispersed nanoparticles. Recent studies have demonstrated potential problems of surfactant due to the interaction with nanoparticles/precursors. To solve the problems, various types of chemical surfactants have been tested, but natural biosurfactants have not received a great deal of attention in engineering application. Here, we report the formation of microemulsions using frog foam nest protein, ranaspumin-2 (RSN-2), based on the hypothesis that RSN-2 assembles at the water-oil interface as a result of conformational change into an extended form. Fluorescence spectroscopic studies showed that RSN-2 undergoes a reversible transition between extended and globular conformation in foams/microemulsions and aqueous solution, respectively. Microemulsions were formulated with RSN-2 to synthesize 8-10 nm superparamagnetic iron oxide nanoparticles by mixing precursor-containing microemulsions with base-containing microemulsions. RSN-2 proteins were recovered from microemulsions and found to be recycled to make foams and microemulsions. Fluorescence spectroscopic analyses showed that RSN-2 maintained its mechanical agitation-induced amphiphilicity throughout multiple foaming/defoaming processes. These results suggest that conformational flexibility and structural stability of RSN-2 in aggressive environments enable the recycled use of RSN-2, elucidating the cost-effective advantage.

  18. Synthesis of nanoparticles with frog foam nest proteins

    Science.gov (United States)

    Choi, Hyo-Jick; Ebersbacher, Charles F.; Myung, Nosang V.; Montemagno, Carlo D.

    2012-09-01

    Microemulsions provide an efficient means of synthesizing monodispersed nanoparticles. Recent studies have demonstrated potential problems of surfactant due to the interaction with nanoparticles/precursors. To solve the problems, various types of chemical surfactants have been tested, but natural biosurfactants have not received a great deal of attention in engineering application. Here, we report the formation of microemulsions using frog foam nest protein, ranaspumin-2 (RSN-2), based on the hypothesis that RSN-2 assembles at the water-oil interface as a result of conformational change into an extended form. Fluorescence spectroscopic studies showed that RSN-2 undergoes a reversible transition between extended and globular conformation in foams/microemulsions and aqueous solution, respectively. Microemulsions were formulated with RSN-2 to synthesize 8-10 nm superparamagnetic iron oxide nanoparticles by mixing precursor-containing microemulsions with base-containing microemulsions. RSN-2 proteins were recovered from microemulsions and found to be recycled to make foams and microemulsions. Fluorescence spectroscopic analyses showed that RSN-2 maintained its mechanical agitation-induced amphiphilicity throughout multiple foaming/defoaming processes. These results suggest that conformational flexibility and structural stability of RSN-2 in aggressive environments enable the recycled use of RSN-2, elucidating the cost-effective advantage.

  19. Reversible Thermoset Adhesives

    Science.gov (United States)

    Mac Murray, Benjamin C. (Inventor); Tong, Tat H. (Inventor); Hreha, Richard D. (Inventor)

    2016-01-01

    Embodiments of a reversible thermoset adhesive formed by incorporating thermally-reversible cross-linking units and a method for making the reversible thermoset adhesive are provided. One approach to formulating reversible thermoset adhesives includes incorporating dienes, such as furans, and dienophiles, such as maleimides, into a polymer network as reversible covalent cross-links using Diels Alder cross-link formation between the diene and dienophile. The chemical components may be selected based on their compatibility with adhesive chemistry as well as their ability to undergo controlled, reversible cross-linking chemistry.

  20. Nest-site selection and nest success of an Arctic-breeding passerine, Smith's Longspur, in a changing climate

    Science.gov (United States)

    McFarland, Heather R.; Kendall, Steve J.; Powell, Abby

    2017-01-01

    Despite changes in shrub cover and weather patterns associated with climate change in the Arctic, little is known about the breeding requirements of most passerines tied to northern regions. We investigated the nesting biology and nest habitat characteristics of Smith's Longspurs (Calcarius pictus) in 2 study areas in the Brooks Range of Alaska, USA. First, we examined variation in nesting phenology in relation to local temperatures. We then characterized nesting habitat and analyzed nest-site selection for a subset of nests (n = 86) in comparison with paired random points. Finally, we estimated the daily survival rate of 257 nests found in 2007–2013 with respect to both habitat characteristics and weather variables. Nest initiation was delayed in years with snow events, heavy rain, and freezing temperatures early in the breeding season. Nests were typically found in open, low-shrub tundra, and never among tall shrubs (mean shrub height at nests = 26.8 ± 6.7 cm). We observed weak nest-site selection patterns. Considering the similarity between nest sites and paired random points, coupled with the unique social mating system of Smith's Longspurs, we suggest that habitat selection may occur at the neighborhood scale and not at the nest-site scale. The best approximating model explaining nest survival suggested a positive relationship with the numbers of days above 21°C that an individual nest experienced; there was little support for models containing habitat variables. The daily nest survival rate was high (0.972–0.982) compared with that of most passerines in forested or grassland habitats, but similar to that of passerines nesting on tundra. Considering their high nesting success and ability to delay nest initiation during inclement weather, Smith's Longspurs may be resilient to predicted changes in weather regimes on the breeding grounds. Thus, the greatest threat to breeding Smith's Longspurs associated with climate change may be the loss of low

  1. Island characteristics within wetlands influence waterbird nest success and abundance

    Science.gov (United States)

    Hartman, Christopher; Ackerman, Josh; Herzog, Mark

    2016-01-01

    Coastal waterbird populations are threatened by habitat loss and degradation from urban and agricultural development and forecasted sea level rise associated with climate change. Remaining wetlands often must be managed to ensure that waterbird habitat needs, and other ecosystem functions, are met. For many waterbirds, the availability of island nesting habitat is important for conserving breeding populations. We used linear mixed models to investigate the influence of pond and island landscape characteristics on nest abundance and nest success of American avocets (Recurvirostra americana), black-necked stilts (Himantopus mexicanus), and Forster's terns (Sterna forsteri) in San Francisco Bay, California, USA, based on a 9-year dataset that included >9,000 nests. Nest abundance and nest success were greatest within ponds and on individual islands located either 4 km from San Francisco Bay. Further, nest abundance was greater within ponds with relatively few islands, and on linear-shaped, highly elongated islands compared to more rounded islands. Nest success was greater on islands located away from the nearest surrounding pond levee. Compared to more rounded islands, linear islands contained more near-water habitat preferred by many nesting waterbirds. Islands located away from pond levees may provide greater protection from terrestrial egg and chick predators. Our results indicate that creating and maintaining a few, relatively small, highly elongated and narrow islands away from mainland levees, in as many wetland ponds as possible would be effective at providing waterbirds with preferred nesting habitat.

  2. Does cooperation mean kinship between spatially discrete ant nests?

    Science.gov (United States)

    Procter, Duncan S; Cottrell, Joan E; Watts, Kevin; A'Hara, Stuart W; Hofreiter, Michael; Robinson, Elva J H

    2016-12-01

    Eusociality is one of the most complex forms of social organization, characterized by cooperative and reproductive units termed colonies. Altruistic behavior of workers within colonies is explained by inclusive fitness, with indirect fitness benefits accrued by helping kin. Members of a social insect colony are expected to be more closely related to one another than they are to other conspecifics. In many social insects, the colony can extend to multiple socially connected but spatially separate nests (polydomy). Social connections, such as trails between nests, promote cooperation and resource exchange, and we predict that workers from socially connected nests will have higher internest relatedness than those from socially unconnected, and noncooperating, nests. We measure social connections, resource exchange, and internest genetic relatedness in the polydomous wood ant Formica lugubris to test whether (1) socially connected but spatially separate nests cooperate, and (2) high internest relatedness is the underlying driver of this cooperation. Our results show that socially connected nests exhibit movement of workers and resources, which suggests they do cooperate, whereas unconnected nests do not. However, we find no difference in internest genetic relatedness between socially connected and unconnected nest pairs, both show high kinship. Our results suggest that neighboring pairs of connected nests show a social and cooperative distinction, but no genetic distinction. We hypothesize that the loss of a social connection may initiate ecological divergence within colonies. Genetic divergence between neighboring nests may build up only later, as a consequence rather than a cause of colony separation.

  3. Experimental nest site limitation affects reproductive strategies and parental investment in a hole-nesting passerine

    NARCIS (Netherlands)

    Jacot, A.; Valcu, M.; Van Oers, K.; Kempenaers, B.

    2009-01-01

    In resource defence mating systems, males monopolize a resource that is of primary importance for breeding females. For secondary cavity nesters, the availability of suitable nesting sites is important in determining the strength of intrasexual competition, whereby phenotypic and behavioural traits

  4. Nested PCR for Rapid Detection of Mumps Virus in Cerebrospinal Fluid from Patients with Neurological Diseases

    OpenAIRE

    Poggio, Gustavo Palacios; Rodriguez, Claudia; Cisterna, Daniel; Freire, María Cecilia; Cello, Jerónimo

    2000-01-01

    In this study, we have developed a reverse transcription (RT)-nested polymerase chain reaction (n-PCR) for the detection of mumps virus RNA in cerebrospinal fluid (CSF) from patients with neurological infections. A specific 112-bp fragment was amplified by this method with primers from the nucleoprotein of the mumps virus genome. The mumps virus RT–n-PCR was capable of detecting 0.001 PFU/ml and 0.005 50% tissue culture infective dose/ml. This method was found to be specific, since no PCR pro...

  5. Reverse logistics - a framework

    OpenAIRE

    Brito, Marisa; Dekker, Rommert

    2002-01-01

    textabstractIn this paper we define and compare Reverse Logistics definitions. We start by giving an understanding framework of Reverse Logistics: the why-what-how. By this means, we put in context the driving forces for Reverse Logistics, a typology of return reasons, a classification of products, processes and actors. In addition we provide a decision framework for Reverse Logistics and we present it according to long, medium and short term decisions, i.e. strategic-tactic-operational decis...

  6. Reverse cholesterol transport revisited

    Institute of Scientific and Technical Information of China (English)

    Astrid; E; van; der; Velde

    2010-01-01

    Reverse cholesterol transport was originally described as the high-density lipoprotein-mediated cholesterol flux from the periphery via the hepatobiliary tract to the intestinal lumen, leading to fecal excretion. Since the introduction of reverse cholesterol transport in the 1970s, this pathway has been intensively investigated. In this topic highlight, the classical reverse cholesterol transport concepts are discussed and the subject reverse cholesterol transport is revisited.

  7. Reverse logistics - a framework

    NARCIS (Netherlands)

    M.P. de Brito (Marisa); R. Dekker (Rommert)

    2002-01-01

    textabstractIn this paper we define and compare Reverse Logistics definitions. We start by giving an understanding framework of Reverse Logistics: the why-what-how. By this means, we put in context the driving forces for Reverse Logistics, a typology of return reasons, a classification of product

  8. Flexibility in nest-site choice and nesting success of Turdus rufiventris (Turdidae) in a montane forest in northwestern argentina

    Science.gov (United States)

    Lomascolo, S.B.; Monmany, A.C.; Malizia, A.; Martin, T.E.

    2010-01-01

    We studied the consequences of nest-site choice on nesting success under differing disturbance levels for the Rufous-bellied Thrush (Turdus rufiventris). We compared nest-site choice and nest success between a disturbed site and an undisturbed site in a montane subtropical forest in northwestern Argentina. We found no overall difference in daily predation rate (DPR) between the disturbed and undisturbed sites. However, DPR of nests on bromeliads was significantly lower at the microhabitat level than on other types of subtrates at the disturbed site. T. rufiventris used bromeliads for nesting more often than expected by chance at the disturbed site. DPR did not differ between substrates at the undisturbed site and T. rufiventris used all substrates according to their availability. Nests had higher predation at the disturbed site when DPR on non-bromeliad substrates was compared between disturbed and undisturbed sites. Nest fate was independent of nest height. Our results suggest T. rufiventris' flexibility in nest-site choice, as reflected by increased use of the safest sites, i.e., bromeliads, in the disturbed site compared to the undisturbed site, may allow this species to survive in an otherwise much riskier habitat. Our results illustrate how microhabitat-scale effects can mediate landscape scale effects. ?? 2010 by the Wilson Ornithological Society.

  9. Nests with numerous SOX10 and MiTF-positive cells in lichenoid inflammation: pseudomelanocytic nests or authentic melanocytic proliferation?

    Science.gov (United States)

    Silva, Claudine Yap; Goldberg, Lynne J; Mahalingam, Meera; Bhawan, Jag; Wolpowitz, Deon

    2011-10-01

    Pseudomelanocytic nests in the setting of lichenoid inflammation can mimic atypical melanocytic proliferations. Both melanocytic and cytokeratin immunohistochemical stains may be utilized to differentiate these entities. Unlike true melanocytic nests, pseudomelanocytic nests contain Melanoma Antigen Recognized by T-cells 1 (MART-1)/ Melan-A-positive cells and cells positive for pan-cytokeratins, CD3 and/or CD68. Recently, rare (1-2 cells/nest) microphthalmia- associated transcription factor (MiTF)-positive cells were also reported in pseudomelanocytic nests. We present a 48-year-old man with a 2 × 3 cm violaceous to hyperpigmented, non-blanching, polygonal patch on the neck. Histopathology showed focal epidermal atrophy, irregularly distributed junctional nests and a lichenoid infiltrate with colloid bodies. Immunoperoxidase studies revealed occasional pan-cytokeratin and MART-1/Melan-A-positive staining in nests as well as focal S-100 protein-positive cells. Importantly, the majority of nests showed numerous cells positive for MiTF and SOX10 (>2 cells/nest and some the majority of cells). This combined staining pattern confounds the above-described immunohistochemical distinction between pseudo and true melanocytic nests. Clinically felt to represent unilateral lichen planus pigmentosus/erythema dyschromicum perstans and not malignant melanoma in situ, this lesion highlights the importance of clinicopathologic correlation and suggests either a new melanocytic entity or a novel pattern of benign melanocytic reorganization in a subset of lichenoid dermatitides.

  10. Essays on pricing dynamics, price dispersion, and nested logit modelling

    Science.gov (United States)

    Verlinda, Jeremy Alan

    The body of this dissertation comprises three standalone essays, presented in three respective chapters. Chapter One explores the possibility that local market power contributes to the asymmetric relationship observed between wholesale costs and retail prices in gasoline markets. I exploit an original data set of weekly gas station prices in Southern California from September 2002 to May 2003, and take advantage of highly detailed station and local market-level characteristics to determine the extent to which spatial differentiation influences price-response asymmetry. I find that brand identity, proximity to rival stations, bundling and advertising, operation type, and local market features and demographics each influence a station's predicted asymmetric relationship between prices and wholesale costs. Chapter Two extends the existing literature on the effect of market structure on price dispersion in airline fares by modeling the effect at the disaggregate ticket level. Whereas past studies rely on aggregate measures of price dispersion such as the Gini coefficient or the standard deviation of fares, this paper estimates the entire empirical distribution of airline fares and documents how the shape of the distribution is determined by market structure. Specifically, I find that monopoly markets favor a wider distribution of fares with more mass in the tails while duopoly and competitive markets exhibit a tighter fare distribution. These findings indicate that the dispersion of airline fares may result from the efforts of airlines to practice second-degree price discrimination. Chapter Three adopts a Bayesian approach to the problem of tree structure specification in nested logit modelling, which requires a heavy computational burden in calculating marginal likelihoods. I compare two different techniques for estimating marginal likelihoods: (1) the Laplace approximation, and (2) reversible jump MCMC. I apply the techniques to both a simulated and a travel mode

  11. Characteristic Formulae for Relations with Nested Fixed Points

    Directory of Open Access Journals (Sweden)

    Luca Aceto

    2012-02-01

    Full Text Available A general framework for the connection between characteristic formulae and behavioral semantics is described in [2]. This approach does not suitably cover semantics defined by nested fixed points, such as the n-nested simulation semantics for n greater than 2. In this study we address this deficiency and give a description of nested fixed points that extends the approach for single fixed points in an intuitive and comprehensive way.

  12. Sandhill crane abundance and nesting ecology at Grays Lake, Idaho

    Science.gov (United States)

    Austin, J.E.; Henry, A.R.; Ball, I.J.

    2007-01-01

    We examined population size and factors influencing nest survival of greater sandhill cranes (Grus canadensis tabida) at Grays Lake National Wildlife Refuge, Idaho, USA, during 1997-2000. Average local population of cranes from late April to early May, 1998-2000, was 735 cranes, 34% higher than that reported for May 1970-1971. We estimated 228 (SE = 30) nests in the basin core (excluding renests), 14% higher than a 1971 estimate. Apparent nest success in our study (x?? = 60%, n = 519 nests) was lower than reported for Grays Lake 30-50 years earlier. Daily survival rates (DSRs) of all nests averaged 0.9707 (41.2%). The best model explaining nest survival included year and water depth and their interaction. Nest survival was highest (DSR = 0.9827) in 1998 compared with other years (0.9698-0.9707). Nest survival changed little relative to water depth in 1998, when flooding was extensive and alternative prey (microtines) irrupted, but declined markedly with lower water levels in 2000, the driest year studied. Hypotheses relating nest survival to vegetation height, land use (idle, summer grazing, fall grazing), and date were not supported. In a before-after-control-impact design using 12 experimental fields, nest survival differed among years but not among management treatments (idle, fall graze, fall burn, and summer-graze-idle rotation), nor was there an interaction between year and treatments. However, DSRs in fall-burn fields declined from 0.9781 in 1997-1998 to 0.9503 in 1999-2000 (posttreatment). Changes in the predator community have likely contributed to declines in nest success since the 1950s and 1970s. Our results did not support earlier concerns about effects of habitat management practices on crane productivity. Nest survival could best be enhanced by managing spring water levels. Managers should continue censuses during late April to evaluate long-term relationships to habitat conditions and management.

  13. Nesting ecology of waterbirds at Grays Lake, Idaho

    Science.gov (United States)

    Austin, J.E.; Pyle, W.H.

    2004-01-01

    Montane wetlands provide valuable habitat for nesting waterfowl and other waterbirds in the western United States, but relatively little information is available about the nesting ecology of their waterbird communities. We describe the general nesting ecology of breeding waterbirds at a large, shallow montane wetland in southeast Idaho during 1997-2000. Habitats included upland grasslands and intermittently to semipermanently flooded wetland habitats. We located a total of 1207 nests of 23 bird species: eared grebe (Podiceps nigricollis), Canada goose (Branta canadensis), mallard (Anas platyrhynchos), gadwall (A. strepera), American wigeon (A. americana), green-winged teal (A. crecca), blue-winged teal (A. discors), cinnamon teal (A. cyanoptera), northern shoveler (A. clypeata), northern pintail (A. acuta), redhead (Aythya americana), canvasback (A. valisineria), lesser scaup (A. affinis), ruddy duck (Oxyuris jamaicensis), northern harrier (Circus cyaneus), American coot (Fulica americana), Virginia rail (Rallus limicola), greater sandhill crane (Grus canadensis tabida), American avocet (Recurvirostra americana), long-billed curlew (Numenius americanus), Wilsons snipe (Gallinago delicta), Wilsons phalarope (Phalaropus tricolor), and short-eared owl (Asio flammeus). Most nests were initiated in May-early June and were terminated (hatched or destroyed) by the third week of June. Mean daily survival rate (DSR) for Canada goose nests was 0.954 0.005 (SE) (n = 127 nests), equivalent to Mayfield nest success of 21%. Mean DSR for dabbling duck nests over all four years was 0.938 0.006 (n = 141), equivalent to Mayfield nest success of 11%. For all other species where we found >10 nests each year (eared grebe, redhead, canvasback, coot, sandhill crane, American avocet, and Wilsons snipe), >50% of nests found hatched at least one young. Success rates for geese, cranes, and ducks were lower than reported for Grays Lake during 1949-1951 and lower than most other wetlands in

  14. Generalized Derivations and Bilocal Jordan Derivations of Nest Algebras

    Directory of Open Access Journals (Sweden)

    Dangui Yan

    2011-01-01

    Full Text Available Let H be a complex Hilbert space and B(H the collection of all linear bounded operators, A is the closed subspace lattice including 0 an H, then A is a nest, accordingly alg A={T∈B(H:TN⊆N,  ∀N∈A} is a nest algebra. It will be shown that of nest algebra, generalized derivations are generalized inner derivations, and bilocal Jordan derivations are inner derivations.

  15. Duck nesting in intensively farmed areas of North Dakota

    Science.gov (United States)

    Higgins, K.F.

    1977-01-01

    A study to determine the major factors limiting duck nesting and production on intensively farmed areas in eastern North Dakota was conducted from 1969 through 1974. A total of 186 duck nests was found during searches on 6,018 ha of upland. Nest density per km2 for 5 major habitat types was 20.2 in untilled upland, 3.7 in standing grain stubble, 1.6 in mulched grain stubble, 1.2 in summer fallow, and 1.1 in growing grain. Pintails (Anas acuta) nested in cultivated cropland types in greater prevalence than other duck species. Nest densities were 12 times greater on untilled upland (20.2/km2) than on annually tilled cropland (1.7/km2), and hatched-clutch densities were 16 times greater on untilled upland (4.8/km2) than on annually tilled cropland (0.3/km2). Hatching success was greater on untilled upland (25%) than on tilled cropland (17%). Of 186 nests found, 77 percent did not hatch; 76 percent of the failures were attributed to predators and 19 percent to farming operations. Poor quality nesting cover, the result of intensive land use practices, and nesting failures caused by machinery and predators mainly mammals, were the principal factors limiting duck nesting and production on intensively farmed areas.

  16. Nest success of grassland sparrows on reclaimed surface mines

    Science.gov (United States)

    Stauffer, G.E.; Diefenbach, D.R.; Marshall, M.R.; Brauning, D.W.

    2011-01-01

    Grasslands resulting from surface mine reclamation support grassland songbird populations in several midwestern and eastern states in the United States, especially where reclaimed mines are large (>1,000ha). However, most reclaimed surface mines in Pennsylvania are small (success is unknown. We evaluated nest success of grasshopper (Ammodramus savannarum), Henslow's (A. henslowii), and Savannah sparrows (Passerculus sandwichensis) on 4 reclaimed surface mines (50-180ha) in western Pennsylvania, USA from 2006 to 2007. Overall nest success based on mean covariate values was 0.435 (95% CI = 0.376-0.504) for grasshopper sparrows, 0.396 (95% CI = 0.295-0.533) for Henslow's sparrows, and 0.158 (95% CI = 0.063-0.392) for Savannah sparrows. These estimates of nest success are comparable to those on larger reclaimed mines and other habitats. Grasshopper and Henslow's sparrow nests that were well concealed were less likely to fail than highly visible nests (??visible = -0.028, CI = -0.051 to -0.005 for grasshopper sparrows; ??visible = -0.063, CI = -0.112 to -0.014 for Henslow's sparrows), and nests in areas with surrounding deep litter were more likely to fail than nests in areas with shallow litter (??litterD = -0.145, CI = -0.335 to 0.045 for grasshopper sparrows; ??litterD = -0.676, CI = -1.187 to -0.116 for Henslow's sparrows). Savannah sparrow nests in areas with high visual obstruction by vegetation were less likely to fail than nests in areas with sparse and short vegetation (??VisOb = 0.048, CI = 0.006-0.091). Daily probability of survival for grasshopper sparrow nests was greatest early and late in the breeding season, and Savannah sparrow nest survival followed a decreasing linear trend. Nest survival of Henslow's sparrows was greater on warm days (??temp = 0.197, CI = 0.014-0.379), whereas for Savannah sparrows nest survival decreased on warm days and on days with rain, but for Savannah sparrows confidence intervals of weather effects included zero (??temp = -0

  17. Edible bird's nest: food or medicine?

    Science.gov (United States)

    Wong, Rebecca S Y

    2013-09-01

    Edible bird's nest (EBN) is derived from the saliva of certain types of swiftlets. It is consumed in many parts of the world for its nutritional and medicinal values. Although many claims have been made on the therapeutic and health-promoting effects of EBN, scientific documentations regarding these effects are very limited in published literature. It is not until recently that the biological effects of EBN are being investigated and evidence-based studies are being conducted. Several studies have found that EBN may enhance cell proliferation and differentiation and various beneficial effects have been reported in vitro as well as in vivo. While these studies point towards the potential use of EBN in the treatment or even prevention of several diseases, the mechanisms of action of EBN remain largely unknown and more explorations are needed. This review is one of the very few scientific reviews on EBN which focuses on recent evidence-based discoveries.

  18. Development of the nested fiber filter

    Science.gov (United States)

    Litt, R. D.; Conkle, H. N.; Raghavan, J. K.

    Battelle has tested the Nested Fiber Filter (NFF) as a particulate control device for high temperature, high-pressure (HTHP) applications. Battelle funded initial bench-scale tests which were the basis for patents and a concept applying the NFF. Subsequent parametric tests in a 6-inch diameter reactor established excellent particulate capture performance, greater than 99 percent, for conditions up to 1600 F and 6 atmospheres. Effective cleaning/regeneration of the NFF was achieved in the 6-inch scale with acoustic and mechanical vibration. A pulse combustor was tested in an integrated NFF arrangement because of compatibility with the HTBP conditions. This arrangement provided the basis for larger scale tests under the subject contract. A 6-sq ft test module was designed and installed with an existing fluidized bed combustor for additional development and testing.

  19. Gene-expression analysis of single cells-nested polymerase chain reaction afte laser microdissection

    Institute of Scientific and Technical Information of China (English)

    Xin Shi; Jorg Kleeff; Zhao-Wen Zhu; Bruno Schmied; Wen-Hao Tang; Arthur Zimmermann; Markus W. Bucher; Helmut Friess

    2003-01-01

    AIM: The structural and functional characteristics of cells are dependent on the specific gene expression profile. The ability to study and compare gene expression at the cellular level will therefore provide valuable insights into cell physiology and pathophysiology. METHODS: Individual cells were isolated from frozen colon tissue sections using laser microdissection. DNA as well as RNA were extracted, and total RNA was reversely transcribed to complementary DNA (cDNA). Both DNA and cDNA were analyzed by nested polymerase chain reaction (PCR). The quality of isolated DNA and RNA was satisfactory. RESULTS: Single cells were successfully microdissected using an ultraviolet laser micromanipulator. Nested PCR amplification products of DNA and cDNA of single cells could clearly be visualized by agarose gel electrophoresis. CONCLUSION: The combined use of laser microdissection and nested-PCR provides an opportunity to analyze geneexpression in single cells. This method allows the analysisand identification of specific genes which are involved inphysiological and pathophysiological processes in a complexof variable cell phenotypes.

  20. Daily survival rate for nests and chicks of Least Terns (Sternula antillarum) at natural nest sites in South Carolina

    Science.gov (United States)

    Brooks, Gillian L.; Sanders, Felicia J.; Gerard, Patrick D.; Jodice, Patrick G.

    2013-01-01

    Although a species of conservation concern, little is known about the reproductive success of Least Terns (Sternula antillarum) throughout the southeastern USA where availability of natural beaches for nesting is limited. Daily survival rate (DSR) of nests and chicks was examined at four natural nesting sites in Cape Romain National Wildlife Refuge, South Carolina, 2009–2010. Measures of nest success (n = 257 nests) ranged from 0–93% among colony sites. The DSR of nests was primarily related to colony site, but year and estimates of predation risk also were related to DSR. Predation was the principal cause of identifiable nest loss, accounting for 47% of nest failures when the two years of data were pooled. The probability (± SE) of a chick surviving from hatching to fledging = 0.449 ± 0.01 (n = 92 chicks). DSR of chicks was negatively related to tide height and rainfall. Therefore, productivity of Least Terns is being lost during both the nesting and chick stage through a combination of biotic and abiotic factors that may prove difficult to fully mitigate or manage. Although natural nesting sites within Cape Romain National Wildlife Refuge intermittently produce successful nests, the consistency of productivity over the long term is still unknown. Given that the long term availability of anthropogenic nest sites (e.g., rooftops, dredge-spoil islands) for Least Terns is questionable, further research is required both locally and throughout the region to assess the extent to which natural sites act as population sources or sinks.

  1. The effect of nesting material on the nest-building and maternal behavior of domestic sows and piglet production.

    Science.gov (United States)

    Chaloupková, H; Illmann, G; Neuhauserová, K; Simecková, M; Kratinová, P

    2011-02-01

    Nest building is an important part of maternal behavior in domestic pigs. The aim of the study was to assess the effect of nesting material sawdust vs. straw on sow behavior 24 h before and after birth of the first piglet (BFP) and piglet production. Sows, housed in farrowing crates, were randomly divided into 2 treatments: sawdust (n = 12) and straw (n = 13). Sawdust and straw were provided during the pre- and parturient period; after parturition, straw was given to both experimental groups. The prepartum nesting period (the time interval between the first and last nest-building records, including all other activity and resting before BFP), the nesting records (number of nesting records), nesting duration (duration of all nesting records), the start and termination of nesting, and the frequency of prepartum postural changes were collected 24 h before BFP. After BFP, number of nesting records and time to first sucking of the litter were collected. Frequency of postural changes and duration of udder access were collected 24 h after BFP during 3 time periods (during parturition, from the end of parturition to 12 h after BFP, and 12 to 24 h after BFP) and the frequency of nursing during 2 time periods (from the end of parturition to 12 h after BFP, and 12 to 24 h after BFP). Piglet BW gain and mortality were estimated 24 h after BFP. Data were analyzed using PROC MIXED and the probability of the piglet mortality using PROC GENMOD in SAS. Nesting material did not affect (P > 0.10) most of sow prepartum nesting behavior and had no effect (P > 0.10) on the prepartum frequency of postural changes. Sows from the sawdust treatment had a longer nesting period (P 0.10) of the nesting material on piglet BW gain and mortality was found. The results suggest that sawdust compared with straw as nesting material provided to sows before and through parturition does not negatively affect maternal behavior during the 24 h before and after parturition or piglet production. Therefore

  2. Hatchling sex ratio, body weight and nest parameters for Chelonia mydas nesting on Sugözü beaches (Turkey

    Directory of Open Access Journals (Sweden)

    Kılıç, Ç.

    2014-12-01

    Full Text Available We investigated the relationship between nest parameters, hatchling body mass, and sex ratio of green turtle, Chelonia mydas, embryos and hatchlings at the temperate nesting rookery of Sugözü Beach (Adana–Turkey. Mean nest temperature and distance from the sea were correlated, while mean nest temperature and incubation period were inversely related. There was no apparent relationship between incubation period and hatchling mass. Hatchling and embryo sex ratios, determined by histological examination, showed a 70.5% and 93.5% female bias, respectively. There was no correlation between sex and body weight of hatchlings,

  3. A hierarchical nest survival model integrating incomplete temporally varying covariates

    Science.gov (United States)

    Converse, Sarah J.; Royle, J. Andrew; Adler, Peter H.; Urbanek, Richard P.; Barzan, Jeb A.

    2013-01-01

    Nest success is a critical determinant of the dynamics of avian populations, and nest survival modeling has played a key role in advancing avian ecology and management. Beginning with the development of daily nest survival models, and proceeding through subsequent extensions, the capacity for modeling the effects of hypothesized factors on nest survival has expanded greatly. We extend nest survival models further by introducing an approach to deal with incompletely observed, temporally varying covariates using a hierarchical model. Hierarchical modeling offers a way to separate process and observational components of demographic models to obtain estimates of the parameters of primary interest, and to evaluate structural effects of ecological and management interest. We built a hierarchical model for daily nest survival to analyze nest data from reintroduced whooping cranes (Grus americana) in the Eastern Migratory Population. This reintroduction effort has been beset by poor reproduction, apparently due primarily to nest abandonment by breeding birds. We used the model to assess support for the hypothesis that nest abandonment is caused by harassment from biting insects. We obtained indices of blood-feeding insect populations based on the spatially interpolated counts of insects captured in carbon dioxide traps. However, insect trapping was not conducted daily, and so we had incomplete information on a temporally variable covariate of interest. We therefore supplemented our nest survival model with a parallel model for estimating the values of the missing insect covariates. We used Bayesian model selection to identify the best predictors of daily nest survival. Our results suggest that the black fly Simulium annulus may be negatively affecting nest survival of reintroduced whooping cranes, with decreasing nest survival as abundance of S. annulus increases. The modeling framework we have developed will be applied in the future to a larger data set to evaluate the

  4. Local individual preferences for nest materials in a passerine bird.

    Directory of Open Access Journals (Sweden)

    Adèle Mennerat

    Full Text Available BACKGROUND: Variation in the behavioural repertoire of animals is acquired by learning in a range of animal species. In nest-building birds, the assemblage of nest materials in an appropriate structure is often typical of a bird genus or species. Yet plasticity in the selection of nest materials may be beneficial because the nature and abundance of nest materials vary across habitats. Such plasticity can be learned, either individually or socially. In Corsican populations of blue tits Cyanistes caeruleus, females regularly add in their nests fragments of several species of aromatic plants during the whole breeding period. The selected plants represent a small fraction of the species present in the environment and have positive effects on nestlings. METHODOLOGY/PRINCIPAL FINDINGS: We investigated spatiotemporal variations of this behaviour to test whether the aromatic plant species composition in nests depends on 1 plant availability in territories, 2 female experience or 3 female identity. Our results indicate that territory plays a very marginal role in the aromatic plant species composition of nests. Female experience is not related to a change in nest plant composition. Actually, this composition clearly depends on female identity, i.e. results from individual preferences which, furthermore, are repeatable both within and across years. A puzzling fact is the strong difference in plant species composition of nests across distinct study plots. CONCLUSIONS/SIGNIFICANCE: This study demonstrates that plant species composition of nests results from individual preferences that are homogeneous within study plots. We propose several hypotheses to interpret this pattern of spatial variation before discussing them in the light of preliminary results. As a conclusion, we cannot exclude the possibility of social transmission of individual preferences for aromatic plants. This is an exciting perspective for further work in birds, where nest construction

  5. Nest survival of forest birds in the Mississippi Alluvial Valley

    Science.gov (United States)

    Twedt, D.J.; Wilson, R.R.; Henne-Kerr, J.L.; Hamilton, R.B.

    2001-01-01

    In the Mississippi Alluvial Valley, flood control has led to a drastic reduction in the area of forest habitat and altered the patchwork of forest cover types. Silvicultural management of the remaining fragmented forests has changed to reflect the altered hydrology of the forests, current economic conditions of the area, and demand for forest products. Because forest type and silvicultural management impact forest birds, differences in avian productivity within these forests directly impact bird conservation. To assist in conservation planning, we evaluated daily nest survival, nest predation rates, and brood parasitism rates of forest birds in relation to different forest cover types and silvicultural management strategies within this floodplain. Within bottomland hardwood forests, nest success of blue-gray gnatcatcher (Polioptila caerulea, 13%), eastern towhee (Pipilo erythrophthalmus, 28%), indigo bunting (Passerina cyanea, 18%), northern cardinal (Cardinalis cardinalis, 22%), and yellow-billed cuckoo (Coccyzus americanus, 18%) did not differ from that within intensively managed cottonwood plantations. However, average daily survival of 542 open-cup nests of 19 bird species in bottomland hardwoods (0.9516 + 0.0028, -27% nest success) was greater than that of 543 nests of 18 species in cotlonwood plantations (0.9298 + 0.0035, -15% nest success). Differences in daily nest survival rates likely resulted from a combination of differences in the predator community--particularly fire ants (Solenopsis invicta)--and a marked difference in species composition of birds breeding within these 2 forest types. At least 39% of nests in bottomland hardwood forests and 65% of nests in cottonwood plantations were depredated. Rates of parasitism by brown-headed cowbirds (Molothrus ater) were greater in managed cottonwoods (24%) than in bottomland hardwoods (9%). Nest success in planted cottonwood plantations for 18 species combined (-14%), and for yellow-breasted chat (Icteria

  6. Factors affecting Culicoides species composition and abundance in avian nests.

    Science.gov (United States)

    Martínez-de la Puente, J; Merino, S; Tomás, G; Moreno, J; Morales, J; Lobato, E; Talavera, S; Sarto I Monteys, V

    2009-08-01

    Mechanisms affecting patterns of vector distribution among host individuals may influence the population and evolutionary dynamics of vectors, hosts and the parasites transmitted. We studied the role of different factors affecting the species composition and abundance of Culicoides found in nests of the blue tit (Cyanistes caeruleus). We identified 1531 females and 2 males of 7 different Culicoides species in nests, with C. simulator being the most abundant species, followed by C. kibunensis, C. festivipennis, C. segnis, C. truncorum, C. pictipennis and C. circumscriptus. We conducted a medicationxfumigation experiment randomly assigning bird's nests to different treatments, thereby generating groups of medicated and control pairs breeding in fumigated and control nests. Medicated pairs were injected with the anti-malarial drug Primaquine diluted in saline solution while control pairs were injected with saline solution. The fumigation treatment was carried out using insecticide solution or water for fumigated and control nests respectively. Brood size was the main factor associated with the abundance of biting midges probably because more nestlings may produce higher quantities of vector attractants. In addition, birds medicated against haemoparasites breeding in non-fumigated nests supported a higher abundance of C. festivipennis than the rest of the groups. Also, we found that the fumigation treatment reduced the abundance of engorged Culicoides in both medicated and control nests, thus indicating a reduction of feeding success produced by the insecticide. These results represent the first evidence for the role of different factors in affecting the Culicoides infracommunity in wild avian nests.

  7. Common loon nest defense against an American mink

    Science.gov (United States)

    McCarthy, Kyle P.; Destefano, Stephen

    2011-01-01

    We describe a successful nest defense strategy of an adult Gavia immer (Common Loon) during an attempted predation event by a Nevison vison (American Mink) at Umbagog National Wildlife Refuge, NH. It is suspected that mink occasionally depredate loon nests, but defense strategies have not been described previously.

  8. Preferences for nest boxes as environmental enrichment for laboratory mice

    NARCIS (Netherlands)

    Van de Weerd, HA; Van Loo, PLP; Van Zutphen, LFM; Koolhaas, JM; Baumans, [No Value

    1998-01-01

    In nature, mice live in burrows with nest chambers where they breed and may hide from predators. In the laboratory, a shelter or refuge is an easily applicable form of enrichment which may enhance the welfare of laboratory mice by giving them more control over their environment. Six nest boxes made

  9. Animating Nested Taylor Polynomials to Approximate a Function

    Science.gov (United States)

    Mazzone, Eric F.; Piper, Bruce R.

    2010-01-01

    The way that Taylor polynomials approximate functions can be demonstrated by moving the center point while keeping the degree fixed. These animations are particularly nice when the Taylor polynomials do not intersect and form a nested family. We prove a result that shows when this nesting occurs. The animations can be shown in class or…

  10. Brunn nests masquerading as bladder tumor: a case report

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jin Hee; Byun, Kyung Hwan; Jeon, Ji Min [College of Medicine, Pochon CHA University, Pochon (Korea, Republic of)

    2005-07-15

    Brunn nests are the most common proliferative lesions of the bladder uroepithelium, but exuberant proliferation can mimic bladder tumor on radiologic imaging and cystoscopy. We describe a case of pathologically proven Brunn nests in a 34-year-old man, misdiagnosed as bladder tumor on preoperative imaging studies.

  11. Nest ectoparasites increase physiological stress in breeding birds: an experiment

    Science.gov (United States)

    Martínez-de La Puente, Josué; Merino, Santiago; Tomás, Gustavo; Moreno, Juan; Morales, Judith; Lobato, Elisa; Martínez, Javier

    2011-02-01

    Parasites are undoubtedly a biotic factor that produces stress. Heat shock proteins (HSPs) are important molecules buffering cellular damage under adverse conditions. During the breeding season, blue tit Cyanistes caeruleus (L.) adults are affected by blood parasites, nest-dwelling parasites and biting flies, potentially affecting their HSP-mediated responses. Here, we treated females with primaquine to reduce blood parasites and fumigated nests with permethrin to reduce nest-dwelling parasites to test whether these treatments affect HSP60 level during the breeding season. Medicated females, but not controls, had a significant reduction of the intensity of infection by Haemoproteus spp. blood parasites. However, final intensity of infection did not differ significantly between groups, and we did not find an effect of medication on change in HSP60 level. Fumigation reduced the abundance of nest-dwelling parasites (mites, fleas and blowfly larvae) and engorged biting midges in nests. Females breeding in non-fumigated nests increased HSP60 levels during the season more than those breeding in fumigated nests. Furthermore, the change in HSP60 level was positively correlated with the abundance of biting midges. These results show how infections by nest ectoparasites during the breeding period can increase the level of HSPs and suggest that biting midges impose physiological costs on breeding female blue tits. Although plausible, the alternative that biting midges prefer to feed on more stressed birds is poorly supported by previous studies.

  12. A new method for wireless video monitoring of bird nests

    Science.gov (United States)

    David I. King; Richard M. DeGraaf; Paul J. Champlin; Tracey B. Champlin

    2001-01-01

    Video monitoring of active bird nests is gaining popularity among researchers because it eliminates many of the biases associated with reliance on incidental observations of predation events or use of artificial nests, but the expense of video systems may be prohibitive. Also, the range and efficiency of current video monitoring systems may be limited by the need to...

  13. Influence of nest box environment on kit survival

    DEFF Research Database (Denmark)

    Lund, V.H.; Malmkvist, Jens

    2012-01-01

    . In conclusion, access to different nesting materials reduced the risk of dying in farm mink in relation with factors as e.g. nest quality and maternal behaviour. A decrease in kit mortality from 20% to 5% would give the Danish mink production a profound number of Danish kroner extra per year....

  14. Long-eared owls nesting in Badlands National Park

    Science.gov (United States)

    Deborah D. Paulson; Carolyn Hull Sieg

    1985-01-01

    Long-eared Owls nest at high densities locally over the Great Plains where suitable habitat is limited (Bent 1938), yet , according to Whitney et al. (1978), this species is rare to uncommon in South Dakota. Especially west of the Missouri River, few nesting records have been reported. This paper reports the occurrence of Long-eared Owls in the Badlands National Park...

  15. Nesting habitat and productivity of Swainson's Hawks in southeastern Arizona

    Science.gov (United States)

    Nishida, Catherine; Boal, Clint W.; DeStefano, Stephen; Hobbs, Royden J.

    2013-01-01

    We studied Swainson's Hawks (Buteo swainsoni) in southeastern Arizona to assess the status of the local breeding population. Nest success (≥1 young fledged) was 44.4% in 1999 with an average of 1.43 ± 0.09 (SE) young produced per successful pair. Productivity was similar in 2000, with 58.2% nesting success and 1.83 ± 0.09 fledglings per successful pair. Mesquite (Prosopis velutina) and cottonwood (Populus fremontii) accounted for >50% of 167 nest trees. Nest trees were taller than surrounding trees and random trees, and overall there was more vegetative cover at nest sites than random sites. This apparent requirement for cover around nest sites could be important for management of the species in Arizona. However, any need for cover at nest sites must be balanced with the need for open areas for foraging. Density of nesting Swainson's Hawks was higher in agriculture than in grasslands and desert scrub. Breeding pairs had similar success in agricultural and nonagricultural areas, but the effect of rapid and widespread land-use change on breeding distribution and productivity continues to be a concern throughout the range of the species.

  16. LOGGERHEAD SEA TURTLE LATE NESTING ECOLOGY IN VIRGINIA BEACH, VIRGINIA

    Science.gov (United States)

    T'he.loggerhead sea turtle (Caretta came is the only recurrent nesting species of sea turtle in southeastern Virginia (Lutcavage & Musick, 1985; Dodd, 1988). Inasmuch as the loggerhead is a federally threatened species, the opportunity to gather data on its nesting ecology is imp...

  17. Reversible cortical blindness: posterior reversible encephalopathy syndrome.

    Science.gov (United States)

    Bandyopadhyay, Sabyasachi; Mondal, Kanchan Kumar; Das, Somnath; Gupta, Anindya; Biswas, Jaya; Bhattacharyya, Subir Kumar; Biswas, Gautam

    2010-11-01

    Cortical blindness is defined as visual failure with preserved pupillary reflexes in structurally intact eyes due to bilateral lesions affecting occipital cortex. Bilateral oedema and infarction of the posterior and middle cerebral arterial territory, trauma, glioma and meningioma of the occipital cortex are the main causes of cortical blindness. Posterior reversible encephalopathy syndrome (PRES) refers to the reversible subtype of cortical blindness and is usually associated with hypertension, diabetes, immunosuppression, puerperium with or without eclampsia. Here, 3 cases of PRES with complete or partial visual recovery following treatment in 6-month follow-up are reported.

  18. Introduction to reversible computing

    CERN Document Server

    Perumalla, Kalyan S

    2013-01-01

    Few books comprehensively cover the software and programming aspects of reversible computing. Filling this gap, Introduction to Reversible Computing offers an expanded view of the field that includes the traditional energy-motivated hardware viewpoint as well as the emerging application-motivated software approach. Collecting scattered knowledge into one coherent account, the book provides a compendium of both classical and recently developed results on reversible computing. It explores up-and-coming theories, techniques, and tools for the application of rever

  19. Nesting behavior of Trypoxylon (Trypargilum agamemnom Richards (Hymenoptera: Crabronidae

    Directory of Open Access Journals (Sweden)

    MLT Buschini

    Full Text Available Nesting behaviour is extremely diversified among solitary nesting sphecids. Thus, the aim of this study was to describe the nesting behaviour of Trypoxylon agamemnon and discuss the advantages of guarding behaviour of males. It was conducted in the Parque Municipal das Araucárias, Guarapuava (PR, Brazil from October/2003 to July/2007. To describe the behaviour of T. agamemnon and construct its ethogram, daily observations were made, totalling 410:19 hours observation. Although the males of T. agamemnon stand guard close to the entrance of the nests, we concluded that this behaviour is not ensuring the protection of nests against parasitoids and that, probably, this behaviour ensures them the paternity, but further studies with microsatellite markers will be necessary to confirm this hypothesis.

  20. Nesting behavior of Trypoxylon (Trypargilum) agamemnom Richards (Hymenoptera: Crabronidae).

    Science.gov (United States)

    Buschini, M L T; Donatti, A J

    2012-05-01

    Nesting behaviour is extremely diversified among solitary nesting sphecids. Thus, the aim of this study was to describe the nesting behaviour of Trypoxylon agamemnon and discuss the advantages of guarding behaviour of males. It was conducted in the Parque Municipal das Araucárias, Guarapuava (PR), Brazil from October/2003 to July/2007. To describe the behaviour of T. agamemnon and construct its ethogram, daily observations were made, totalling 410:19 hours observation. Although the males of T. agamemnon stand guard close to the entrance of the nests, we concluded that this behaviour is not ensuring the protection of nests against parasitoids and that, probably, this behaviour ensures them the paternity, but further studies with microsatellite markers will be necessary to confirm this hypothesis.

  1. Nest predation research: Recent findings and future perspectives

    Science.gov (United States)

    Chalfoun, Anna D.; Ibanez-Alamo, J. D.; Magrath, R. D.; Schmidt, Kenneth A.; Thomson, R. L.; Oteyza, Juan C.; Haff, T. M.; Martin, T.E.

    2016-01-01

    Nest predation is a key source of selection for birds that has attracted increasing attention from ornithologists. The inclusion of new concepts applicable to nest predation that stem from social information, eavesdropping or physiology has expanded our knowledge considerably. Recent methodological advancements now allow focus on all three players within nest predation interactions: adults, offspring and predators. Indeed, the study of nest predation now forms a vital part of avian research in several fields, including animal behaviour, population ecology, evolution and conservation biology. However, within nest predation research there are important aspects that require further development, such as the comparison between ecological and evolutionary antipredator responses, and the role of anthropogenic change. We hope this review of recent findings and the presentation of new research avenues will encourage researchers to study this important and interesting selective pressure, and ultimately will help us to better understand the biology of birds.

  2. Reversible Logic Circuit Synthesis

    CERN Document Server

    Shende, V V; Markov, I L; Prasad, A K; Hayes, John P.; Markov, Igor L.; Prasad, Aditya K.; Shende, Vivek V.

    2002-01-01

    Reversible, or information-lossless, circuits have applications in digital signal processing, communication, computer graphics and cryptography. They are also a fundamental requirement for quantum computation. We investigate the synthesis of reversible circuits that employ a minimum number of gates and contain no redundant input-output line-pairs (temporary storage channels). We propose new constructions for reversible circuits composed of NOT, Controlled-NOT, and TOFFOLI gates (the CNT gate library) based on permutation theory. A new algorithm is given to synthesize optimal reversible circuits using an arbitrary gate library. We also describe much faster heuristic algorithms. We also pursue applications of the proposed techniques to the synthesis of quantum circuits.

  3. Reverse Core Engine with Thrust Reverser

    Science.gov (United States)

    Suciu, Gabriel L. (Inventor); Chandler, Jesse M. (Inventor)

    2017-01-01

    An engine system has a gas generator, a bi-fi wall surrounding at least a portion of the gas generator, a casing surrounding a fan, and the casing having first and second thrust reverser doors which in a deployed position abut each other and the bi-fi wall.

  4. Directed random polymers via nested contour integrals

    Science.gov (United States)

    Borodin, Alexei; Bufetov, Alexey; Corwin, Ivan

    2016-05-01

    We study the partition function of two versions of the continuum directed polymer in 1 + 1 dimension. In the full-space version, the polymer starts at the origin and is free to move transversally in R, and in the half-space version, the polymer starts at the origin but is reflected at the origin and stays in R-. The partition functions solve the stochastic heat equation in full-space or half-space with mixed boundary condition at the origin; or equivalently the free energy satisfies the Kardar-Parisi-Zhang equation. We derive exact formulas for the Laplace transforms of the partition functions. In the full-space this is expressed as a Fredholm determinant while in the half-space this is expressed as a Fredholm Pfaffian. Taking long-time asymptotics we show that the limiting free energy fluctuations scale with exponent 1 / 3 and are given by the GUE and GSE Tracy-Widom distributions. These formulas come from summing divergent moment generating functions, hence are not mathematically justified. The primary purpose of this work is to present a mathematical perspective on the polymer replica method which is used to derive these results. In contrast to other replica method work, we do not appeal directly to the Bethe ansatz for the Lieb-Liniger model but rather utilize nested contour integral formulas for moments as well as their residue expansions.

  5. Fermi Surface Nesting in UGe_2

    Science.gov (United States)

    Wang, F.; Allen, J. W.; Denlinger, J. D.; Rossnagel, Kai; Huxley, A. D.; Flouquet, J.

    2004-03-01

    UGe2 is of high current interest in connection with the possible role of ferromagnetic fluctuations in its pressure induced superconductivity, for which the Fermi surface (FS) is thought to be important. The band structure and FS contours of a single crystal have been measured using resonant angle-resolved photoemission near the U 5d to 5f edge. The measured dominant large sheet Fermi surface contour shows good agreement with magneto-oscillatory orbit frequencies, but with a much simpler diamond-like shape as compared to LDA and LDA+U band calculations. The measured FS topology is suggestive of a possible diagonal nesting condition different than previously proposed for SCDW models of the ferromagnetic transition(s) in UGe2 and allows assessment of FS topology-driven models of the ferromagnetic superconductor phase diagram.(e.g. K.G. Sandeman et al.), Phys. Rev. Lett. 90, 167005 (2003). Supported by the U.S. NSF at U. Mich. (DMR-03-02825) and by the DOE at the Advanced Light Source (DE-AC03-76SF00098).

  6. Nest Success and Cause-Specific Nest Failure of Grassland Passerines Breeding in Prairie Grazed by Livestock

    Science.gov (United States)

    This manuscript describes two years of field research on ground-nesting songbird species at Zumwalt Prairie Reserve, northeastern Oregon, USA. Cattle-grazing has long been suspected in declines of ground-nesting songbirds in grazed grassland, primarily due to increased trampling...

  7. Effects of timber size-class on predation of artificial nests in extensive forest

    Science.gov (United States)

    Richard M. DeGraaf; Per. Angelstam

    1993-01-01

    Depredation on artificial ground and cup nests in even-aged seedling/sapling, pole, and mature stands of continuous northern hardwood forest was studied in the White Mountain National Forest in New Hampshire, USA from May to June 1988. Track-board nests were used to identify predators of ground nests; plain ground nests and cup nests were used to investigate the...

  8. Contrasting Effects of Cattle Grazing Intensity on Upland-Nesting Duck Production at Nest and Field Scales in the Aspen Parkland, Canada

    Directory of Open Access Journals (Sweden)

    Jeffrey M. Warren

    2008-12-01

    Full Text Available The Aspen Parkland of Canada is one of the most important breeding areas for temperate nesting ducks in North America. The region is dominated by agricultural land use, with approximately 9.3 million ha in pasture land for cattle grazing. However, the effects of using land for cattle grazing on upland-nesting duck production are poorly understood. The current study was undertaken during 2001 and 2002 to investigate how nest density and nesting success of upland-nesting ducks varied with respect to the intensity of cattle grazing in the Aspen Parkland. We predicted that the removal and trampling of vegetation through cattle grazing would reduce duck nest density. Both positive and negative responses of duck nesting success to grazing have been reported in previous studies, leading us to test competing hypotheses that nesting success would (1 decline linearly with grazing intensity or (2 peak at moderate levels of grazing. Nearly 3300 ha of upland cover were searched during the study. Despite extensive and severe drought, nest searches located 302 duck nests. As predicted, nest density was higher in fields with lower grazing intensity and higher pasture health scores. A lightly grazed field with a pasture score of 85 out of a possible 100 was predicted to have 16.1 nests/100 ha (95% CI = 11.7–22.1, more than five times the predicted nest density of a heavily grazed field with a pasture score of 58 (3.3 nests/100 ha, 95% CI = 2.2–4.5. Nesting success was positively related to nest-site vegetation density across most levels of grazing intensity studied, supporting our hypothesis that reductions in vegetation caused by grazing would negatively affect nesting success. However, nesting success increased with grazing intensity at the field scale. For example, nesting success for a well-concealed nest in a lightly grazed field was 11.6% (95% CI = 3.6–25.0%, whereas nesting success for a nest with the same level of nest-site vegetation in a heavily

  9. Quantum reverse hypercontractivity

    Energy Technology Data Exchange (ETDEWEB)

    Cubitt, Toby [Department of Computer Science, University College London, London, United Kingdom and Centre for Quantum Information and Foundations, DAMTP, University of Cambridge, Cambridge (United Kingdom); Kastoryano, Michael [NBIA, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen (Denmark); Montanaro, Ashley [School of Mathematics, University of Bristol, Bristol (United Kingdom); Temme, Kristan [Institute for Quantum Information and Matter, California Institute of Technology, Pasadena, California 91125 (United States)

    2015-10-15

    We develop reverse versions of hypercontractive inequalities for quantum channels. By generalizing classical techniques, we prove a reverse hypercontractive inequality for tensor products of qubit depolarizing channels. We apply this to obtain a rapid mixing result for depolarizing noise applied to large subspaces and to prove bounds on a quantum generalization of non-interactive correlation distillation.

  10. Clocked Thrust Reversers

    Science.gov (United States)

    Suciu, Gabriel L. (Inventor); Chandler, Jesse M. (Inventor)

    2017-01-01

    An aircraft includes a fuselage including a propulsion system supported within an aft portion. A thrust reverser is mounted proximate to the propulsion system for directing thrust in a direction to slow the aircraft. The thrust reverser directs thrust at an angle relative to a vertical plane to reduce interference on control surfaces and reduce generation of underbody lift.

  11. Atrioventricular Pacemaker Lead Reversal

    Directory of Open Access Journals (Sweden)

    Mehmet K Aktas, MD

    2007-01-01

    Full Text Available During cardiac surgery temporary epicardial atrial and ventricular leads are placed in case cardiac pacing is required postoperatively. We present the first reported series of patients with reversal of atrioventricular electrodes in the temporary pacemaker without any consequent deleterious hemodynamic effect. We review the electrocardiographic findings and discuss the findings that lead to the discovery of atrioventricular lead reversal.

  12. Reversible cerebral vasoconstriction syndrome

    Directory of Open Access Journals (Sweden)

    Saini Monica

    2009-01-01

    Full Text Available Reversible cerebral vasoconstriction syndromes (RCVS are a group of disorders that have in common an acute presentation with headache, reversible vasoconstriction of cerebral arteries, with or without neurological signs and symptoms. In contrast to primary central nervous system vasculitis, they have a relatively benign course. We describe here a patient who was diagnosed with RCVS.

  13. Towards Reversible Sessions

    Directory of Open Access Journals (Sweden)

    Francesco Tiezzi

    2014-06-01

    Full Text Available In this work, we incorporate reversibility into structured communication-based programming, to allow parties of a session to automatically undo, in a rollback fashion, the effect of previously executed interactions. This permits taking different computation paths along the same session, as well as reverting the whole session and starting a new one. Our aim is to define a theoretical basis for examining the interplay in concurrent systems between reversible computation and session-based interaction. We thus enrich a session-based variant of pi-calculus with memory devices, dedicated to keep track of the computation history of sessions in order to reverse it. We discuss our initial investigation concerning the definition of a session type discipline for the proposed reversible calculus, and its practical advantages for static verification of safe composition in communication-centric distributed software performing reversible computations.

  14. Nesting ecology of roseate spoonbills at Nueces Bay, Texas

    Science.gov (United States)

    White, D.H.; Mitchell, C.A.; Cromartie, E.

    1982-01-01

    We conducted a study in 1978-1980 of the nesting ecology of Roseate Spoonbills (Ajaia ajaja) in a relatively polluted environment at Nueces Bay, Texas. For 154 marked nests, the average clutch size was 3.0 eggs; 73% of the eggs hatched, and 87% of the nests were successful (hatched at least 1 young). The average nest success rate (total fledglings:total eggs) was 50% or 1.5 fledglings per total nests. Incubation began the day after the first egg was laid, and the incubation period for each egg was 22 days. Eggs hatched in the order that they were laid; the first and second eggs hatched on consecutive days, and the second, third, and fourth eggs hatched every other day. Nest composition and size were highly consistent, but nest placement varied considerably and was dependent on the vegetative configuration of the dredge-material islands. Growth rate of nestlings conformed to a 'standard' growth curve, where body weight of nestlings at fledging equaled that of adults. There was no difference in weight gain among siblings based on actual age. Nestlings fledged at about 6 weeks of age, when feather development was complete. At fledging, the bills of juveniles had almost reached adult width, but bill length was only 67% that of adults. In general, environmental pollutants were low (Nueces Bay, Texas, though the area is surrounded by industries and agricultural lands. Apparently, spoonbills are less sensitive to these contaminants than are other aquatic species

  15. Red-shouldered hawk nesting habitat preference in south Texas

    Science.gov (United States)

    Strobel, Bradley N.; Boal, Clint W.

    2010-01-01

    We examined nesting habitat preference by red-shouldered hawks Buteo lineatus using conditional logistic regression on characteristics measured at 27 occupied nest sites and 68 unused sites in 2005–2009 in south Texas. We measured vegetation characteristics of individual trees (nest trees and unused trees) and corresponding 0.04-ha plots. We evaluated the importance of tree and plot characteristics to nesting habitat selection by comparing a priori tree-specific and plot-specific models using Akaike's information criterion. Models with only plot variables carried 14% more weight than models with only center tree variables. The model-averaged odds ratios indicated red-shouldered hawks selected to nest in taller trees and in areas with higher average diameter at breast height than randomly available within the forest stand. Relative to randomly selected areas, each 1-m increase in nest tree height and 1-cm increase in the plot average diameter at breast height increased the probability of selection by 85% and 10%, respectively. Our results indicate that red-shouldered hawks select nesting habitat based on vegetation characteristics of individual trees as well as the 0.04-ha area surrounding the tree. Our results indicate forest management practices resulting in tall forest stands with large average diameter at breast height would benefit red-shouldered hawks in south Texas.

  16. Extreme sequential polyandry insures against nest failure in a frog.

    Science.gov (United States)

    Byrne, Phillip G; Keogh, J Scott

    2009-01-07

    Sequential polyandry may evolve as an insurance mechanism to reduce the risk of choosing a mate that is infertile, closely related, genetically inferior or incompatible, but polyandry also might insure against nest failure in unpredictable environments. Most animals are oviparous, and in species where males provide nest sites whose quality varies substantially and unpredictably, polyandrous females might insure offspring success by distributing their eggs across multiple nests. Here, we test this hypothesis in a wild population of an Australian terrestrial toadlet, a polyandrous species, where males construct nests and remain with broods. We found that females partitioned their eggs across the nests of two to eight males and that more polyandrous females gained a significant increase in mean offspring survivorship. Our results provide evidence for the most extreme case of sequential polyandry yet discovered in a vertebrate and also suggest that insurance against nest failure might favour the evolution of polyandry. We propose that insurance against nest failure might be widespread among oviparous taxa and provide an important explanation for the prevalence of sequential polyandry in nature.

  17. An object-oriented approach to nested data parallelism

    Science.gov (United States)

    Sheffler, Thomas J.; Chatterjee, Siddhartha

    1994-01-01

    This paper describes an implementation technique for integrating nested data parallelism into an object-oriented language. Data-parallel programming employs sets of data called 'collections' and expresses parallelism as operations performed over the elements of a collection. When the elements of a collection are also collections, then there is the possibility for 'nested data parallelism.' Few current programming languages support nested data parallelism however. In an object-oriented framework, a collection is a single object. Its type defines the parallel operations that may be applied to it. Our goal is to design and build an object-oriented data-parallel programming environment supporting nested data parallelism. Our initial approach is built upon three fundamental additions to C++. We add new parallel base types by implementing them as classes, and add a new parallel collection type called a 'vector' that is implemented as a template. Only one new language feature is introduced: the 'foreach' construct, which is the basis for exploiting elementwise parallelism over collections. The strength of the method lies in the compilation strategy, which translates nested data-parallel C++ into ordinary C++. Extracting the potential parallelism in nested 'foreach' constructs is called 'flattening' nested parallelism. We show how to flatten 'foreach' constructs using a simple program transformation. Our prototype system produces vector code which has been successfully run on workstations, a CM-2, and a CM-5.

  18. Nested RT-PCR method for the detection of European avian-like H1 swine inlfuenza A virus

    Institute of Scientific and Technical Information of China (English)

    WEI Yan-di; PEI Xing-yao; ZHANG Yuan; YU Chen-fang; SUN Hong-lei; LIU Jin-hua; PU Juan

    2016-01-01

    Swine inlfuenza A virus (swine IAV) circulates worldwide in pigs and poses a serious public health threat, as evidenced by the 2009 H1N1 inlfuenza pandemic. Among multiple subtypes/lineages of swine inlfuenza A viruses, European avian-like (EA) H1N1 swine IAV has been dominant since 2005 in China and caused infections in humans in 2010. Highly sensitive and speciifc methods of detection are required to differentiate EA H1N1 swine IAVs from viruses belonging to other lineages and subtypes. In this study, a nested reverse transcription (RT)-PCR assay was developed to detect EA H1 swine IAVs. Two primer sets (outer and inner) were designed speciifcaly to target the viral hemagglutinin genes. Speciifc PCR products were obtained from al tested EA H1N1 swine IAV isolates, but not from other lineages of H1 swine IAVs, other subtypes of swine IAVs, or other infectious swine viruses. The sensitivity of the nested RT-PCR was improved to 1 plaque forming unit (PFU) mL–1which was over 104 PFU mL–1 for a previously established multiplex RT-PCR method. The nested RT-PCR results obtained from screening 365 clinical samples were consistent with those obtained using conventional virus isolation methods combined with sequencing. Thus, the nested RT-PCR assay reported herein is more sensitive and suitable for the diagnosis of clinical infections and surveilance of EA H1 swine IAVs in pigs and humans.

  19. Interspecific nest parasitism by chukar on greater sage-grouse

    Science.gov (United States)

    Fearon, Michelle L.; Coates, Peter S.

    2014-01-01

    Nest parasitism occurs when a female bird lays eggs in the nest of another and the host incubates the eggs and may provide some form of parental care for the offspring (Lyon and Eadie 1991). Precocial birds (e.g., Galliformes and Anseriformes) are typically facultative nest parasites of both their own and other species (Lyon and Eadie 1991). This behavior increases a female’s reproductive success when she parasitizes other nests while simultaneously raising her own offspring. Both interspecific and conspecific nest parasitism have been well documented in several families of the order Galliformes, particularly the Phasianidae (Lyon and Eadie 1991, Geffen and Yom-Tov 2001, Krakauer and Kimball 2009). The Chukar (Alectoris chukar) has been widely introduced as a game bird to western North America from Eurasia and is now well established within the Great Basin from northeastern California east to Utah and north to Idaho and Oregon (Christensen 1996). Over much of this range the Chukar occurs with other phasianids, including the native Greater Sage-Grouse (Centrocercus urophasianus), within sagebrush (Artemisia spp.) steppe (Christensen 1996, Schroeder et al. 1999, Connelly et al. 2000). Chukar typically exploit a broader range of habitats than do sage-grouse, but both species use the same species of sagebrush and other shrubs for nesting cover (Christensen 1996, Schroeder et al. 1999). Chukar are known to parasitize nests of other individuals of their own species (Geffen and Yom-Tov 2001), but we are unaware of reported evidence that Chukar may parasitize nests of sage-grouse. Here we describe a case of a Chukar parasitizing a sage-grouse nest in the sagebrush steppe of western Nevada.

  20. Dual Biochemical Oscillators May Control Cellular Reversals in Myxococcus xanthus

    Science.gov (United States)

    Eckhert, Erik; Rangamani, Padmini; Davis, Annie E.; Oster, George; Berleman, James E.

    2014-01-01

    Myxococcus xanthus is a Gram-negative, soil-dwelling bacterium that glides on surfaces, reversing direction approximately once every 6 min. Motility in M. xanthus is governed by the Che-like Frz pathway and the Ras-like Mgl pathway, which together cause the cell to oscillate back and forth. Previously, Igoshin et al. (2004) suggested that the cellular oscillations are caused by cyclic changes in concentration of active Frz proteins that govern motility. In this study, we present a computational model that integrates both the Frz and Mgl pathways, and whose downstream components can be read as motor activity governing cellular reversals. This model faithfully reproduces wildtype and mutant behaviors by simulating individual protein knockouts. In addition, the model can be used to examine the impact of contact stimuli on cellular reversals. The basic model construction relies on the presence of two nested feedback circuits, which prompted us to reexamine the behavior of M. xanthus cells. We performed experiments to test the model, and this cell analysis challenges previous assumptions of 30 to 60 min reversal periods in frzCD, frzF, frzE, and frzZ mutants. We demonstrate that this average reversal period is an artifact of the method employed to record reversal data, and that in the absence of signal from the Frz pathway, Mgl components can occasionally reverse the cell near wildtype periodicity, but frz- cells are otherwise in a long nonoscillating state. PMID:25468349

  1. Archiving California’s historical duck nesting data

    Science.gov (United States)

    Ackerman, Joshua T.; Herzog, Mark P.; Brady, Caroline; Eadie, John M.; Yarris, Greg S.

    2015-07-14

    The U.S. Geological Survey (USGS), in partnership with the California Waterfowl Association (CWA) and other organizations, have compiled large datasets on the nesting ecology and management of dabbling ducks and associated upland nesting birds (Northern Harriers [Circus cyaneus], Short-eared Owls [Asio flammeus], Ring-necked Pheasants [Phasianus colchicus], and American Bitterns [Botaurus lentiginosus]) throughout California on Federal Refuges, State Wildlife Areas, and private lands, some participating in State and Federal habitat programs. These datasets encompass several long-term monitoring programs at multiple sites throughout California, and include data from more than 26,000 nests and span nearly 30 years.

  2. Nested Hilbert schemes on surfaces: Virtual fundamental class

    DEFF Research Database (Denmark)

    Gholampour, Amin; Sheshmani, Artan; Yau, Shing-Tung

    2017-01-01

    We construct natural virtual fundamental classes for nested Hilbert schemes on a nonsingular projective surface S. This allows us to define new invariants of S that recover some of the known important cases such as Poincare invariants of Durr-Kabanov-Okonek and the stable pair invariants of Kool......-Thomas. In the case of the nested Hilbert scheme of points, we can express these invariants in terms of integrals over the products of Hilbert scheme of points on S, and relate them to the vertex operator formulas found by Carlsson-Okounkov. The virtual fundamental classes of the nested Hilbert schemes play a crucial...

  3. Spatiotemporal patterns of duck nest density and predation risk: a multi-scale analysis of 18 years and more than 10,000 nests

    Science.gov (United States)

    Ringelman, Kevin M.; Eadie, John M.; Ackerman, Joshua T.; Sih, Andrew; Loughman, Daniel L.; Yarris, Gregory S.; Oldenburger, Shaun L.; McLandress, M. Robert

    2017-01-01

    Many avian species are behaviorally-plastic in selecting nest sites, and may shift to new locations or habitats following an unsuccessful breeding attempt. If there is predictable spatial variation in predation risk, the process of many individuals using prior experience to adaptively change nest sites may scale up to create shifting patterns of nest density at a population level. We used 18 years of waterfowl nesting data to assess whether there were areas of consistently high or low predation risk, and whether low-risk areas increased, and high-risk areas decreased in nest density the following year. We created kernel density maps of successful and unsuccessful nests in consecutive years and found no correlation in predation risk and no evidence for adaptive shifts, although nest density was correlated between years. We also examined between-year correlations in nest density and nest success at three smaller spatial scales: individual nesting fields (10–28 ha), 16-ha grid cells and 4-ha grid cells. Here, results were similar across all scales: we found no evidence for year-to-year correlation in nest success but found strong evidence that nest density was correlated between years, and areas of high nest success increased in nest density the following year. Prior research in this system has demonstrated that areas of high nest density have higher nest success, and taken together, our results suggest that ducks may adaptively select nest sites based on the local density of conspecifics, rather than the physical location of last year's nest. In unpredictable environments, current cues, such as the presence of active conspecific nests, may be especially useful in selecting nest sites. The cues birds use to select breeding locations and successfully avoid predators deserve continued attention, especially in systems of conservation concern.

  4. Incorporation of cigarette butts into nests reduces nest ectoparasite load in urban birds: new ingredients for an old recipe?

    Science.gov (United States)

    Suárez-Rodríguez, Monserrat; López-Rull, Isabel; Garcia, Constantino Macías

    2013-02-23

    Birds are known to respond to nest-dwelling parasites by altering behaviours. Some bird species, for example, bring fresh plants to the nest, which contain volatile compounds that repel parasites. There is evidence that some birds living in cities incorporate cigarette butts into their nests, but the effect (if any) of this behaviour remains unclear. Butts from smoked cigarettes retain substantial amounts of nicotine and other compounds that may also act as arthropod repellents. We provide the first evidence that smoked cigarette butts may function as a parasite repellent in urban bird nests. The amount of cellulose acetate from butts in nests of two widely distributed urban birds was negatively associated with the number of nest-dwelling parasites. Moreover, when parasites were attracted to heat traps containing smoked or non-smoked cigarette butts, fewer parasites reached the former, presumably due to the presence of nicotine. Because urbanization changes the abundance and type of resources upon which birds depend, including nesting materials and plants involved in self-medication, our results are consistent with the view that urbanization imposes new challenges on birds that are dealt with using adaptations evolved elsewhere.

  5. Using rational numbers to key nested sets

    CERN Document Server

    Hazel, Dan

    2008-01-01

    This report details the generation and use of tree node ordering keys in a single relational database table. The keys for each node are calculated from the keys of its parent, in such a way that the sort order places every node in the tree before all of its descendants and after all siblings having a lower index. The calculation from parent keys to child keys is simple, and reversible in the sense that the keys of every ancestor of a node can be calculated from that node's keys without having to consult the database. Proofs of the above properties of the key encoding process and of its correspondence to a finite continued fraction form are provided.

  6. Interaction between the solitary bee Chelostoma florisomne and its nest parasite Sapyga clavicornis-empty cells reduce the impact of parasites

    DEFF Research Database (Denmark)

    Munster-Swendsen, Mikael; Calabuig, Isabel

    2000-01-01

    Chelostoma, empty cells, interaction, mortality, nest architecture, nest parasite, protection, Sapyga, solitary bee......Chelostoma, empty cells, interaction, mortality, nest architecture, nest parasite, protection, Sapyga, solitary bee...

  7. An algebra of reversible computation

    OpenAIRE

    2016-01-01

    We design an axiomatization for reversible computation called reversible ACP (RACP). It has four extendible modules, basic reversible processes algebra (BRPA), algebra of reversible communicating processes (ARCP), recursion and abstraction. Just like process algebra ACP in classical computing, RACP can be treated as an axiomatization foundation for reversible computation.

  8. An Algebra of Reversible Computation

    OpenAIRE

    Yong WANG

    2014-01-01

    We design an axiomatization for reversible computation called reversible ACP (RACP). It has four extendible modules, basic reversible processes algebra (BRPA), algebra of reversible communicating processes (ARCP), recursion and abstraction. Just like process algebra ACP in classical computing, RACP can be treated as an axiomatization foundation for reversible computation.

  9. An algebra of reversible computation.

    Science.gov (United States)

    Wang, Yong

    2016-01-01

    We design an axiomatization for reversible computation called reversible ACP (RACP). It has four extendible modules: basic reversible processes algebra, algebra of reversible communicating processes, recursion and abstraction. Just like process algebra ACP in classical computing, RACP can be treated as an axiomatization foundation for reversible computation.

  10. 1990 Flathead Valley duck nesting study progress report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This informal progress report describes predator removal practices in the Lake County area, and observed waterfowl nest success. Species-specific data are...

  11. Inkjet printing of silk nest arrays for cell hosting.

    Science.gov (United States)

    Suntivich, Rattanon; Drachuk, Irina; Calabrese, Rossella; Kaplan, David L; Tsukruk, Vladimir V

    2014-04-14

    An inkjet printing approach is presented for the facile fabrication of microscopic arrays of biocompatible silk "nests" capable of hosting live cells for prospective biosensors. The patterning of silk fibroin nests were constructed by the layer-by-layer (LbL) assembly of silk polyelectrolytes chemically modified with poly-(l-lysine) and poly-(l-glutamic acid) side chains. The inkjet-printed silk circular regions with a characteristic "nest" shape had diameters of 70-100 μm and a thickness several hundred nanometers were stabilized by ionic pairing and by the formation of the silk II crystalline secondary structure. These "locked-in" silk nests remained anchored to the substrate during incubation in cell growth media to provide a biotemplated platform for printing-in, immobilization, encapsulation and growth of cells. The process of inkjet-assisted printing is versatile and can be applied on any type of substrate, including rigid and flexible, with scalability and facile formation.

  12. 1993 waterfowl nesting success on Fish Springs National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Report on an investigation of nesting success and factors affecting it on Fish Springs National Wildlife Refuge. Baseline information on trust species within the...

  13. Wading bird nesting survey Fish Springs National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report discusses results of a wading bird survey conducted at Fish Springs National Wildlife Refuge. The objectives of the survey include; 1) quantify nest site...

  14. 2005 nest success data : Klettke WPA predator exclosure

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Report summarizing nest success at Klettke Waterfowl Production Area predator exclosure on Kulm wetland Management District in 2005. In 2005, the Klettke predator...

  15. Contaminant exposure of white pelicans nesting at Anaho Island NWR

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Reproductive success of American white pelicans (Pelecanus erythrorhynchus) was monitored at a nesting colony on Anaho Island, Pyramid Lake, Nevada in 1996. Eggs...

  16. Bald Eagle Summary Report for New York Nesting Territories 1991

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Observations at New York bald eagle nest sites one, three and four in Livingston, Genesee, and Seneca Counties respectively, continued during the 1991 breeding...

  17. Application of nested sampling in statistical physics: the Potts model

    CERN Document Server

    Pfeifenberger, Manuel J

    2016-01-01

    We present a systematic benchmark study of the nested sampling algorithm on the basis of the Potts model. This model exhibits a first order phase transition for $q>4$ at the critical temperature. The numerical evaluation of the partition function and thermodynamic observables, which involves high dimensional sums of sharply structured multi-modal density functions, represents a major challenge to most standard numerical techniques, such as Markov Chain Monte Carlo. Nested sampling, on the other hand, is particularly suited for such problems. In this paper we will employ both, nested sampling and thermodynamic integration to evaluate the partition function of the Potts model. In both cases individual moves are based on Swendsen-Wang updates. A autocorrelation time analysis of both algorithms shows that the severe slowing down of thermodynamic integration around the critical temperature does not occur in nested sampling. In addition we show, how thermodynamic variables can be computed with high accuracy from th...

  18. The Food and nesting Habits of the Bald Eagle

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the observations of the author who watched a bald eagle and studied its food habits at two nests. At the time of the report, the bald eagle...

  19. Bald Eagle Summary Report for New York Nesting Territories 1990

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Observations at New York bald eagle nest sites one, three and four in Livingston, Genesee, and Seneca Counties respectively, continued during the 1990 breeding...

  20. Nest losses in grazed vs. ungrazed waterfowl habitat

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — A fair number of managers, with student help, have just completed a series of dummy nest studies which sampled grazed and ungrazed habitat. I have examined 40...

  1. History of Waterfowl Nesting on the Patuxent Research Center

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report is a summary of waterfowl counts, waterfowl research, waterfowl nesting, and waterfowl records at Patuxent Research Refuge from 1963 through 2008, as...

  2. Medium Range Forecast (MRF) and Nested Grid Model (NGM)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Nested Grid Model (NGM) and Medium Range Forecast (MRF) Archive is historical digital data set DSI-6140, archived at the NOAA National Centers for Environmental...

  3. 1970 American Eagle Nest Survey of the Chesapeake Bay Region.

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Data refers to the 1970 nesting season for the Bald Eagle in the Chesapeake area to include Virginia and Maryland. The 1970 results are most disappointing since...

  4. Bald Eagle Summary Report for New York Nesting Territories 1989

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Observations at New York bald eagle nest sites one, three and four in Livingston, Genesee, and Seneca Counties respectively, continued during the 1989 breeding...

  5. Inventory and monitoring of red-cockaded woodpecker Nesting

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Report provides nesting monitoring and group size summary data associated with the red-cockaded woodpecker population at Noxubee NWR in 2012.

  6. EXTREME POINTS IN DIAGONAL-DISJOINT IDEALS OF NEST ALGEBRAS

    Institute of Scientific and Technical Information of China (English)

    董浙; 鲁世杰

    2002-01-01

    In this paper, the extreme points of the unit ball of diagonal-disjoint ideals in nest algebras are characterized completely; Furthermore, it is shown that every extreme point of the unit ball of 2 has essential-norm one.

  7. [Proposal] Loggerhead sea turtle nest monitoring on seven refuges

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The purpose of this project is to continue FWS involvement in the long-term, consistent monitoring of loggerhead sea turtle nesting to assess changes in phenological...

  8. Shorebird Nesting Success Report : Bear River Migratory Bird Refuge : 2003

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This preliminary study was initiated to establish a baseline of nesting success for one of the most important breeding sites of shorebirds within the Greater Salt...

  9. 1982 Bald Eagle Nest Survey, Chesapeake Bay Region.

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Data refers to the 1982 nesting season for the Bald Eagle in the Chesapeake area to include Virginia, Maryland and Delaware. For the third year in succession we have...

  10. Black Tern Nesting, Missisquoi National Wildlife Refuge, 2009-2014

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Black tern breeding pair surveys have been conducted in Vermont every year since 1990, except during 2006. Initially, there were 3 separate nesting populations of...

  11. Effects Of Predator Exclosures On Nesting Success Of Killdeer

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Nests of shorebirds are often destroyed by predators and in some instances predation may cause severe local declines in breeding success and in size of a breeding...

  12. Proposal - Inventory and Monitoring for Red-cockaded Woodpecker Nesting

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Proposal is to monitor the nesting success and productivity of the red-cockaded woodpecker population at the Sam D. Hamilton Noxubee National Wildlife Refuge during...

  13. Nesting birds of the Malheur environmental field station

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The purpose of this paper is to expose the reader to the various birds nesting on the Malheur environmental field station (MEFS). Each species will be discussed...

  14. Variation in nesting behavior of eight species of spider mites, Stigmaeopsis having sociality

    Science.gov (United States)

    Saito, Yutaka; Zhang, Yan-Xuan; Mori, Kotaro; Ito, Katsura; Sato, Yukie; Chittenden, Anthony R.; Lin, Jian-Zhen; Chae, Younghae; Sakagami, Takane; Sahara, Ken

    2016-10-01

    Nesting behavior is considered to be an important element of social living in animals. The spider mites belonging to the genus Stigmaeopsis spend their lives within nests produced from silk threads. Several of these species show cooperative sociality, while the others are subsocial. In order to identify the origins of this social behavior, comparisons of nest sizes, nesting behaviors (making nests continuously or separately), and their associated traits (fecal deposition patterns) were made for eight cogeneric Stigmaeopsis species showing various levels of social development. All of these species inhabit bamboo plants (Poaceae). We initially addressed the proximate factor of nest size variation. The variation in nest size of the eight species corresponded well with the variation in dorsal seta sc1 length, suggesting that nest size variation among species may have a genetic basis. The time spent within a nest (nest duration) increased with nest size on the respective host plants. Nest arrangement patterns varied among species showing different sized nests: Large nest builders continuously extended their nests, while middle and small nest-building species built new separate nests, which resulted in different social interaction times among species, and is thought to be closely related to social development. Fecal deposition behaviors also varied among Stigmaeopsis species, suggesting diversity in anti-predatory adaptations. Finally, we discuss how the variation in sociality observed within this genus is likely the result of nest size variation that initially evolved as anti-predator strategies.

  15. Reversible Data Hiding Techniques

    Directory of Open Access Journals (Sweden)

    Dhananjay Yadav

    2012-03-01

    Full Text Available Reversible data hiding is a technique that is used to hide data inside an image. The data is hidden in such a way that the exact or original data is not visible. The hidden data can be retrieved as and when required. There are several methods that are used in reversible data hiding techniques like Watermarking, Lossless embedding and encryption. In this paper we present a review of reversible watermarking techniques and show different methods that are used to get reversible data hiding technique with higher embedding capacity and invisible objects. Watermark need not be hidden. Watermarking can be applied to 1. Images, 2. Text, 3. Audio/video, 4. Software.

  16. Reversible flowchart languages and the structured reversible program theorem

    DEFF Research Database (Denmark)

    Yokoyama, Tetsuo; Axelsen, Holger Bock; Glück, Robert

    2008-01-01

    Many irreversible computation models have reversible counterparts, but these are poorly understood at present. We introduce reversible flowcharts with an assertion operator and show that any reversible flowchart can be simulated by a structured reversible flowchart using only three control flow o...... justification for low-level machine code for reversible microprocessors as well as high-level block-structured reversible languages. We give examples for both such languages and illustrate them with a lossless encoder for permutations given by Dijkstra....

  17. Adapted nested force-gradient integrators for the Schwinger model

    CERN Document Server

    Shcherbakov, Dmitry; Günther, Michael; Finkenrath, Jacob; Knechtli, Francesco; Peardon, Michael

    2016-01-01

    We study a novel class of numerical integrators, the adapted nested force-gradient schemes, used within the molecular dynamics step of the Hybrid Monte Carlo (HMC) algorithm. We test these methods in the Schwinger model on the lattice, a well known benchmark problem. We derive the analytical basis of nested force-gradient type methods and demonstrate the advantage of the proposed approach, namely reduced computational costs compared with other numerical integration schemes in HMC.

  18. Nest sanitation elicits egg discrimination in cuckoo hosts.

    Science.gov (United States)

    Yang, Canchao; Chen, Min; Wang, Longwu; Liang, Wei; Møller, Anders Pape

    2015-11-01

    Nest sanitation is a nearly universal behavior in birds, while egg discrimination is a more specific adaptation that has evolved to counter brood parasitism. These two behaviors are closely related with nest sanitation being the ancestral behavior, and it has been hypothesized to constitute a preadaptation for egg discrimination. However, previous studies found little evidence to support this hypothesis. Here, we conducted an empirical test of the association between nest sanitation and egg discrimination in the barn swallow (Hirundo rustica) by inserting a single non-mimetic model egg or a non-mimetic model egg plus half a peanut shell into host nests. Compared to the rejection rate of single model eggs, barn swallows significantly increased egg rejection frequency if a half peanut shell was simultaneously introduced. Our result for the first time shows the impact of nest sanitation on egg discrimination and demonstrates that nest sanitation can elicit egg discrimination in hosts of brood parasites. This study provided evidence for nest sanitation being a preadaptation to egg discrimination by facilitating egg rejection, thereby significantly advancing our understanding of avian cognition of foreign objects. Furthermore, we suggest that egg discrimination behavior in many accepters and intermediate rejecters may be lost or diluted. Such egg discrimination can be elicited and restored after nest sanitation, implying a sensitive and rapid phenotypic response to increased risk of parasitism. Our study offers a novel perspective for investigating the role of so-called intermediate rejecter individuals or species in the long-term coevolutionary cycle between brood parasites and their hosts.

  19. Adaptive Pairing Reversible Watermarking.

    Science.gov (United States)

    Dragoi, Ioan-Catalin; Coltuc, Dinu

    2016-05-01

    This letter revisits the pairwise reversible watermarking scheme of Ou et al., 2013. An adaptive pixel pairing that considers only pixels with similar prediction errors is introduced. This adaptive approach provides an increased number of pixel pairs where both pixels are embedded and decreases the number of shifted pixels. The adaptive pairwise reversible watermarking outperforms the state-of-the-art low embedding bit-rate schemes proposed so far.

  20. Nesting behavior of Podium denticulatum Smith (Hymenoptera: Sphecidae).

    Science.gov (United States)

    Ribeiro, Favi; Garófalo, Carlos A

    2010-01-01

    The nesting behavior of Podium denticulatum Smith was studied on the campus of Ribeirão Preto of the Universidade de São Paulo, SP, Brazil, from September 2003 to August 2005. The wasps established their nests in bamboo canes ranging from 11.4 cm to 26.2 cm in length and from 0.7 cm to 1.8 cm in internal diameter. Podium denticulatum nested almost exclusively in the hot and wet season (September-April), producing at least five generations per year. The cell provisioning was made with adult and nymphal cockroaches (Blattellidae) which were arranged venter-up and with the head inward toward the inner end of the cell. The construction of a temporary closure occurred in cells that took more than one day to be provisioned. The cells provisioned with a greater number of prey were more likely to produce females than males. The nests included 1-6 brood cells separated by mud partitions and arranged in a linear series. The innermost cells of the nests produced females, and the outermost cells produced males. Nests were parasitized by Eulophidae (Melittobia sp.), Chrysididae and Tachinidae.

  1. Plastic and the nest entanglement of urban and agricultural crows.

    Directory of Open Access Journals (Sweden)

    Andrea K Townsend

    Full Text Available Much attention has been paid to the impacts of plastics and other debris on marine organisms, but the effects of plastic on terrestrial organisms have been largely ignored. Detrimental effects of terrestrial plastic could be most pronounced in intensively human-modified landscapes (e.g., urban and agricultural areas, which are a source of much anthropogenic debris. Here, we examine the occurrence, types, landscape associations, and consequences of anthropogenic nest material in the American crow (Corvus brachyrhynchos, a North American species that breeds in both urban and agricultural landscapes. We monitored 195 nestlings in 106 nests across an urban and agricultural gradient in the Sacramento Valley, California, USA. We found that 85.2% of crow nests contained anthropogenic material, and 11 of 195 nestlings (5.6% were entangled in their nests. The length of the material was greater in nests in agricultural territories than in urban territories, and the odds of entanglement increased 7.55 times for each meter of anthropogenic material in the nest. Fledging success was significantly lower for entangled than for unentangled nestlings. In all environments, particularly urban, agricultural, and marine, careful disposal of potential hazards (string, packing and hay bale twine, balloon ribbon, wire, fishing line could reduce the occurrence of entanglement of nestling birds.

  2. Plastic and the nest entanglement of urban and agricultural crows.

    Science.gov (United States)

    Townsend, Andrea K; Barker, Christopher M

    2014-01-01

    Much attention has been paid to the impacts of plastics and other debris on marine organisms, but the effects of plastic on terrestrial organisms have been largely ignored. Detrimental effects of terrestrial plastic could be most pronounced in intensively human-modified landscapes (e.g., urban and agricultural areas), which are a source of much anthropogenic debris. Here, we examine the occurrence, types, landscape associations, and consequences of anthropogenic nest material in the American crow (Corvus brachyrhynchos), a North American species that breeds in both urban and agricultural landscapes. We monitored 195 nestlings in 106 nests across an urban and agricultural gradient in the Sacramento Valley, California, USA. We found that 85.2% of crow nests contained anthropogenic material, and 11 of 195 nestlings (5.6%) were entangled in their nests. The length of the material was greater in nests in agricultural territories than in urban territories, and the odds of entanglement increased 7.55 times for each meter of anthropogenic material in the nest. Fledging success was significantly lower for entangled than for unentangled nestlings. In all environments, particularly urban, agricultural, and marine, careful disposal of potential hazards (string, packing and hay bale twine, balloon ribbon, wire, fishing line) could reduce the occurrence of entanglement of nestling birds.

  3. Nesting biology of Centris (Centris aenea Lepeletier (Hymenoptera, Apidae, Centridini

    Directory of Open Access Journals (Sweden)

    Cândida Maria Lima Aguiar

    2003-12-01

    Full Text Available Nesting activity of Centris aenea Lepeletier, 1841 was studied in two Brazilian habitats, Caatinga (Monte Santo, Bahia and Cerrado (Palmeiras, Bahia and Luiz Antônio, São Paulo. Nests were excavated in the ground and did not tend to be aggregated together at the two sites, but at Palmeiras, nests were in a large aggregation. Nest architecture consists of a single unbranched tunnel, sloping to vertical, which leads to a linear series of four cells, placed from 8 to 26 cm in depth. Cells are urn-shaped with a rounded base, and their cell caps have a central hollow process, as in other Centridini. Nest architecture of C. aenea was compared to other species of Centris Fabricius, 1804. Provisions are composed of a pollen mass covered by a thin liquid layer on which the egg is placed. Females were observed gathering oil on Mcvaughia bahiana W.R. Anderson flowers from October to March in the Caatinga, and on Byrsonima intermedia A.Juss. as well as other Malpighiaceae species from August to December in the Cerrado. Pollen is gathered by buzzing flowers of Solanaceae, Caesalpiniaceae, Malpighiaceae, and Ochnaceae. Several nectar sources were recorded. There is indirect evidence that Mesoplia sp. parasitizes nests of C. aenea in the Cerrado.

  4. Japanese queenless ants, Pristomyrmex punctatus, prefer the traces of both nestmates and strangers in nest selection.

    Science.gov (United States)

    Satow, Show; Saitow, Yuka; Yamaki, Shōtarō; Hirota, Tadao

    2013-07-01

    Conspecific avoidance may influence the spatial distribution of colonies in some ants. House-hunting ants (Temnothorax albipennis) avoid nesting in areas where non-nestmates have nested previously. However, no reports are available on conspecific avoidance during nest selection in other ants. In the present study, we investigated nest selection in another nomadic species, the Japanese queenless ant, Pristomyrmex punctatus. Two-choice tests revealed that, similar to house-hunting ants, P. punctatus preferred nests soiled by nestmates to clean nests. However, unlike house-hunting ants, P. punctatus also preferred nests soiled by non-nestmates to a clean nest. Given the choice between a nest soiled by nestmates and one soiled by strangers, P. punctatus, unlike house-haunting ants, showed no significant preference. Thus, conspecific avoidance in nest selection was not observed in P. punctatus. Interspecific differences in ecological factors may drive the evolution of different nest selection strategies.

  5. Analytical solutions for Tokamak equilibria with reversed toroidal current

    Energy Technology Data Exchange (ETDEWEB)

    Martins, Caroline G. L.; Roberto, M.; Braga, F. L. [Departamento de Fisica, Instituto Tecnologico de Aeronautica, Sao Jose dos Campos, Sao Paulo 12228-900 (Brazil); Caldas, I. L. [Instituto de Fisica, Universidade de Sao Paulo, 05315-970 Sao Paulo, SP (Brazil)

    2011-08-15

    In tokamaks, an advanced plasma confinement regime has been investigated with a central hollow electric current with negative density which gives rise to non-nested magnetic surfaces. We present analytical solutions for the magnetohydrodynamic equilibria of this regime in terms of non-orthogonal toroidal polar coordinates. These solutions are obtained for large aspect ratio tokamaks and they are valid for any kind of reversed hollow current density profiles. The zero order solution of the poloidal magnetic flux function describes nested toroidal magnetic surfaces with a magnetic axis displaced due to the toroidal geometry. The first order correction introduces a poloidal field asymmetry and, consequently, magnetic islands arise around the zero order surface with null poloidal magnetic flux gradient. An analytic expression for the magnetic island width is deduced in terms of the equilibrium parameters. We give examples of the equilibrium plasma profiles and islands obtained for a class of current density profile.

  6. On thermodynamic and microscopic reversibility

    Energy Technology Data Exchange (ETDEWEB)

    Crooks, Gavin E.

    2011-07-12

    The word 'reversible' has two (apparently) distinct applications in statistical thermodynamics. A thermodynamically reversible process indicates an experimental protocol for which the entropy change is zero, whereas the principle of microscopic reversibility asserts that the probability of any trajectory of a system through phase space equals that of the time reversed trajectory. However, these two terms are actually synonymous: a thermodynamically reversible process is microscopically reversible, and vice versa.

  7. Striped-tailed Yellow-finch nesting success in abandoned mining pits from central Brazilian cerrado

    Directory of Open Access Journals (Sweden)

    DT. Gressler

    Full Text Available Suitability of degraded areas as breeding habitats can be tested through assessment of nest predation rates. In this study we estimated nest success in relation to several potential predictors of nest survival in the Stripe-tailed Yellow-finch (Sicalis citrina breeding in abandoned mining pits at Brasília National Park. We monitored 73 nests during the 2007-breeding season. Predation was the main cause of nest failure (n = 48, 66%; while six nests were abandoned (8% and 19 nests produced young (26%. Mayfield’s daily survival rates and nest success were 0.94 and 23%, respectively. Our results from nest survival models on program MARK indicated that daily survival rates increase linearly towards the end of the breeding season and decrease as nests aged. None of the nest individual covariates we tested - nest height, nest size, nest substrate, and edge effect - were important predictors of nest survival; however, nests placed on the most common plant tended to have higher survival probabilities. Also, there was no observer effect on daily survival rates. Our study suggests that abandoned mining pits may be suitable alternative breeding habitats for Striped-tailed Yellow-finches since nest survival rates were similar to other studies in the central cerrado region.

  8. A review of the nest protection hypothesis: does inclusion of fresh green plant material in birds' nests reduce parasite infestation?

    Science.gov (United States)

    Scott-Baumann, James F; Morgan, Eric R

    2015-07-01

    The use of aromatic plants and their essential oils for ectoparasite treatment is a field of growing interest. Several species of birds regularly introduce aromatic herbs into their nests putatively to reduce parasites. The behaviour is most often seen in cavity nesting birds and after nest building has finished. The plants are included in a non-structural manner and are often strongly aromatic. Various different hypotheses have been proposed regarding the function of this behaviour; from the plants altering some non-living factor in the nest (crypsis, water loss and insulation hypotheses) to them being involved in mate selection (mate hypothesis) or even having a beneficial effect, direct or indirect, on chicks (drug or nest protection hypothesis, NPH). Many studies have been carried out over the years observing and experimentally testing these hypotheses. This review focuses on studies involving the most popular of these hypotheses, the NPH: that plants decrease nest parasites or pathogens, thereby conveying positive effects to the chicks, allowing the behaviour to evolve. Studies providing observational evidence towards this hypothesis and those experimentally testing it are discussed.

  9. Variation in clutch size in relation to nest size in birds

    Science.gov (United States)

    Møller, Anders P; Adriaensen, Frank; Artemyev, Alexandr; Bańbura, Jerzy; Barba, Emilio; Biard, Clotilde; Blondel, Jacques; Bouslama, Zihad; Bouvier, Jean-Charles; Camprodon, Jordi; Cecere, Francesco; Charmantier, Anne; Charter, Motti; Cichoń, Mariusz; Cusimano, Camillo; Czeszczewik, Dorota; Demeyrier, Virginie; Doligez, Blandine; Doutrelant, Claire; Dubiec, Anna; Eens, Marcel; Eeva, Tapio; Faivre, Bruno; Ferns, Peter N; Forsman, Jukka T; García-Del-Rey, Eduardo; Goldshtein, Aya; Goodenough, Anne E; Gosler, Andrew G; Góźdź, Iga; Grégoire, Arnaud; Gustafsson, Lars; Hartley, Ian R; Heeb, Philipp; Hinsley, Shelley A; Isenmann, Paul; Jacob, Staffan; Järvinen, Antero; Juškaitis, Rimvydas; Korpimäki, Erkki; Krams, Indrikis; Laaksonen, Toni; Leclercq, Bernard; Lehikoinen, Esa; Loukola, Olli; Lundberg, Arne; Mainwaring, Mark C; Mänd, Raivo; Massa, Bruno; Mazgajski, Tomasz D; Merino, Santiago; Mitrus, Cezary; Mönkkönen, Mikko; Morales-Fernaz, Judith; Morin, Xavier; Nager, Ruedi G; Nilsson, Jan-Åke; Nilsson, Sven G; Norte, Ana C; Orell, Markku; Perret, Philippe; Pimentel, Carla S; Pinxten, Rianne; Priedniece, Ilze; Quidoz, Marie-Claude; Remeš, Vladimir; Richner, Heinz; Robles, Hugo; Rytkönen, Seppo; Senar, Juan Carlos; Seppänen, Janne T; da Silva, Luís P; Slagsvold, Tore; Solonen, Tapio; Sorace, Alberto; Stenning, Martyn J; Török, János; Tryjanowski, Piotr; van Noordwijk, Arie J; von Numers, Mikael; Walankiewicz, Wiesław; Lambrechts, Marcel M

    2014-01-01

    Nests are structures built to support and protect eggs and/or offspring from predators, parasites, and adverse weather conditions. Nests are mainly constructed prior to egg laying, meaning that parent birds must make decisions about nest site choice and nest building behavior before the start of egg-laying. Parent birds should be selected to choose nest sites and to build optimally sized nests, yet our current understanding of clutch size-nest size relationships is limited to small-scale studies performed over short time periods. Here, we quantified the relationship between clutch size and nest size, using an exhaustive database of 116 slope estimates based on 17,472 nests of 21 species of hole and non-hole-nesting birds. There was a significant, positive relationship between clutch size and the base area of the nest box or the nest, and this relationship did not differ significantly between open nesting and hole-nesting species. The slope of the relationship showed significant intraspecific and interspecific heterogeneity among four species of secondary hole-nesting species, but also among all 116 slope estimates. The estimated relationship between clutch size and nest box base area in study sites with more than a single size of nest box was not significantly different from the relationship using studies with only a single size of nest box. The slope of the relationship between clutch size and nest base area in different species of birds was significantly negatively related to minimum base area, and less so to maximum base area in a given study. These findings are consistent with the hypothesis that bird species have a general reaction norm reflecting the relationship between nest size and clutch size. Further, they suggest that scientists may influence the clutch size decisions of hole-nesting birds through the provisioning of nest boxes of varying sizes. PMID:25478150

  10. Social waves in giant honeybees (Apis dorsata) elicit nest vibrations.

    Science.gov (United States)

    Kastberger, Gerald; Weihmann, Frank; Hoetzl, Thomas

    2013-07-01

    Giant honeybees (Apis dorsata) nest in the open and have developed a wide array of strategies for colony defence, including the Mexican wave-like shimmering behaviour. In this collective response, the colony members perform upward flipping of their abdomens in coordinated cascades across the nest surface. The time-space properties of these emergent waves are response patterns which have become of adaptive significance for repelling enemies in the visual domain. We report for the first time that the mechanical impulse patterns provoked by these social waves and measured by laser Doppler vibrometry generate vibrations at the central comb of the nest at the basic (='natural') frequency of 2.156 ± 0.042 Hz which is more than double the average repetition rate of the driving shimmering waves. Analysis of the Fourier spectra of the comb vibrations under quiescence and arousal conditions provoked by mass flight activity and shimmering waves gives rise to the proposal of two possible models for the compound physical system of the bee nest: According to the elastic oscillatory plate model, the comb vibrations deliver supra-threshold cues preferentially to those colony members positioned close to the comb. The mechanical pendulum model predicts that the comb vibrations are sensed by the members of the bee curtain in general, enabling mechanoreceptive signalling across the nest, also through the comb itself. The findings show that weak and stochastic forces, such as general quiescence or diffuse mass flight activity, cause a harmonic frequency spectrum of the comb, driving the comb as an elastic plate. However, shimmering waves provide sufficiently strong forces to move the nest as a mechanical pendulum. This vibratory behaviour may support the colony-intrinsic information hypothesis herein that the mechanical vibrations of the comb provoked by shimmering do have the potential to facilitate immediate communication of the momentary defensive state of the honeybee nest to

  11. Reproductive ecology of American Oystercatchers nesting on shell rakes

    Science.gov (United States)

    Jodice, Patrick G.; Thibault, Janet M.; Collins, S.A.; Spinks, Mark D.; Sanders, Felicia J.

    2014-01-01

    Degradation of nesting habitat for coastal birds has led to the use of nontraditional nesting habitat. The American Oystercatcher (Haematopus palliatus) is listed as a "Species of High Concern'' by the U. S. Shorebird Conservation Plan and is declining in the southern portion of its U. S. breeding range, where ~ 50% of breeding oystercatchers nest on shell substrate instead of beachfront habitat. We measured daily survival rates during incubation and chick rearing in shell rake habitats over five breeding seasons in the Cape Romain region of South Carolina, USA. Of 354 nesting attempts monitored, 16.1% hatched at least one egg. During incubation, daily survival rate was 0.938, corresponding to 22.8% success to hatching (nest success). For broods, daily survival was 0.991, or 74.0% success from hatching to fledging. Productivity in the Cape Romain region is primarily being lost during the incubation phase, when nests are exposed to overwash and predation. Mobile chicks may, however, be able to avoid flood events or predators by relocating to higher or more protected portions of a shell rake. Based on comparative data for American Oystercatchers from elsewhere in their range, it does not appear that shell rakes in the Cape Romain region are inferior breeding habitat. Our data suggest that conservation actions targeting nest and chick loss from flooding and predation have the greatest opportunity to enhance reproductive success in this core breeding area, and that an assessment of the availability, structure, avian use, and protection status of shell rakes is warranted.

  12. Is it safe to nest near conspicuous neighbours? Spatial patterns in predation risk associated with the density of American Golden-Plover nests

    Directory of Open Access Journals (Sweden)

    Marie-Andrée Giroux

    2016-08-01

    Full Text Available Predation is one of the main factors explaining nesting mortality in most bird species. Birds can avoid nest predation or reduce predation pressure by breeding at higher latitude, showing anti-predator behaviour, selecting nest sites protected from predators, and nesting in association with protective species. American Golden-Plovers (Pluvialis dominica defend their territory by using various warning and distraction behaviours displayed at varying levels of intensity (hereafter “conspicuous behaviour”, as well as more aggressive behaviours such as aerial attacks, but only in some populations. Such antipredator behaviour has the potential to repel predators and thus benefit the neighbouring nests by decreasing their predation risk. Yet, conspicuous behaviour could also attract predators by signalling the presence of a nest. To test for the existence of a protective effect associated with the conspicuous antipredator behaviour of American Golden-Plovers, we studied the influence of proximity to plover nests on predation risk of artificial nests on Igloolik Island (Nunavut, Canada in July 2014. We predicted that the predation risk of artificial nests would decrease with proximity to and density of plover nests. We monitored 18 plover nests and set 35 artificial nests at 30, 50, 100, 200, and 500 m from seven of those plover nests. We found that the predation risk of artificial nests increases with the density of active plover nests. We also found a significant negative effect of the distance to the nearest active protector nest on predation risk of artificial nests. Understanding how the composition and structure of shorebird communities generate spatial patterns in predation risks represents a key step to better understand the importance of these species of conservation concern in tundra food webs.

  13. Variation in clutch size in relation to nest size in birds

    NARCIS (Netherlands)

    Møller, Anders P.; Adriaensen, Frank; Artemyev, Alexandr; Bańbura, Jerzy; Barba, Emilio; Biard, Clotilde; Blondel, Jacques; Bouslama, Zihad; Bouvier, Jean-Charles; Camprodon, Jordi; Cecere, Francesco; Charmantier, Anne; Charter, Motti; Cichoń, Mariusz; Cusimano, Camillo; Czeszczewik, Dorota; Demeyrier, Virginie; Doligez, Blandine; Doutrelant, Claire; Dubiec, Anna; Eens, Marcel; Eeva, Tapio; Faivre, Bruno; Ferns, Peter N.; Forsman, Jukka T.; García-Del-Rey, Eduardo; Goldshtein, Aya; Goodenough, Anne E.; Gosler, Andrew G.; Góźdź, Iga; Grégoire, Arnaud; Gustafsson, Lars; Hartley, Ian R.; Heeb, Philipp; Hinsley, Shelley A.; Isenmann, Paul; Jacob, Staffan; Järvinen, Antero; Juškaitis, Rimvydas; Korpimäki, Erkki; Krams, Indrikis; Laaksonen, Toni; Leclercq, Bernard; Lehikoinen, Esa; Loukola, Olli; Lundberg, Arne; Mainwaring, Mark C.; Mänd, Raivo; Massa, Bruno; Mazgajski, Tomasz D.; Merino, Santiago; Mitrus, Cezary; Mönkkönen, Mikko; Morales-Fernaz, Judith; Morin, Xavier; Nager, Ruedi G.; Nilsson, Jan-Åke; Nilsson, Sven G.; Norte, Ana C.; Orell, Markku; Perret, Philippe; Pimentel, Carla S.; Pinxten, Rianne; Priedniece, Ilze; Quidoz, Marie-Claude; Remeš, Vladimir; Richner, Heinz; Robles, Hugo; Rytkönen, Seppo; Senar, Juan Carlos; Seppänen, Janne T.; da Silva, Luís P.; Slagsvold, Tore; Solonen, Tapio; Sorace, Alberto; Stenning, Martyn J.; Török, János; Tryjanowski, Piotr; van Noordwijk, Arie J.; von Numers, Mikael; Walankiewicz, Wiesław; Lambrechts, Marcel M.

    2014-01-01

    Nests are structures built to support and protect eggs and/or offspring from predators, parasites, and adverse weather conditions. Nests are mainly constructed prior to egg laying, meaning that parent birds must make decisions about nest site choice and nest building behavior before the start of

  14. Predicting nest success from habitat features in aspen forests of the central Rocky Mountains

    Science.gov (United States)

    Heather M. Struempf; Deborah M. Finch; Gregory Hayward; Stanley Anderson

    2001-01-01

    We collected nesting data on bird use of aspen stands in the Routt and Medicine Bow National Forests between 1987 and 1989. We found active nest sites of 28 species of small nongame birds on nine study plots in undisturbed aspen forests. We compared logistic regression models predicting nest success (at least one nestling) from nest-site or stand-level habitat...

  15. Male Rock Sparrow (Petronia petronia) Nest Defence Correlates with Female Ornament Size

    DEFF Research Database (Denmark)

    Griggio, Matteo; Matessi, Giuliano; Pilastro, Andrea

    2003-01-01

    We investigated the relationship between male nest defence and female breast patch size in an alpine population of rock sparrow (Petronia petronia) in northern Italy. We presented a mounted weasel (Mustela nivalis), a common nest predator, to 28 pairs breeding in nest boxes, with 12-13-d-old nest...

  16. Breeding phenology of birds: mechanisms underlying seasonal declines in the risk of nest predation.

    Directory of Open Access Journals (Sweden)

    Kathi L Borgmann

    Full Text Available Seasonal declines in avian clutch size are well documented, but seasonal variation in other reproductive parameters has received less attention. For example, the probability of complete brood mortality typically explains much of the variation in reproductive success and often varies seasonally, but we know little about the underlying cause of that variation. This oversight is surprising given that nest predation influences many other life-history traits and varies throughout the breeding season in many songbirds. To determine the underlying causes of observed seasonal decreases in risk of nest predation, we modeled nest predation of Dusky Flycatchers (Empidonax oberholseri in northern California as a function of foliage phenology, energetic demand, developmental stage, conspecific nest density, food availability for nest predators, and nest predator abundance. Seasonal variation in the risk of nest predation was not associated with seasonal changes in energetic demand, conspecific nest density, or predator abundance. Instead, seasonal variation in the risk of nest predation was associated with foliage density (early, but not late, in the breeding season and seasonal changes in food available to nest predators. Supplemental food provided to nest predators resulted in a numerical response by nest predators, increasing the risk of nest predation at nests that were near supplemental feeders. Our results suggest that seasonal changes in foliage density and factors associated with changes in food availability for nest predators are important drivers of temporal patterns in risk of avian nest predation.

  17. Assessing nest-building behavior of mice using a 3D depth camera.

    Science.gov (United States)

    Okayama, Tsuyoshi; Goto, Tatsuhiko; Toyoda, Atsushi

    2015-08-15

    We developed a novel method to evaluate the nest-building behavior of mice using an inexpensive depth camera. The depth camera clearly captured nest-building behavior. Using three-dimensional information from the depth camera, we obtained objective features for assessing nest-building behavior, including "volume," "radius," and "mean height". The "volume" represents the change in volume of the nesting material, a pressed cotton square that a mouse shreds and untangles in order to build its nest. During the nest-building process, the total volume of cotton fragments is increased. The "radius" refers to the radius of the circle enclosing the fragments of cotton. It describes the extent of nesting material dispersion. The "radius" averaged approximately 60mm when a nest was built. The "mean height" represents the change in the mean height of objects. If the nest walls were high, the "mean height" was also high. These features provided us with useful information for assessment of nest-building behavior, similar to conventional methods for the assessment of nest building. However, using the novel method, we found that JF1 mice built nests with higher walls than B6 mice, and B6 mice built nests faster than JF1 mice. Thus, our novel method can evaluate the differences in nest-building behavior that cannot be detected or quantified by conventional methods. In future studies, we will evaluate nest-building behaviors of genetically modified, as well as several inbred, strains of mice, with several nesting materials.

  18. Radiation controlling reversible window

    Energy Technology Data Exchange (ETDEWEB)

    Gell, H.A. Jr.

    1980-01-01

    A coated glass glazing system is presented including a transparent glass substrate having one surface coated with a radiation absorptive film which is overcoated with a radiation reflective film by a technique which renders the radiation reflective film radiation absorptive at the surface contracting the radiating absorptive film. The coated glass system is used as glazing for storm windows which are adapted to be reversible so that the radiation reflective surface may be exposed to the outside of the dwelling during the warm seasons to prevent excessive solar radiation from entering a dwelling and reversed during cold seasons to absorb solar radiation and utilize it to aid in keeping the dwelling interior warm.

  19. Correlates of nest-defense behavior of common terns

    Science.gov (United States)

    Erwin, R.M.

    1988-01-01

    Nest-defense behavior was studied at seven Common Tern (Sterna hirundo) colonies in southern coastal New Jersey during June and July 1981. Data were collected weekly on numbers of adults, nests, eggs, and young in relation to the frequency and intensity of dive attacks on a human intruder by nesting terns. I explored the relationships between attack behavior and colony size/density, seasonality, and brood survival. The results provide little support for social facilitation since neither colony size (range 30-250 nests) nor density was related to mean attack frequency; however, in larger colonies, fewer birds participated in dive attacks. Although the intensity of attacks was strongly seasonal, patterns were very different among colonies and peak attack rates did not always coincide with peak hatching periods. Defense levels declined late in the season in most colonies regardless of whether brood survival was high or low. Colonies with individuals that attacked early in the season had higher overall nesting success than in colonies where individuals showed little early season aggression.

  20. Commitments to aggression and nest sites in male Betta splendens.

    Science.gov (United States)

    Bronstein, P M

    1981-06-01

    Male Siamese fighting fish construct nests that are relatively isolated from conspecific males. Following nest construction, the presence of a male opponent elicits (a) nest fixation, (b) further nest building, and (c) Betta's agonistic sequence, i.e., attacks alternating with flight movements, along with gill displays occurring near the opponent. The form of a male-male encounter depends upon the distance between a resident's nest and the opponent as well as upon the individual differences in combatants' tolerance for the presence of a conspecific nearby. Also, the intensity of aggression early in an encounter is positively correlated with the intensity of subsequent fighting. Male Bettas appear to compete for space through the use of aggressive behavior and to coordinate their fighting activities by means of visual signals. An incentive model of visual communication is proposed in which visual cues emanating from a displaying male opponent elicit attack with an intensity that is directly proportional to the persistence of the opponent and inversely proportional to the distance between fish.

  1. Hydrodynamic modeling of Singapore's coastal waters: Nesting and model accuracy

    Science.gov (United States)

    Hasan, G. M. Jahid; van Maren, Dirk Sebastiaan; Ooi, Seng Keat

    2016-01-01

    The tidal variation in Singapore's coastal waters is influenced by large-scale, complex tidal dynamics (by interaction of the Indian Ocean and the South China Sea) as well as monsoon-driven low frequency variations, requiring a model with large spatial coverage. Close to the shores, the complex topography, influenced by headlands and small islands, requires a high resolution model to simulate tidal dynamics. This can be achieved through direct nesting or multi-scale nesting, involving multiple model grids. In this paper, we investigate the effect of grid resolution and multi-scale nesting on the tidal dynamics in Singapore's coastal waters, by comparing model results with observations using different statistical techniques. The results reveal that the intermediate-scale model is generally sufficiently accurate (equal to or better than the most refined model), but also that the most refined model is only more accurate when nested in the intermediate scale model (requiring multi-scale nesting). This latter is the result of the complex tidal dynamics around Singapore, where the dominantly diurnal tidal currents are decoupled from the semi-diurnal water level variations. Furthermore, different techniques to quantify model accuracy (harmonic analysis, basic statistics and more complex statistics) are inconsistent in determining which model is more accurate.

  2. Does habitat fragmentation influence nest predation in the shortgrass prairie?

    Science.gov (United States)

    Howard, M.N.; Skagen, S.K.; Kennedy, P.L.

    2001-01-01

    We examined the effects of habitat fragmentation and vegetation structure of shortgrass prairie and Conservation Reserve Program (CRP) lands on predation rates of artificial and natural nests in northeastern Colorado. The CRP provides federal payments to landowners to take highly erodible cropland out of agricultural production. In our study area, CRP lands have been reseeded primarily with non-native grasses, and this vegetation is taller than native shortgrass prairie. We measured three indices of habitat fragmentation (patch size, degree of matrix fragmentation, and distance from edge), none of which influenced mortality rates of artificial or natural nests. Vegetation structure did influence predation rates of artificial nests; daily mortality decreased significantly with increasing vegetation height. Vegetation structure did not influence predation rates of natural nests. CRP lands and shortgrass sites did not differ with respect to mortality rates of artificial nests. Our study area is only moderately fragmented; 62% of the study area is occupied by native grassland. We conclude that the extent of habitat fragmentation in our study area does not result in increased predation in remaining patches of shortgrass prairie habitat.

  3. Homing to nest baskets by wild female mallards

    Science.gov (United States)

    Doty, H.A.; Lee, F.B.

    1974-01-01

    A high rate of homing to nest baskets by adult female mallards (Anas platyrhynchos) was observed in prairie potholes of North Dakota. One hundred and thirteen female mallards were caught on nest baskets, banded, and marked with nasal saddles. Forty-six percent homed at least once to nest baskets in the marshes where they were previously captured. Two-thirds of the returnees were observed in the same baskets where they had been caught. The observed rate of homing by previously successful nesters (52 percent) was significantly (P old ducklings that hatched in nest baskets were recaptured as nesting adults in baskets. Five of these hens returned to their natal marshes, and two others were found within 2 km of their natal marshes. Band recovery data indicated that 91 percent of the hunting mortality occurred within 10 km of the banding locations. Information on estimated rate of annual survival and the observed rate of homing suggests that nearly all surviving marked adults returned to within 10 km of the marshes where they were banded.

  4. Sequential Polarity-Reversing Circuit

    Science.gov (United States)

    Labaw, Clayton C.

    1994-01-01

    Proposed circuit reverses polarity of electric power supplied to bidirectional dc motor, reversible electro-mechanical actuator, or other device operating in direction depending on polarity. Circuit reverses polarity each time power turned on, without need for additional polarity-reversing or direction signals and circuitry to process them.

  5. Lifespan analyses of forest raptor nests: patterns of creation, persistence and reuse.

    Science.gov (United States)

    Jiménez-Franco, María V; Martínez, José E; Calvo, José F

    2014-01-01

    Structural elements for breeding such as nests are key resources for the conservation of bird populations. This is especially true when structural elements require a specific and restricted habitat, or if the construction of nests is costly in time and energy. The availability of nesting-platforms is influenced by nest creation and persistence. In a Mediterranean forest in southeastern Spain, nesting-platforms are the only structural element for three forest-dwelling raptor species: booted eagle Aquila pennata, common buzzard Buteo buteo and northern goshawk Accipiter gentilis. From 1998 to 2013, we tracked the fate of 157 nesting-platforms built and reused by these species with the aim of determining the rates of creation and destruction of nesting-platforms, estimating nest persistence by applying two survival analyses, describing the pattern of nest reuse and testing the effects of nest use on breeding success. Nest creation and destruction rates were low (0.14 and 0.05, respectively). Using Kaplan Meier survival estimates and Cox proportional-hazards regression models we found that median nest longevity was 12 years and that this was not significantly affected by nest characteristics, nest-tree dimensions, nest-builder species, or frequency of use of the platform. We also estimated a transition matrix, considering the different stages of nest occupation (vacant or occupied by one of the focal species), to obtain the fundamental matrix and the average life expectancies of nests, which varied from 17.9 to 19.7 years. Eighty six percent of nests were used in at least one breeding attempt, 67.5% were reused and 17.8% were successively occupied by at least two of the study species. The frequency of nest use had no significant effects on the breeding success of any species. We conclude that nesting-platforms constitute an important resource for forest raptors and that their longevity is sufficiently high to allow their reuse in multiple breeding attempts.

  6. Exploring Multi-Modal Distributions with Nested Sampling

    CERN Document Server

    Feroz, F

    2013-01-01

    In performing a Bayesian analysis, two difficult problems often emerge. First, in estimating the parameters of some model for the data, the resulting posterior distribution may be multi-modal or exhibit pronounced (curving) degeneracies. Secondly, in selecting between a set of competing models, calculation of the Bayesian evidence for each model is computationally expensive using existing methods such as thermodynamic integration. Nested Sampling is a Monte Carlo method targeted at the efficient calculation of the evidence, but also produces posterior inferences as a by-product and therefore provides means to carry out parameter estimation as well as model selection. The main challenge in implementing Nested Sampling is to sample from a constrained probability distribution. One possible solution to this problem is provided by the Galilean Monte Carlo (GMC) algorithm. We show results of applying Nested Sampling with GMC to some problems which have proven very difficult for standard Markov Chain Monte Carlo (MC...

  7. Characterising equilibrium logic and nested logic programs: Reductions and complexity

    CERN Document Server

    Pearce, David; Woltran, Stefan

    2009-01-01

    Equilibrium logic is an approach to nonmonotonic reasoning that extends the stable-model and answer-set semantics for logic programs. In particular, it includes the general case of nested logic programs, where arbitrary Boolean combinations are permitted in heads and bodies of rules, as special kinds of theories. In this paper, we present polynomial reductions of the main reasoning tasks associated with equilibrium logic and nested logic programs into quantified propositional logic, an extension of classical propositional logic where quantifications over atomic formulas are permitted. We provide reductions not only for decision problems, but also for the central semantical concepts of equilibrium logic and nested logic programs. In particular, our encodings map a given decision problem into some formula such that the latter is valid precisely in case the former holds. The basic tasks we deal with here are the consistency problem, brave reasoning, and skeptical reasoning. Additionally, we also provide encoding...

  8. Nest architecture shapes the collective behaviour of harvester ants.

    Science.gov (United States)

    Pinter-Wollman, Noa

    2015-10-01

    Structures influence how individuals interact and, therefore, shape the collective behaviours that emerge from these interactions. Here I show that the structure of a nest influences the collective behaviour of harvester ant colonies. Using network analysis, I quantify nest architecture and find that as chamber connectivity and redundancy of connections among chambers increase, so does a colony's speed of recruitment to food. Interestingly, the volume of the chambers did not influence speed of recruitment, suggesting that the spatial organization of a nest has a greater impact on collective behaviour than the number of workers it can hold. Thus, by changing spatial constraints on social interactions organisms can modify their behaviour and impact their fitness.

  9. Welfare indicators in laying hens in relation to nest exclusion

    DEFF Research Database (Denmark)

    Alm, M; Tauson, R; Holm, L

    2016-01-01

    . The assessed indicators were: corticosterone metabolites in droppings (FCM), corticosterone concentration in yolk, corticosterone concentration in plasma, irregularities of eggshells, heterophil to lymphocyte (H:L) ratio, tonic immobility duration, and feather cover. Behavioral observations showed...... that the birds had a clear preference for using the secluded nest sites, confirming that they were likely to perceive nest exclusion as an undesirable experience. Further, elevated levels of FCM in droppings, yolk corticosterone concentrations, H:L ratios and irregular eggshells were detected in both nest...... between FCM in droppings and eggshell irregularities, also supporting the use of eggshell irregularities as a potential non-invasive welfare indicator. However, the pattern of the stress response varied between indicators and correlations were generally few and inconsistent, highlighting the complexity...

  10. Time reversal communication system

    Science.gov (United States)

    Candy, James V.; Meyer, Alan W.

    2008-12-02

    A system of transmitting a signal through a channel medium comprises digitizing the signal, time-reversing the digitized signal, and transmitting the signal through the channel medium. The channel medium may be air, earth, water, tissue, metal, and/or non-metal.

  11. Engineering Encounters: Reverse Engineering

    Science.gov (United States)

    McGowan, Veronica Cassone; Ventura, Marcia; Bell, Philip

    2017-01-01

    This column presents ideas and techniques to enhance your science teaching. This month's issue shares information on how students' everyday experiences can support science learning through engineering design. In this article, the authors outline a reverse-engineering model of instruction and describe one example of how it looked in our fifth-grade…

  12. Reverse Coherent Information

    Science.gov (United States)

    García-Patrón, Raúl; Pirandola, Stefano; Lloyd, Seth; Shapiro, Jeffrey H.

    2009-05-01

    In this Letter we define a family of entanglement distribution protocols assisted by feedback classical communication that gives an operational interpretation to reverse coherent information, i.e., the symmetric counterpart of the well-known coherent information. This leads to the definition of a new entanglement distribution capacity that exceeds the unassisted capacity for some interesting channels.

  13. Reversed extension flow

    DEFF Research Database (Denmark)

    Nielsen, Jens Kromann; Rasmussen, Henrik K.

    2008-01-01

    Afilament stretching rheometer (FSR) was used for measuring the start-up of uni-axial elongational flow followed by reversed bi-axial flow, both with a constant elongational rate. A narrow molecular mass distribution linear polystyrene with a molecular weight of 145 kg / mole wis subjected to the...

  14. REVERSE SUPPLY CHAIN

    Directory of Open Access Journals (Sweden)

    Tomasz DOMAGAŁA

    2013-10-01

    Full Text Available The paper focuses on the presentation of the reverse supply chain, of which the role in the modern business grows along with the increasing number of environmental regulations and possibilities of reducing an operating cost. The paper also describes main problems in developing the profitable chain and possibilities to take an action in order to overcome them.

  15. On reverse hypercontractivity

    CERN Document Server

    Mossel, Elchanan; Sen, Arnab

    2011-01-01

    We study the notion of reverse hypercontractivity. We show that reverse hypercontractive inequalities are implied by standard hypercontractive inequalities as well as by the modified log-Sobolev inequality. Our proof is based on a new comparison lemma for Dirichlet forms and an extension of the Strook-Varapolos inequality. A consequence of our analysis is that {\\em all} simple operators $L=Id-\\E$ as well as their tensors satisfy uniform reverse hypercontractive inequalities. That is, for all $qreverse hypercontractive inequalities established here imply new mixing and isoperimetric results for short random walks in product spaces, for certain card-shufflings, for Glauber dynamics in high-temperat...

  16. Reversing Discrimination: A Perspective

    Science.gov (United States)

    Pati, Gopal; Reilly, Charles W.

    1977-01-01

    Examines the debate over affirmative action and reverse discrimination, and discusses how and why the present dilemma has developed. Suggests that organizations can best address the problem through an honest, in-depth analysis of their organizational structure and management practices. (JG)

  17. Factors affecting detection of burrowing owl nests during standardized surveys

    Science.gov (United States)

    Conway, C.J.; Garcia, V.; Smith, M.D.; Hughes, K.

    2008-01-01

    Identifying causes of declines and evaluating effects of management practices on persistence of local populations of burrowing owls (Athene cunicularia) requires accurate estimates of abundance and population trends. Moreover, regulatory agencies in the United States and Canada typically require surveys to detect nest burrows prior to approving developments or other activities in areas that are potentially suitable for nesting burrowing owls. In general, guidelines on timing of surveys have been lacking and surveys have been conducted at different times of day and in different stages of the nesting cycle. We used logistic regression to evaluate 7 factors that could potentially affect probability of a surveyor detecting a burrowing owl nest. We conducted 1,444 detection trials at 323 burrowing owl nests within 3 study areas in Washington and Wyoming, USA, between February and August 2000-2002. Detection probability was highest during the nestling period and increased with ambient temperature. The other 5 factors that we examined (i.e., study area, time of day, timing within the breeding season, wind speed, % cloud cover) interacted with another factor to influence detection probability. Use of call-broadcast surveys increased detection probability, even during daylight hours when we detected >95% of owls visually. Optimal timing of surveys will vary due to differences in breeding phenology and differences in nesting behavior across populations. Nevertheless, we recommend ???3 surveys per year: one that coincides with the laying and incubation period, another that coincides with the early nestling period, and a third that coincides with the late nestling period. In northern latitudes, surveys can be conducted throughout the day.

  18. Fleas (Siphonaptera) in the Nests of Dormice (Gliridae: Rodentia) in Lithuania.

    Science.gov (United States)

    Lipatova, I; Stanko, M; Paulauskas, A; Spakovaite, S; Gedminas, V

    2015-05-01

    Negative effects of flea (Siphonaptera) parasitism on the host may be expressed in different ways. The aim of this study was to assess distribution of the flea fauna in nests of dormice in Lithuania. Nests of Glis glis (L.), Dryomys nitedula (Pallas), and Muscardinus avellanarius (L.) were collected from nest boxes in 2012 and 2013. Fleas were collected from nests in the laboratory and put into plastic tubes with 70% ethanol. Flea species were identified using morphological keys. From 400 nest boxes, 112 nests of dormice were collected from eight sites from mixed forests of central Lithuania. Twenty-three nests of G. glis were collected from nest boxes, with 16 of them containing 286 fleas belonging to four species: Ceratophyllus sciurorum (Schrank) (259), C. gallinae (Schrank) (23), Hystrichopsylla talpae (Curtis) (3), and Megabothris turbidus (Rothschild) (1). Fourteen nests of M. avellanarius were collected from nest boxes, 4 of which contained 224 fleas belonging to two species: C. sciurorum (221) and C. gallinae (3). Twenty-four nests of D. nitedula were collected from nest boxes, including 17 containing 207 fleas belonging to two species: C. sciurorum (205) and C. gallinae (2). Fifty-one nests of undetermined dormice species also were collected from nest boxes, 12 of them contained 395 fleas belonging to three species: C. sciurorum (374), Ctenophthalmus agyrtes (Heller) (19), and Ctenophthalmus assimilis (Taschenberg) (2). C. sciurorum was a predominant species in the nests of dormice. The occurrence of C. gallinae was documented in Lithuania for the first time.

  19. Coping with shifting nest predation refuges by European reed Warblers Acrocephalus scirpaceus.

    Directory of Open Access Journals (Sweden)

    Lucyna Halupka

    Full Text Available Predation, the most important source of nest mortality in altricial birds, has been a subject of numerous studies during past decades. However, the temporal dynamics between changing predation pressures and parental responses remain poorly understood. We analysed characteristics of 524 nests of European reed warblers monitored during six consecutive breeding seasons in the same area, and found some support for the shifting nest predation refuge hypothesis. Nest site characteristics were correlated with nest fate, but a nest with the same nest-site attributes could be relatively safe in one season and vulnerable to predation in another. Thus nest predation refuges were ephemeral and there was no between-season consistency in nest predation patterns. Reed warblers that lost their first nests in a given season did not disperse farther for the subsequent reproductive attempt, compared to successful individuals, but they introduced more changes to their second nest sites. In subsequent nests, predation risk remained constant for birds that changed nest-site characteristics, but increased for those that did not. At the between-season temporal scale, individual birds did not perform better with age in terms of reducing nest predation risk. We conclude that the experience acquired in previous years may not be useful, given that nest predation refuges are not stable.

  20. Pseudoxylaria as stowaway of the fungus-growing termite nest:

    DEFF Research Database (Denmark)

    Visser, Anna A.; Kooij, Pepijn Wilhelmus; Debets, Alfons J. M.

    2011-01-01

    Though inconspicuous in healthy nests, Pseudoxylaria species are almost always present and overgrow deteriorating fungus-growing termite gardens. Whether these fungi are detrimental to the fungus-garden, benign, or even beneficial is unclear. We hypothesize that Pseudoxylaria is a stowaway...... that practices a sit-and-wait strategy to survive in the termite nest. Using isolates from three different termite genera to test our hypothesis, we compared Pseudoxylaria’s growth on 40 carbon sources with that of Termitomyces and tested its interaction with Termitomyces. The C-source use of both fungi largely...

  1. Imperfect nesting and transport properties in unconventional density waves

    Science.gov (United States)

    Dóra, Balázs; Maki, Kazumi; Virosztek, Attila

    2002-10-01

    We consider the effect of imperfect nesting in quasi-one-dimensional unconventional density waves (DW's). The phase diagram is very close to those in a conventional DW's. The linear and non-linear aspects of the electric conductivity are discussed. At T=0 the frequency dependent electric conductivity develops a small dip at low frequencies. The threshold electric field depends strongly on the imperfect nesting parameter, allowing us to describe very well the measured threshold electric field in the low temperature phase of the quasi-two-dimensional organic conductor, α-(BEDT-TTF)2KHg(SCN)4.

  2. Efficient use of iterative solvers in nested topology optimization

    DEFF Research Database (Denmark)

    Amir, Oded; Stolpe, Mathias; Sigmund, Ole

    2010-01-01

    In the nested approach to structural optimization, most of the computational effort is invested in the solution of the analysis equations. In this study, it is suggested to reduce this computational cost by using an approximation to the solution of the analysis problem, generated by a Krylov...... subspace iterative solver. By choosing convergence criteria for the iterative solver that are strongly related to the optimization objective and to the design sensitivities, it is possible to terminate the iterative solution of the nested equations earlier compared to traditional convergence measures...

  3. Don't Mess with the NEST

    Energy Technology Data Exchange (ETDEWEB)

    Larson, M

    2012-03-15

    NEST stands for Nuclear Emergency Support Team. The NEST Mission Statement as first established: (1) Conduct, direct, coordinate search and recovery operations for nuclear material, weapons or devices; and (2) Assist in identification and deactivation of Improvised Nuclear Devices (INDs) and Radiological Dispersal Devices (RDDs). Then in 1980 a very sophisticated improvised explosive device was found at Harvey's Casino at Lake Tahoe, Nevada. The FBI and Bomb Squads were unprepared and it detonated. As a result the additional phrase 'and Sophisticated Improvised Explosive Devices (SIEDs)' was added to the Mission Statement.

  4. Detection of cancer cells in peripheral blood with nested RT-PCR and itssignificance in patients with gastric carcinomas

    Institute of Scientific and Technical Information of China (English)

    Jia Zeng Xia; Hao Ran Yin; Zheng Gang Zhu; Min yan

    2000-01-01

    AIM To study the detection of micrometastasis in peripheral blood of patients with gastric carcinomas andits clinical significance.METHODS A cytokeratin 19 (CK19)-specific nested reverse transcriptase-polimerase chain reaction (RT-PCR) assay was developed to detect CK19 expressing cancer cells, the sensitivity was determined by serialdilution method using CK19 expressing gastric cancer cells, the specificity was assessed by examining 12negative controls and 12 positive controls. Then pre-operative peripheral blood from 42 patients with gastriccancer was detected and the relationship between positive results and biological behavior was studied.RESULTS CK19mRNA was expressed in all the 12 gastric cancer tissues but not in peripheral blood from12 healthy individuals;sensitivity of nested RT-PCR amplification for CK19mRNA was confirmed to be 1/106 by serial dilution method using human gastric cancer line SGC-7901; micrometastases in pre-operativeperipheral blood were detected in 13 (30,9%) patients with gastric carcinomas, the frequency ofmicrometastasis in peripheral blood was significantly correlated with tumor size,depth of invasion and TNMstage (x2 test, P<0.05).CONCLUSION Nested RT-PCR amplification for CK19mRNA is a sensitive and specific method for thedetection of micrometastases in peripheral blood in gastric cancer patients; pre-operative detection ofmicrometastasis in peripheral blood may be helpful in the prediction of tumor progression.

  5. The path to the nest of spiders The path to the nest of spiders

    Directory of Open Access Journals (Sweden)

    Eliane Luz Bayer

    2008-04-01

    Full Text Available Italo Calvino writes in his preface to The Path to the Nest of Spiders that the novel answers to the "ripeness of the time" since ht wrote it after wartime, a period when everyone had a tale to tell. He tells us that this is a story in which iobody is a hero and nobody has the class consciousness necessary to unify them in the struggle. Calvino acknowledges that it was difficult to conciliate his experiences with the postwar literary movement which he calls Neo-expresSionism, a term which, he thinks, describes better Italian Neo-realism. This is a book with a full realistic depictior of the incongruousness of the whole situation, showing rumen beings driven by loneliness, aggressiveness, unfulfilment and failure to meet, their nerves frayed by the War. It reveals human beings in their weaknesses, subjected to deterministic fates changing roles according to circumstance. Partisans shift to the Nazi side and inform on their f rmer allies and vice-versa, being later chased in revenge. The novel has as its setting Italy under Fascism and unde German occupation, the Italian people being divided betw en the fascists of the "Black Brigade" and the "Partisa4s" who belonged to the Resistance. Although this is a pOlitical book, it has universal appeal. At the same time that it livens up historical facts about the period, it moves our feelings. Calvino's book is about World War II as it is viewed and felt by a small outcast, Pin, who makes considerable efforts to be accepted and understood by adults. In his daily life Pinsuffers the consequences Of the war. His aggressive disposition reflects the environment which he has been brought up in: since he was born, his country has been at war. Besides that, his only sister is a whore, whom he hates and despises. Italo Calvino writes in his preface to The Path to the Nest of Spiders that the novel answers to the "ripeness of the time" since ht wrote it after wartime, a period when everyone had a tale to tell

  6. Reversible quantum cellular automata

    CERN Document Server

    Schumacher, B

    2004-01-01

    We define quantum cellular automata as infinite quantum lattice systems with discrete time dynamics, such that the time step commutes with lattice translations and has strictly finite propagation speed. In contrast to earlier definitions this allows us to give an explicit characterization of all local rules generating such automata. The same local rules also generate the global time step for automata with periodic boundary conditions. Our main structure theorem asserts that any quantum cellular automaton is structurally reversible, i.e., that it can be obtained by applying two blockwise unitary operations in a generalized Margolus partitioning scheme. This implies that, in contrast to the classical case, the inverse of a nearest neighbor quantum cellular automaton is again a nearest neighbor automaton. We present several construction methods for quantum cellular automata, based on unitaries commuting with their translates, on the quantization of (arbitrary) reversible classical cellular automata, on quantum c...

  7. Partial Reversible Gates(PRG) for Reversible BCD Arithmetic

    CERN Document Server

    Thapliyal, Himanshu; Bajpai, Rajnish; Sharma, Kamal K

    2007-01-01

    IEEE 754r is the ongoing revision to the IEEE 754 floating point standard and a major enhancement to the standard is the addition of decimal format. Furthermore, in the recent years reversible logic has emerged as a promising computing paradigm having its applications in low power CMOS, quantum computing, nanotechnology, and optical computing. The major goal in reversible logic is to minimize the number of reversible gates and garbage outputs. Thus, this paper proposes the novel concept of partial reversible gates that will satisfy the reversibility criteria for specific cases in BCD arithmetic. The partial reversible gate is proposed to minimize the number of reversible gates and garbage outputs, while designing the reversible BCD arithmetic circuits.

  8. A unique nest-protection strategy in a new species of spider wasp.

    Directory of Open Access Journals (Sweden)

    Michael Staab

    Full Text Available Hymenoptera show a great variation in reproductive potential and nesting behavior, from thousands of eggs in sawflies to just a dozen in nest-provisioning wasps. Reduction in reproductive potential in evolutionary derived Hymenoptera is often facilitated by advanced behavioral mechanisms and nesting strategies. Here we describe a surprising nesting behavior that was previously unknown in the entire animal kingdom: the use of a vestibular cell filled with dead ants in a new spider wasp (Hymenoptera: Pompilidae species collected with trap nests in South-East China. We scientifically describe the 'Bone-house Wasp' as Deuteragenia ossarium sp. nov., named after graveyard bone-houses or ossuaries. We show that D. ossarium nests are less vulnerable to natural enemies than nests of other sympatric trap-nesting wasps, suggesting an effective nest protection strategy, most likely by utilizing chemical cues emanating from the dead ants.

  9. Nesting Biology and Behavior of Euodynerus dantici (Rossi, 1790 (Hymenoptera: Vespidae: Eumeninae in Central Mongolia

    Directory of Open Access Journals (Sweden)

    Batchuluun Buyanjargal

    2015-12-01

    Full Text Available Nesting biology of Euodynerus dantici (Rossi, 1790 was studied in the Khugnu- Khaan Mountains of Khugnu-Tarna National Park, central Mongolia in 2014 using nest traps. Euodynerus dantici is univoltine in the study site, with one generation per growth season. Nest architecture and its structural parts were described in details. The inner cells of the nests were longer and contained a proportionately larger amount of food than the shorter outer cells. Females developed in inner cells and males developed in outer cells. Developmental stages of E. dantici is studied with details of pupation period. All basic behavioral elements of nesting females are described. A nest parasitoid, Chrysis ignita (Linnaeus, 1758 (Hymenoptera, Chrysididae was reared from E. dantici nests for the fi rst time. For provisioning, caterpillars of the family Noctuidae (Lepidoptera were hunted by females. Diversity in nest architecture is possibly a result of nest parasite pressure

  10. Multilevel Analysis Methods for Partially Nested Cluster Randomized Trials

    Science.gov (United States)

    Sanders, Elizabeth A.

    2011-01-01

    This paper explores multilevel modeling approaches for 2-group randomized experiments in which a treatment condition involving clusters of individuals is compared to a control condition involving only ungrouped individuals, otherwise known as partially nested cluster randomized designs (PNCRTs). Strategies for comparing groups from a PNCRT in the…

  11. Xylaria species associated with nests of Odontotermes formosanus in Taiwan.

    Science.gov (United States)

    Ju, Yu-Ming; Hsieh, Huei-Mei

    2007-01-01

    Nine species of Xylaria were collected in Taiwan from nests of Odontotermes formosanus, the only known macrotermitine termite in Taiwan. These include six newly described species, X. acuminatilongissima, X. atrodivaricata, X. brunneovinosa, X. griseosepiacea, X. intraflava and X. ochraceostroma, and three previously known species, X. cirrata, X. escharoidea and X. nigripes. We obtained cultures and ITS sequences from the nine species found in Taiwan and describe anamorphs for eight of them. Before the current study teleomorph-anamorph connections in the Xylaria species associated with termite nests have been established unequivocally in X. escharoidea only. Xylaria angulosa, X. fimbriata, X. kedahae, X. micrura, X. radicans, X. reinkingii and X. tolosa also are considered and annotated because they were reported to grow on ground and likely are associated with termite nests. Epitypifications are made for X. cirrata, X. escharoidea and X. nigripes. Xylaria sanchezii is considered a nomen dubium. Photographs are presented for most of the aforementioned species. A dichotomous key to 25 Xylaria species growing on termite nests or ground also is given.

  12. Multi-Core Nested Depth-First Search

    NARCIS (Netherlands)

    Laarman, Alfons; Langerak, Rom; Pol, van de Jaco; Weber, Michael; Wijs, Anton; Bultan, T.; Hsiung, P.-A.

    2011-01-01

    The LTL Model Checking problem is reducible to finding accepting cycles in a graph. The Nested Depth-First Search (NDFS) algorithm detects accepting cycles efficiently: on-the-fly, with linear-time complexity and negligible memory overhead. The only downside of the algorithm is that it relies on an

  13. Improved Multi-Core Nested Depth-First Search

    NARCIS (Netherlands)

    Evangelista, Sami; Laarman, Alfons; Petrucci, Laure; Pol, van de Jaco; Ramesh, S.

    2012-01-01

    This paper presents CNDFS, a tight integration of two earlier multi-core nested depth-first search (NDFS) algorithms for LTL model checking. CNDFS combines the different strengths and avoids some weaknesses of its predecessors. We compare CNDFS to an earlier ad-hoc combination of those two algorithm

  14. Repeatability in nest construction by male three-spined sticklebacks

    NARCIS (Netherlands)

    Rushbrook, B. J.; Dingemanse, N. J.; Barber, I.

    Structures built by animals may convey useful information about the builder that may be used by conspecifics in quality assessment. In fish, nest construction has been suggested to reflect qualities of individual builders, but little is known about how consistent individual differences are over

  15. Sea turtle nesting distributions and oceanographic constraints on hatchling migration.

    Science.gov (United States)

    Putman, Nathan F; Bane, John M; Lohmann, Kenneth J

    2010-12-07

    Patterns of abundance across a species's reproductive range are influenced by ecological and environmental factors that affect the survival of offspring. For marine animals whose offspring must migrate long distances, natural selection may favour reproduction in areas near ocean currents that facilitate migratory movements. Similarly, selection may act against the use of potential reproductive areas from which offspring have difficulty emigrating. As a first step towards investigating this conceptual framework, we analysed loggerhead sea turtle (Caretta caretta) nest abundance along the southeastern US coast as a function of distance to the Gulf Stream System (GSS), the ocean current to which hatchlings in this region migrate. Results indicate that nest density increases as distance to the GSS decreases. Distance to the GSS can account for at least 90 per cent of spatial variation in regional nest density. Even at smaller spatial scales, where local beach conditions presumably exert strong effects, at least 38 per cent of the variance is explained by distance from the GSS. These findings suggest that proximity to favourable ocean currents strongly influences sea turtle nesting distributions. Similar factors may influence patterns of abundance across the reproductive ranges of diverse marine animals, such as penguins, eels, salmon and seals.

  16. Nested structures approach for bulk 3D negative index materials

    DEFF Research Database (Denmark)

    Andryieuski, Andrei; Malureanu, Radu; Lavrinenko, Andrei

    2009-01-01

    We propose a generic conceptual idea to obtain bulk 3D negative index metamaterials, which exhibit isotropic properties. The design is based on the nested structures approach, when one element providing magnetic response is inserted into another design with negative dielectric constant. Both...

  17. Using Gesture to Teach Seneca in a Language Nest School

    Science.gov (United States)

    Borgia, Melissa Elayne

    2014-01-01

    Seneca elder Sandy Dowdy and her granddaughter Autumn Crouse direct a language nest school for children aged two to five years in a small longhouse-shaped building, "Ganöhsesge:kha:' Hë:nödeyë:sta'":, or the Faithkeepers School, on the Seneca Allegany Territory in upstate New York. They practice immersion teaching and use forms of…

  18. Behavior of greedy sparse representation algorithms on nested supports

    DEFF Research Database (Denmark)

    Mailhé, Boris; Sturm, Bob L.; Plumbley, Mark

    2013-01-01

    We study the links between recovery properties of Orthogonal Matching Pursuit (OMP) and the whole General MP class for sparse signals with nested supports, i.e., supports that share an inclusion relationship. In particular, we show that the support recovery optimality of those algorithms is not l...

  19. Nested Genetic Algorithm for Resolving Overlapped Spectral Bands

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A nested genetic algorithm, including genetic parameter level and genetic implemented level for peak parameters, was proposed and applied for resolving overlapped spectral bands. By the genetic parameter level, parameters of genetic algorithm were optimized; moreover, the number of overlapped peaks was determined simultaneously. Then parameters of individual peaks were computed with the genetic implemented level.

  20. NEST-SITE SELECTION IN THE CAPE SUGARBIRD We dedicate ...

    African Journals Online (AJOL)

    to fluctuations in wind-speed, an average value was determined for five .... where k is a constant (6,17 x 10-8) having units so that Hc is in cal em-I min-l (porter ...... predators constitute a major force limiting birds nesting on or near the ground.

  1. Urine Nested Polymerase Chain Reaction in Neonatal Septicemia.

    Science.gov (United States)

    Das, B K; Suri, Shipra; Nath, Gopal; Prasad, Rajniti

    2015-08-01

    This cross-sectional study was done to evaluate diagnostic efficacy of urine nested polymerase chain reaction (PCR) using broad-range 16SrDNA PCR-based amplification, followed by restriction analysis and sequencing in neonatal septicemia. The study included 50 babies; 48% had vaginal delivery, 46% were preterm, 20% had a history of prolonged rupture of membranes and 56% were low birth weight (≤2500 g). Clinical presentations were lethargy (96%), respiratory distress (80%) and bleeding diathesis (16%). Absolute neutrophil count <1800/mm(3) was observed in 60%, and positive C-reactive protein in 46%. Thirty neonates had positive blood culture, and Klebsiella pneumoniae (22%) was the predominant organism. Nested urine PCR was positive in 38 (76%) and detected bacterial DNA in 8 neonates with negative blood cultures. The sensitivity, specificity, positive predictive value, negative predictive value and accuracy of nested PCR were 100, 60, 78.9, 100 and 84%, respectively, compared with blood culture. Nested PCR can detect most bacteria in single assay and identify unusual and unexpected causal agents.

  2. Comparison of nest shapes and densities of two sympatric species ...

    African Journals Online (AJOL)

    Comparison of nest shapes and densities of two sympatric species of ... there are significant, though small, differences in height, diameter, number of caps, surface ... the addition of a first cap decreases the volume/surface ratio but a second or ...

  3. Improved Multi-Core Nested Depth-First Search

    NARCIS (Netherlands)

    Evangelista, Sami; Laarman, Alfons; Petrucci, Laure; van de Pol, Jan Cornelis; Ramesh, S.

    2012-01-01

    This paper presents CNDFS, a tight integration of two earlier multi-core nested depth-first search (NDFS) algorithms for LTL model checking. CNDFS combines the different strengths and avoids some weaknesses of its predecessors. We compare CNDFS to an earlier ad-hoc combination of those two

  4. Multi-Core Nested Depth-First Search

    NARCIS (Netherlands)

    Laarman, Alfons; Langerak, Romanus; van de Pol, Jan Cornelis; Weber, M.; Wijs, Anton; Bultan, T.; Hsiung, P.-A.

    2011-01-01

    The LTL Model Checking problem is reducible to finding accepting cycles in a graph. The Nested Depth-First Search (NDFS) algorithm detects accepting cycles efficiently: on-the-fly, with linear-time complexity and negligible memory overhead. The only downside of the algorithm is that it relies on an

  5. The Empty Nest Syndrome: Ways to Enhance Quality of Life

    Science.gov (United States)

    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…

  6. Unit 9 Bird Nesting Survey : Biological Summary Report : May 2015

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is the second year of the proposed 3 year survey project in Unit 9 of the Monte Vista NWR to look at breeding and nesting birds that use wet meadow/ wetland...

  7. Efficient use of iterative solvers in nested topology optimization

    DEFF Research Database (Denmark)

    Amir, Oded; Stolpe, Mathias; Sigmund, Ole

    2009-01-01

    by a Krylov subspace iterative solver. By choosing convergence criteria for the iterative solver that are strongly related to the optimization objective and to the design sensitivities, it is possible to terminate the iterative solution of the nested equations earlier compared to traditional convergence...

  8. Efficient Thread Labeling for Monitoring Programs with Nested Parallelism

    Science.gov (United States)

    Ha, Ok-Kyoon; Kim, Sun-Sook; Jun, Yong-Kee

    It is difficult and cumbersome to detect data races occurred in an execution of parallel programs. Any on-the-fly race detection techniques using Lamport's happened-before relation needs a thread labeling scheme for generating unique identifiers which maintain logical concurrency information for the parallel threads. NR labeling is an efficient thread labeling scheme for the fork-join program model with nested parallelism, because its efficiency depends only on the nesting depth for every fork and join operation. This paper presents an improved NR labeling, called e-NR labeling, in which every thread generates its label by inheriting the pointer to its ancestor list from the parent threads or by updating the pointer in a constant amount of time and space. This labeling is more efficient than the NR labeling, because its efficiency does not depend on the nesting depth for every fork and join operation. Some experiments were performed with OpenMP programs having nesting depths of three or four and maximum parallelisms varying from 10,000 to 1,000,000. The results show that e-NR is 5 times faster than NR labeling and 4.3 times faster than OS labeling in the average time for creating and maintaining the thread labels. In average space required for labeling, it is 3.5 times smaller than NR labeling and 3 times smaller than OS labeling.

  9. Reversible hysteresis loop tuning

    Science.gov (United States)

    Berger, A.; Binek, Ch.; Margulies, D. T.; Moser, A.; Fullerton, E. E.

    2006-02-01

    We utilize antiferromagnetically coupled bilayer structures to magnetically tune hysteresis loop properties. Key element of this approach is the non-overlapping switching field distribution of the two magnetic layers that make up the system: a hard magnetic CoPtCrB layer (HL) and a soft magnetic CoCr layer (SL). Both layers are coupled antiferromagnetically through an only 0.6-nm-thick Ru interlayer. The non-overlapping switching field distribution allows the measurement of magnetization reversal in the SL at low fields while keeping the magnetization state of the HL unperturbed. Applying an appropriate high field or high field sequence changes the magnetic state of the HL, which then influences the SL magnetization reversal due to the interlayer coupling. In this way, the position and shape of the SL hysteresis loop can be changed or tuned in a fully reversible and highly effective manner. Here, we study specifically how the SL hysteresis loop characteristics change as we move the HL through an entire high field hysteresis loop sequence.

  10. Nest success of snowy plovers (Charadrius nivosus) in the Southern high plains of Texas

    Science.gov (United States)

    Saalfeld, S.T.; Conway, Warren C.; Haukos, D.A.; Johnson, W.P.

    2011-01-01

    Snowy Plovers (Charadrius nivosus) nesting on edges of saline lakes within the Southern High Plains (SHP) of Texas are threatened by habitat degradation due to reduced artesian spring flow, making many saline lakes unsuitable for nesting and migrating shorebirds. Factors influencing nest success were evaluated, current nest success estimates in the SHP of Texas were compared to estimates obtained ten years prior, and causes and timing of nest failures determined. Overall, 215 nests were monitored from three saline lakes in 20082009, with nest success estimates from Program MARK ranging from 7-33% ( x??= 22%). The leading causes of nest failures were attributed to predation (40%) and weather (36%). Nest success was negatively influenced by number of plants within 707-cm 2 plot, positively influenced by percent surface water availability, and at one saline lake, negatively influenced by day during the nesting season (i.e., nest success declined later in the nesting season). When compared to estimates ten years prior (19981999), mean nest success has declined by 31%. If nesting Snowy Plovers continue to experience increased predation rates, decreased hydrological integrity, and habitat alterations, populations will continue to decline throughout this region.

  11. Artificial Cavities and Nest Site Selection by Puerto Rican Parrots: a Multiscale Assessment

    Directory of Open Access Journals (Sweden)

    Thomas H. White, Jr.

    2006-12-01

    Full Text Available We examined nest site selection by Puerto Rican Parrots, a secondary cavity nester, at several spatial scales using the nest entrance as the central focal point relative to 20 habitat and spatial variables. The Puerto Rican Parrot is unique in that, since 2001, all known nesting in the wild has occurred in artificial cavities, which also provided us with an opportunity to evaluate nest site selection without confounding effects of the actual nest cavity characteristics. Because of the data limitations imposed by the small population size of this critically endangered endemic species, we employed a distribution-free statistical simulation approach to assess site selection relative to characteristics of used and unused nesting sites. Nest sites selected by Puerto Rican Parrots were characterized by greater horizontal and vertical visibility from the nest entrance, greater density of mature sierra palms, and a more westerly and leeward orientation of nest entrances than unused sites. Our results suggest that nest site selection in this species is an adaptive response to predation pressure, to which the parrots respond by selecting nest sites offering advantages in predator detection and avoidance at all stages of the nesting cycle. We conclude that identifying and replicating the “nest gestalt” of successful nesting sites may facilitate conservation efforts for this and other endangered avian species.

  12. Nested-grid simulation of mercury over North America

    Directory of Open Access Journals (Sweden)

    Y. Zhang

    2012-01-01

    Full Text Available We have developed a new high-resolution (1/2° latitude by 2/3° longitude nested-grid mercury (Hg simulation over North America employing the GEOS-Chem global chemical transport model. Emissions, chemistry, deposition, and meteorology are self-consistent between the global and nested domains. Compared to the global model (4° latitude by 5° longitude, the nested model shows improved skill at capturing the high spatial and temporal variability of Hg wet deposition over North America observed by the Mercury Deposition Network (MDN in 2008–2009. The nested simulation resolves features such as land/ocean contrast and higher deposition due to orographic precipitation, and predicts more efficient convective rain scavenging of Hg over the southeast United States. However, the nested model overestimates Hg wet deposition over the Ohio River Valley region (ORV by 27%. We modify anthropogenic emission speciation profiles in the US EPA National Emission Inventory (NEI to account for the rapid in-plume reduction of reactive to elemental Hg (IPR simulation. This leads to a decrease in the model bias to +3% over the ORV region. Over the contiguous US, the correlation coefficient (r between MDN observations and our IPR simulation increases from 0.63 to 0.78. The IPR nested simulation generally reproduces the seasonal cycle in surface concentrations of speciated Hg from the Atmospheric Mercury Network (AMNet and Canadian Atmospheric Mercury Network (CAMNet. In the IPR simulation, annual mean reactive gaseous and particulate-bound Hg are within 80% and 10% of observations, respectively. In contrast, the simulation with unmodified anthropogenic Hg speciation profiles overestimates these observations by factors of 2 to 4. The nested model shows improved skill at capturing the horizontal variability of Hg observed over California during the ARCTAS aircraft campaign. We find that North American anthropogenic emissions account for 10–22% of Hg wet

  13. Reversible multi-head finite automata characterize reversible logarithmic space

    DEFF Research Database (Denmark)

    Axelsen, Holger Bock

    2012-01-01

    Deterministic and non-deterministic multi-head finite automata are known to characterize the deterministic and non- deterministic logarithmic space complexity classes, respectively. Recently, Morita introduced reversible multi-head finite automata (RMFAs), and posed the question of whether RMFAs...... characterize reversible logarithmic space as well. Here, we resolve the question affirmatively, by exhibiting a clean RMFA simulation of logarithmic space reversible Turing machines. Indirectly, this also proves that reversible and deterministic multi-head finite automata recognize the same languages....

  14. [Reverse Chaddock sign].

    Science.gov (United States)

    Tashiro, Kunio

    2011-08-01

    It is widely accepted that the Babinski reflex is the most well-known and important pathological reflex in clinical neurology. Among many other pathological reflexes that elicit an upgoing great toe, such as Chaddock, Oppenheim, Gordon, Schaefer, and Stransky, only the Chaddock reflex is said to be as sensitive as the Babinski reflex. The optimal receptive fields of the Babinski and Chaddock reflexes are the lateral plantar surface and the external inframalleolar area of the dorsum, respectively. It has been said that the Babinski reflex, obtained by stroking the sole, is by far the best and most reliable method of eliciting an upgoing great toe. However, the Chaddock reflex, the external malleolar sign, is also considered sensitive and reliable according to the literature and everyday neurological practice. The major problems in eliciting the Babinski reflex by stroking the lateral part of the sole are false positive or negative responses due to foot withdrawal, tonic foot response, or some equivocal movements. On the other hand, according to my clinical experience, the external inframalleolar area, which is the receptive field of the Chaddock reflex, is definitely suitable for eliciting the upgoing great toe. In fact, the newly proposed method to stimulate the dorsum of the foot from the medial to the lateral side, which I term the "reversed Chaddock method," is equally sensitive to demonstrate pyramidal tract involvement. With the "reversed Chaddock method", the receptive field of the Chaddock reflex may be postulated to be in the territory of the sural nerve, which could be supported by the better response obtained on stimulation of the postero-lateral calf than the anterior shin. With regard to the receptive fields of the Babinski and Chaddock reflexes, the first sacral dermatome (S1) is also considered a reflexogenous zone, but since the dermatome shows marked overlapping, the zones vary among individuals. As upgoing toe responses are consistently observed in

  15. Nest and brood attentiveness in female black ducks

    Science.gov (United States)

    Ringelman, J.K.; Longcore, J.R.; Owen, R.B.

    1982-01-01

    Incubation rhythms and brood attentiveness of radio-marked Black Ducks (Anas rubripes) were studied in southcentral Maine during 1977-1980. Recess duration and frequency differed between three females nesting near wetlands (x = 82 min, 2.3 recesses/day) and two nesting at upland sites(x = 183 min, I. I recesses/day), but incubation constancy was similar for all birds (x = 86.7%). A fourth wetland-nesting female apparently responded to the absence of down and concealing cover at the nest site by taking shorter and fewer recesses (x= 34 min, 1.0 recesses/day) than did other wetland-nesters with typical nests. Wetland-nesters took longer recesses with increasing air temperature and following long incubation sessions. After their ducklings were two weeks old, two brood-rearing females began leaving their broods to forage on nearby wetlands. Duration of rearing recess (x = 56 min) and total recess time (x = 94 min/day) were less during this mid-rearing stage than during the latter part of rearing (x = 265 min, 488 min/day). The two hen-brood bonds terminated at 43 and 48 days. We suggest that small endogenous nutrient reserves and the low density of invertebrate foods, typical of Black Duck breeding habitat, were critical factors affecting the evolution of Black Duck incubation behavior. Bouts of inattention during brood rearing may have also evolved in relation to food requirements; by foraging on wetlands away from their broods, females avoid competing with offspring for common food resources.

  16. Interacting effects of aromatic plants and female age on nest-dwelling ectoparasites and blood-sucking flies in avian nests.

    Science.gov (United States)

    Tomás, G; Merino, S; Martínez-de la Puente, J; Moreno, J; Morales, J; Lobato, E; Rivero-de Aguilar, J; Del Cerro, S

    2012-06-01

    Some avian species incorporate aromatic plants to their nests. The "nest protection hypothesis", which posits that volatile secondary compounds contained in these plants may have antiparasite properties, has not received full support. All previous tests of this hypothesis have only considered effects on nest-dwelling ectoparasites, but not on blood-sucking flies. The "drug hypothesis" posits that aromatic plants may stimulate nestling immune system, development, or condition. We tested these hypotheses experimentally in wild blue tits, Cyanistes caeruleus, a species that adds aromatic plants to their nests. We supplemented aromatic plants to half of a sample of nests, while adding grass to the other half of nests. We quantified abundance of two groups of blood-sucking flies (blackflies and biting midges) at two different stages of the reproductive period, and abundance of three nest-dwelling ectoparasites (fleas, mites, and blowflies). Experimental supplementation of aromatic plants reduced abundance of fleas only in nests of yearling females and not in nests of older females. Blackflies and biting midges were both more numerous in nests of yearling females than in nests of older females. Mass of aromatic plants added by females was negatively related with abundance of fleas in control nests but not in experimental nests supplied with aromatic plants. Mass of plants added by females was also positively related with abundance of blackflies during the nestling stage. Finally, aromatic plants did not affect nestling growth or immune responses. We conclude that several factors such as female experience and their ability to add plants to the nest interact to explain effects of aromatic plants on different parasites.

  17. Sunrise nest attendance and aggression by least Bell's vireos fail to deter cowbird parasitism

    Science.gov (United States)

    Sharp, Bryan L.; Kus, Barbara E.

    2004-01-01

    We video-recorded three, natural, brood-parasitism events by Brown-headed Cowbirds (Molothrus ater) at nests of Least Bell's Vireos (Vireo bellii pusillus). All instances occurred near dawn, during both egg-laying and incubation stages of the nesting cycle. In each case, an adult vireo was on the nest when the female cowbird arrived. Both members of each parasitized pair vigorously attacked the intruding cowbird, but in no encounter did a pair of vireos successfully defend its nest from parasitism. Thus, Least Bell's Vireos in our study were unable to prevent a female cowbird from parasitizing their nests once the cowbird had reached the nest.

  18. Determinants of abundance and effects of blood-sucking flying insects in the nest of a hole-nesting bird

    NARCIS (Netherlands)

    Tomás, G.; Merino, S.; Martínez-de la Puente, J.; Moreno, J.; Morales, J.; Lobato, E.

    2008-01-01

    Compared to non-flying nest-dwelling ectoparasites, the biology of most species of flying ectoparasites and its potential impact on avian hosts is poorly known and rarely, if ever, reported. In this study we explore for the first time the factors that may affect biting midge (Diptera:

  19. PCP-induced deficits in murine nest building activity: employment of an ethological rodent behavior to mimic negative-like symptoms of schizophrenia.

    Science.gov (United States)

    Pedersen, Christian Spang; Sørensen, Dorte Bratbo; Parachikova, Anna I; Plath, Niels

    2014-10-15

    Schizophrenia is a severe psychiatric disorder characterized by three symptom domains, positive (hallucinations, obsession), negative (social withdrawal, apathy, self-neglect) and cognitive (impairment in attention, memory and executive function). Whereas current medication ameliorates positive symptomatology, negative symptoms as well as cognitive dysfunctions remain untreated. The development of improved therapies for negative symptoms has proven particularly difficult, in part due to the inability of mimicking these in rodents. Here, we address the predictive validity of combining an ethologically well preserved behavior in rodents, namely nest building activity, with an established animal model of schizophrenia, the sub-chronic PCP model, for negative symptoms. Decline in rodent nesting activity has been suggested to mirror domains of negative symptoms of schizophrenia, including social withdrawal, anhedonia and self-neglect, whereas repeated treatment with the NMDAR antagonist PCP induces and exacerbates schizophrenia-like symptoms in rodents and human subjects. Using a back-translational approach of pharmacological validation, we tested the effects of two agents targeting the nicotinic α7 receptor (EVP-6124 and TC-5619) that were reported to exert some beneficial effect on negative symptoms in schizophrenic patients. Sub-chronic PCP treatment resulted in a significant nest building deficit in mice and treatment with EVP-6124 and TC-5619 reversed this PCP-induced deficit. In contrast, the atypical antipsychotic drug risperidone remained ineffective in this assay. In addition, EVP-6124, TC-5619 and risperidone were tested in the Social Interaction Test (SIT), an assay suggested to address negative-like symptoms. Results obtained in SIT were comparable to results in the nest building test (NEST). Based on these findings, we propose nest building in combination with the sub-chronic PCP model as a novel approach to assess negative-like symptoms of schizophrenia

  20. Development and evaluation of a simple assay for Marburg virus detection using a reverse transcription-loop-mediated isothermal amplification method.

    Science.gov (United States)

    Kurosaki, Yohei; Grolla, Allen; Fukuma, Aiko; Feldmann, Heinz; Yasuda, Jiro

    2010-07-01

    Marburg virus (MARV) causes a severe hemorrhagic fever in humans with a high mortality rate. The rapid and accurate identification of the virus is required to appropriately provide infection control and outbreak management. Here, we developed and evaluated a one-step reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the rapid and simple detection of MARV. By combining two sets of primers specific for the Musoke and Ravn genetic lineages, a multiple RT-LAMP assay detected MARV strains of both lineages, and no cross-reactivity with other hemorrhagic fever viruses (Ebola virus and Lassa virus) was observed. The assay could detect 10(2) copies of the viral RNA per tube within 40 min by real-time monitoring of the turbidities of the reaction mixtures. The assay was further evaluated using viral RNA extracted from clinical specimens collected in the 2005 Marburg hemorrhagic fever outbreak in Angola and yielded positive results for samples containing MARV at greater than 10(4) 50% tissue culture infective doses/ml, exhibiting 78% (14 of 18 samples positive) consistency with the results of a reverse transcription-PCR assay carried out in the field laboratory. The results obtained by both agarose gel electrophoresis and naked-eye judgment indicated that the RT-LAMP assay developed in this study is an effective tool for the molecular detection of MARV. Furthermore, it seems suitable for use for field diagnostics or in laboratories in areas where MARV is endemic.

  1. Optimal reservoir operation policies using novel nested algorithms

    Science.gov (United States)

    Delipetrev, Blagoj; Jonoski, Andreja; Solomatine, Dimitri

    2015-04-01

    Historically, the two most widely practiced methods for optimal reservoir operation have been dynamic programming (DP) and stochastic dynamic programming (SDP). These two methods suffer from the so called "dual curse" which prevents them to be used in reasonably complex water systems. The first one is the "curse of dimensionality" that denotes an exponential growth of the computational complexity with the state - decision space dimension. The second one is the "curse of modelling" that requires an explicit model of each component of the water system to anticipate the effect of each system's transition. We address the problem of optimal reservoir operation concerning multiple objectives that are related to 1) reservoir releases to satisfy several downstream users competing for water with dynamically varying demands, 2) deviations from the target minimum and maximum reservoir water levels and 3) hydropower production that is a combination of the reservoir water level and the reservoir releases. Addressing such a problem with classical methods (DP and SDP) requires a reasonably high level of discretization of the reservoir storage volume, which in combination with the required releases discretization for meeting the demands of downstream users leads to computationally expensive formulations and causes the curse of dimensionality. We present a novel approach, named "nested" that is implemented in DP, SDP and reinforcement learning (RL) and correspondingly three new algorithms are developed named nested DP (nDP), nested SDP (nSDP) and nested RL (nRL). The nested algorithms are composed from two algorithms: 1) DP, SDP or RL and 2) nested optimization algorithm. Depending on the way we formulate the objective function related to deficits in the allocation problem in the nested optimization, two methods are implemented: 1) Simplex for linear allocation problems, and 2) quadratic Knapsack method in the case of nonlinear problems. The novel idea is to include the nested

  2. Nesting biology of Centris (Hemisiella tarsata Smith (Hymenoptera, Apidae, Centridini

    Directory of Open Access Journals (Sweden)

    Cândida M. L. Aguiar

    2004-09-01

    Full Text Available Nests of Centris tarsata Smith, 1874 were obtained from trap-nests in areas of dry semi-deciduous forest (Baixa Grande and caatinga (Ipirá, in the State of Bahia. Nesting occurred in bamboo canes and in tubes of black cardboard with 5.8 cm (= small tube and 10.5 cm (= large tube in length and 0.6 and 0.8 cm in diameter, respectively. In both areas C. tarsata nested during the wet season producing four generations in Baixa Grande and three generations in Ipirá. The immatures of one generation underwent diapause at both sites. The bees constructed their nests with a mixture of sand and oil. In general, the cells were elongated and arranged in linear series with its opening pointing towards the nest entrance. Completed nests had two to three cells in small tubes, one to seven cells in large tubes, and two to 13 cells in bamboo canes. The nest plug resembled an uncompleted cell and was externally covered with oil. The cells were provisioned with pollen, oil, and nectar. Nests were parasitized by Mesocheira bicolor (Fabricius, 1804 (Hymenoptera: Apidae and other not identify bee species.Ninhos de Centris tarsata Smith, 1874 foram obtidos através da utilização de ninhos-armadilha, em áreas de floresta estacional semi-decídua (Baixa Grande e de caatinga (Ipirá, no Estado da Bahia. A nidificação ocorreu em gomos de bambus e em tubos de cartolina preta, estes com comprimentos de 5,8 cm (= tubos pequenos e 10,5 cm (= tubos grandes, e diâmetro de 0,6 e 0,8 cm, respectivamente. Em ambas as áreas C. tarsata nidificou durante a estação úmida, produzindo quatro gerações anuais em Baixa Grande e três em Ipirá. Os imaturos de uma das gerações passaram por diapausa em ambos os locais. As abelhas construíram seus ninhos com uma mistura de areia e óleo. Em geral, as células foram alongadas e arranjadas em série linear, com sua abertura dirigida para a entrada do ninho. Os ninhos completados tinham de duas a três células nos tubos pequenos

  3. Reverse Engineering of RFID devices

    OpenAIRE

    Bokslag, Wouter

    2015-01-01

    This paper discusses the relevance and potential impact of both RFID and reverse engineering of RFID technology, followed by a discussion of common protocols and internals of RFID technology. The focus of the paper is on providing an overview of the different approaches to reverse engineering RFID technology and possible countermeasures that could limit the potential of such reverse engineering attempts.

  4. Potential influences of climate and nest structure on spotted owl reproductive success: a biophysical approach.

    Science.gov (United States)

    Rockweit, Jeremy T; Franklin, Alan B; Bakken, George S; Gutiérrez, R J

    2012-01-01

    Many bird species do not make their own nests; therefore, selection of existing sites that provide adequate microclimates is critical. This is particularly true for owls in north temperate climates that often nest early in the year when inclement weather is common. Spotted owls use three main types of nest structures, each of which are structurally distinct and may provide varying levels of protection to the eggs or young. We tested the hypothesis that spotted owl nest configuration influences nest microclimate using both experimental and observational data. We used a wind tunnel to estimate the convective heat transfer coefficient (h(c)) of eggs in 25 potential nest configurations that mimicked 2 nest types (top-cavity and platform nests), at 3 different wind speeds. We then used the estimates of h(c) in a biophysical heat transfer model to estimate how long it would take unattended eggs to cool from incubation temperature (~36 °C) to physiological zero temperature (PZT; ~26 °C) under natural environmental conditions. Our results indicated that the structural configuration of nests influences the cooling time of the eggs inside those nests, and hence, influences the nest microclimate. Estimates of time to PZT ranged from 10.6 minutes to 33.3 minutes. Nest configurations that were most similar to platform nests always had the fastest egg cooling times, suggesting that platform nests were the least protective of those nests we tested. Our field data coupled with our experimental results suggested that nest choice is important for the reproductive success of owls during years of inclement weather or in regions characterized by inclement weather during the nesting season.

  5. Potential influences of climate and nest structure on spotted owl reproductive success: a biophysical approach.

    Directory of Open Access Journals (Sweden)

    Jeremy T Rockweit

    Full Text Available Many bird species do not make their own nests; therefore, selection of existing sites that provide adequate microclimates is critical. This is particularly true for owls in north temperate climates that often nest early in the year when inclement weather is common. Spotted owls use three main types of nest structures, each of which are structurally distinct and may provide varying levels of protection to the eggs or young. We tested the hypothesis that spotted owl nest configuration influences nest microclimate using both experimental and observational data. We used a wind tunnel to estimate the convective heat transfer coefficient (h(c of eggs in 25 potential nest configurations that mimicked 2 nest types (top-cavity and platform nests, at 3 different wind speeds. We then used the estimates of h(c in a biophysical heat transfer model to estimate how long it would take unattended eggs to cool from incubation temperature (~36 °C to physiological zero temperature (PZT; ~26 °C under natural environmental conditions. Our results indicated that the structural configuration of nests influences the cooling time of the eggs inside those nests, and hence, influences the nest microclimate. Estimates of time to PZT ranged from 10.6 minutes to 33.3 minutes. Nest configurations that were most similar to platform nests always had the fastest egg cooling times, suggesting that platform nests were the least protective of those nests we tested. Our field data coupled with our experimental results suggested that nest choice is important for the reproductive success of owls during years of inclement weather or in regions characterized by inclement weather during the nesting season.

  6. Neighbourhood society: nesting dynamics, usurpations and social behaviour in solitary bees.

    Directory of Open Access Journals (Sweden)

    Kateřina Černá

    Full Text Available Intraspecific cleptoparasitism represents a facultative strategy advantageous for reducing time and energy costs. However, only a few studies about nesting dynamics have described intraspecific cleptoparasitic behaviour in obligate solitary bees. We focused on nesting dynamics with the characterisation of nest owner replacements and frequency of true usurpation in four aggregating species belonging to different phylogenetic lineages--Andrena vaga (Andrenidae, Anthophora plumipes (Apidae, Colletes cunicularius (Colletidae, and Osmia rufa (Megachilidae. Our study, based on the regular observation of individually marked females, shows that nest owner replacement affects 10-45% of nests across all of the studied species and years. However, 39-90% of these nests had been abandoned before owner change and thus true nest usurpations represent only a part of observed nest replacement cases. Females tend to abandon their nests regularly and found new ones when they live long enough, which is in accordance with risk-spreading strategy. We suggest that the original facultative strategy of observed solitary bees during nest founding is not cleptoparasitism per se but rather reuse of any pre-existing nest (similar to "entering" strategy in apoid wasps. This is supported by gradual increase of nests founded by "entering" during the season with an increase in the number of available nests. Although the frequent reuse of conspecific nests results in frequent contact between solitary females, and rarely, in the short-term coexistence of two females in one nest, we detected unexpectedly low level of conflict in these neighbourhood societies. We suggest that nesting dynamics with regular nest switching and reusing reduces long-term and costly intraspecific aggression, a key factor for the origin and evolution of sociality.

  7. Arctic foxes, lemmings, and canada goose nest survival at cape Churchill, Manitoba

    Science.gov (United States)

    Reiter, M.E.; Andersen, D.E.

    2011-01-01

    We examined factors influencing Canada Goose (Branta canadensis interior) annual nest success, including the relative abundance of collared lemmings (Dicrostonyx richardsoni), arctic fox (Alopex lagopus) den occupancy, nest density, and spring phenology using data collected during annual Canada Goose breeding area surveys at Cape Churchill, Manitoba. Nest density and arctic fox den occupancy strongly influenced Canada Goose nest success. High nest density resulted in higher nest success and high den occupancy reduced nest success. Nest success was not influenced by lemming abundance in the current or previous year as predicted by the "bird-lemming" hypothesis. Reducing arctic fox abundance through targeted management increased nest survival of Canada Geese; a result that further emphasizes the importance of arctic fox as nest predators in this system. The spatial distribution of nest predators, at least for dispersed-nesting geese, may be most important for nest survival, regardless of the abundance of small mammals in the local ecosystem. Further understanding of the factors influencing the magnitude and variance in arctic fox abundance in this region, and the spatial scale at which these factors are realized, is necessary to fully explain predator-prey-alternative prey dynamics in this system. ?? 2011 by the Wilson Ornithological Society.

  8. Common blackbirdsTurdus merula use anthropogenic structures as nesting sites in an urbanized landscape

    Institute of Scientific and Technical Information of China (English)

    Yanping WANG; Qin HUANG; Sisi LAN; Qin ZHANG; Shuihua CHEN

    2015-01-01

    The common blackbirdTurdus merula is one of the most highly urbanized bird species. However, to date, the use of anthropogenic structures as nesting sites in the common blackbird is rarely documented, and the factors influencing its use of the anthropogenic structures as nesting sites remain unclear. In this study, we systematically quantified and determined the factors in-fluencing the use of anthropogenic structures as nesting sites in common blackbirds in a highly urbanized city of Hangzhou, Chi-na. We searched for nests of common blackbirds during four breeding seasons from 2010 to 2013. Among the 60 nests found, 34 nests were in anthropogenic structures such as wall ledges, air condition mounts, window canopies, cable poles, guardrails, eaves, balcony frames, flowerpots and flower shelves on balconies. We found that the available anthropogenic nest sites and the availa-ble nesting trees were main factors determining the use of anthropogenic structures as nesting sites in common blackbirds. In ur-ban environments, the amount of available anthropogenic nesting sites increased significantly, whereas the number of natural nesting sites reduced greatly. Our results suggest that common blackbirds can adjust their nest sites in response to urbanization and such nesting behavior shifts may aid them to colonize urban environments. From a management viewpoint, our results indi-cate that behavioral flexibility should be taken into account for effective urban wildlife management and conservation [Current Zoology 61 (3): 435–443, 2015].

  9. Reverse Engineering Malicious Applications

    Directory of Open Access Journals (Sweden)

    Ioan Cristian Iacob

    2015-06-01

    Full Text Available Detecting new and unknown malware is a major challenge in today’s software. Security profession. A lot of approaches for the detection of malware using data mining techniques have already been proposed. Majority of the works used static features of malware. However, static detection methods fall short of detecting present day complex malware. Although some researchers proposed dynamic detection methods, the methods did not use all the malware features. In this work, an approach for the detection of new and unknown malware was proposed and implemented. Each sample was reverse engineered for analyzing its effect on the operating environment and to extract the static and behavioral features. 

  10. Does nest luminosity play a role in recognition of parasitic eggs in domed nests? A case study of the red bishop

    Science.gov (United States)

    Honza, Marcel; Šulc, Michal; Cherry, Michael I.

    2014-12-01

    Certain light environments may hinder egg discrimination by hosts of foreign eggs, which could in some circumstances lead to the acceptance of non-mimetic eggs by hosts. We measured light parameters at red bishop ( Euplectes orix) nests and used a model of avian visual processing to quantify the detectability of eggs in the light environment in which they are perceived. We found that the overall amount of light was very variable between red bishop nests and always sufficient for colour discrimination. A model of avian visual processing revealed that nest luminosity had no influence on host responses towards eggs which were painted dark brown. Dark eggs do not appear to be cryptic in red bishop nests and can be distinguished with ease, whereas natural red bishop eggs are usually accepted, despite the domed structure of the nest. We found little variation in both chromatic and achromatic contrasts between host and artificial eggs, indicating that there was very little variation in the light quality inside nests. We suggest that nest luminosity is likely to play a role in egg recognition in situations when light reaches threshold values for colour discrimination, i.e. in scotopic as opposed to photopic vision. Rejection rates for dark eggs were higher than for bright (conspecific) foreign eggs. More investigation of domed nest-building species is required, as this type of nest appears to have a highly variable light environment, dependent on both nest structure and habitat.

  11. Infectious bronchitis virus: detection and vaccine Strain differentiation by semi-nested RT-PCR

    Directory of Open Access Journals (Sweden)

    CH Okino

    2005-03-01

    Full Text Available A semi-nested reverse transcription-polymerase chain reaction (Semi-N-RT-PCR was developed and used to detect the S glycoprotein gene of infectious bronchitis virus (IBV strains and to discriminate H120 vaccine strain from other strains. Viral RNA was extracted from the allantoic fluid of chicken embryos and from tissues of chickens experimentally infected with different strains of IBV. Amplification and identification of the viral RNA was performed using two sets of primers complementary to a region of the S glycoprotein gene in the Semi-N-RT-PCR assay. The pair of primers used in the first PCR consisted of universal oligonucleotides flanking a more variable region of S1-S2 gene. The second primer pair was used in the Semi-N-RT-PCR and was comprised of one of the primers from the first universal pair together with either another universal internal oligolucleotide or a oligonucleotide sequence specific for the H120 strain of IBV. The universal primers detected all reference IBV strains and field isolates tested herein. The Semi-N-RT-PCR had high sensitivity and specificity, and was able to differentiate the H120 vaccine strain from other reference IBV strains; including M41 strain. All tissue samples collected from chickens experimentally infected with H120 or M41 strains were positive in the semi-nested RT-PCR using universal primers, while only the H120-infected tissue samples were amplified by the set of primers containing the H120-oligonucleotide. In conclusion, the ability of Semi-N-RT-PCR to detect distinct IBV strains and preliminarily discriminate the vaccine strain (H120 closes a diagnostic gap and offers the opportunity to use comprehensive PCR procedures for the IBV diagnosis.

  12. Reversibly Bistable Flexible Electronics

    KAUST Repository

    Alfaraj, Nasir

    2015-05-01

    Introducing the notion of transformational silicon electronics has paved the way for integrating various applications with silicon-based, modern, high-performance electronic circuits that are mechanically flexible and optically semitransparent. While maintaining large-scale production and prototyping rapidity, this flexible and translucent scheme demonstrates the potential to transform conventionally stiff electronic devices into thin and foldable ones without compromising long-term performance and reliability. In this work, we report on the fabrication and characterization of reversibly bistable flexible electronic switches that utilize flexible n-channel metal-oxide-semiconductor field-effect transistors. The transistors are fabricated initially on rigid (100) silicon substrates before they are peeled off. They can be used to control flexible batches of light-emitting diodes, demonstrating both the relative ease of scaling at minimum cost and maximum reliability and the feasibility of integration. The peeled-off silicon fabric is about 25 µm thick. The fabricated devices are transferred to a reversibly bistable flexible platform through which, for example, a flexible smartphone can be wrapped around a user’s wrist and can also be set back to its original mechanical position. Buckling and cyclic bending of such host platforms brings a completely new dimension to the development of flexible electronics, especially rollable displays.

  13. Monitoring of Nesting Spectacled Eiders on Kigigak Island, Yukon Delta NWR, 2011

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Nesting spectacled eiders were monitored for the 20th consecutive year on Kigigak Island, Alaska in 2011. Clutch size, hatch date, and final nest status were...

  14. Report of Black Duck Nesting on the Blackwater River Migratory Bird Refuge 1932

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The purpose of this investigation is to determine the extent of nesting in the area by ducks and the amount of destruction during the nesting season by predacious...

  15. Fighting fish (Betta splendens) bubble nests do not inhibit microbial growth.

    Science.gov (United States)

    Brown, Alexandria C; Clotfelter, Ethan D

    2012-12-01

    Some organisms produce antimicrobial substances in nesting foam to favorably manipulate the environment to which their developing offspring are exposed. We tested if fighting fish Betta splendens foamy nest material, which is comprised of bubbles produced in the oral cavity of nesting males, has antimicrobial properties against a pathogenic bacteria (Edwardsiella tarda), a nonpathogenic bacteria (Escherichia coli), or a pathogenic oomycete (Saprolegnia parasitica). We also tested if exposure to nest material increases larval survival by performing in vitro fertilizations and individually incubating eggs in bubble nest extract or tank water (control). Our results show no evidence of antimicrobial properties of bubble nests. On the contrary, bubble nests provided favorable microenvironments for the growth of Saprolegnia parasitica. Our results confirm earlier work citing the importance of male nest attendance, and suggest that the mechanism responsible for decreased survival in the absence of attending males is pathogenic microbes.

  16. A survey of potential raptor nesting sites in the southern Askinuk Mountains, Alaska

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — During June 1989, selected areas of the southern Askinuk Mountains were surveyed for raptor nests. Ten nests were located on rock outcroppings at seven locations....

  17. Evaluation of the 100 meter protective zone for bald eagle nests in southeast Alaska

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Bald eagle (Haliaeetus leucocephalus) nests in southeast Alaska have been protected by a 100 m buffer zone since 1968. Nests near logging developments were surveyed...

  18. Nested by design: model fitting and interpretation in a mixed model era

    National Research Council Canada - National Science Library

    Schielzeth, Holger; Nakagawa, Shinichi; Freckleton, Robert

    2013-01-01

    ...‐effects models offer a powerful framework to do so. Nested effects can usually be fitted using the syntax for crossed effects in mixed models, provided that the coding reflects implicit nesting...

  19. Nesting survey for Aleutian Canada geese at Nizki-Alaid, Alaska in 1990

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Nesting success was high in 1990, and moderate numbers of subadult birds, which may nest in future years, were present. Furthermore, a translocation of 38 geese...

  20. Leucophora Satellite Flies (Diptera: Anthomyiidae) as Nest Parasites of Sweat Bees (Hymenoptera: Halictidae) in the Neotropics

    National Research Council Canada - National Science Library

    Polidori, C; Michelsen, V; Nieves-Aldrey, J L

    2015-01-01

    .... Females of both species perch on small stones or sticks within a dense nest aggregation of the bees and then track pollen-loaded bees in flight with great precision, eventually following them into their nests...

  1. Survey of Nesting Osprey at Back Bay National Wildlife Refuge and False Cape State Park

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — A survey of nesting Osprey (Pandion Haliaetus) was conducted during the nesting season of 1990. The survey was conducted in the bay waters of Back Bay National...

  2. A survey for cliff-nesting birds of prey along the Noatak River, Alaska

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The primary objective of the study was to locate peregrine falcon nesting sites and to locate nest sites of other raptor species and assess their location in...

  3. Survey of Nesting Osprey at Back Bay National Wildlife Refuge and False Cape State Park

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — A survey of nesting Osprey (Pandion Haliaetus) was conducted during the nesting season of 1989. The survey was conducted in the bay waters of Back Bay National...

  4. Spectacled eider (Somateria fischeri) nest records Kashunuk River and Kigigak Island, Alaska, 1991-2004

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Data set containing nest records for Spectacled Eiders near the Kashunuk River and on Kigigak Island, within the Yukon-Kuskokwim Delta, Alaska. Nests were visited...

  5. Fundamentals of reversible flowchart languages

    DEFF Research Database (Denmark)

    Yokoyama, Tetsuo; Axelsen, Holger Bock; Glück, Robert

    2016-01-01

    . Although reversible flowcharts are superficially similar to classical flowcharts, there are crucial differences: atomic steps are limited to locally invertible operations, and join points require an explicit orthogonalizing conditional expression. Despite these constraints, we show that reversible......Abstract This paper presents the fundamentals of reversible flowcharts. They are intended to naturally represent the structure and control flow of reversible (imperative) programming languages in a simple computation model, in the same way classical flowcharts do for conventional languages......, structured reversible flowcharts are as expressive as unstructured ones, as shown by a reversible version of the classic Structured Program Theorem. We illustrate how reversible flowcharts can be concretized with two example programming languages, complete with syntax and semantics: a low-level unstructured...

  6. Food use and nutrition of black ducks nesting in Maine

    Science.gov (United States)

    Reinecke, K.J.; Owen, R.B.

    1980-01-01

    Based on 32 adult black ducks (Anas rubripes) collected during the nesting seasons of 1974-76, the proportion of macro invertebrates (as aggregate [average] percent of dry weight) in the diet of males, egg-laying females, and postlaying females was 60, 75, and 55%, respectivey. Sample sizes were small, and the differences associated with sex and reproductive condition were not signficant. Molluscs, Isopods, ephemeropteran and odonate nymphs, and coleopteran, trichopteran, and dipteran larvae contributed 74% of the dry weight and 64% of the gross energy ingested. Data from proximate analyses of 9 invertebrate and 9 plant foods were combined with food habits data to estimate the nutrients available to breeding hens. We concluded that females with access to an adequate amount of natural food including invertebrates and the seeds and tubers of aquatic plants would obtain sufficient minerals, protein, and energy for reproduction. Food quality does not appear to limit the density of black ducks nesting in Maine.

  7. Clustered nested sampling: efficient Bayesian inference for cosmology

    CERN Document Server

    Shaw, R; Hobson, M P

    2007-01-01

    Bayesian model selection provides the cosmologist with an exacting tool to distinguish between competing models based purely on the data, via the Bayesian evidence. Previous methods to calculate this quantity either lacked general applicability or were computationally demanding. However, nested sampling (Skilling 2004), which was recently applied successfully to cosmology by Muhkerjee et al. 2006, overcomes both of these impediments. Their implementation restricts the parameter space sampled, and thus improves the efficiency, using a decreasing ellipsoidal bound in the $n$-dimensional parameter space centred on the maximum likelihood point. However, if the likelihood function contains any multi-modality, then the ellipse is prevented from constraining the sampling region efficiently. In this paper we introduce a method of clustered ellipsoidal nested sampling which can form multiple ellipses around each individual peak in the likelihood. In addition we have implemented a method for determining the expectation...

  8. Experimental demonstration of an inertial collimation mechanism in nested outflows

    CERN Document Server

    Yurchak, R; Pelka, A; Pikuz, S; Falize, E; Vinci, T; Koenig, M; Loupias, B; Benuzzi-Mounaix, A; Fatenejad, M; Tzeferacos, P; Lamb, D Q; Blackman, E G

    2014-01-01

    Interaction between a central outflow and a surrounding wind is common in astrophysical sources powered by accretion. Understanding how the interaction might help to collimate the inner central outflow is of interest for assessing astrophysical jet formation paradigms. In this context, we studied the interaction between two nested supersonic plasma flows generated by focusing a long pulse high-energy laser beam onto a solid target. A nested geometry was created by shaping the energy distribution at the focal spot with a dedicated phase plate. Optical and X-ray diagnostics were used to study the interacting flows. Experimental results and numerical hydrodynamic simulations indeed show the formation of strongly collimated jets. Our work experimentally confirms the "shock-focused inertial confinement" mechanism proposed in previous theoretical astrophysics investigations.

  9. NANOFIBROUS MATS WITH BIRD'S NEST PATTERNS BY ELECTROSPINNING

    Institute of Scientific and Technical Information of China (English)

    Xiang-yu Ye; Xiao-jun Huang; Zhi-kang Xu

    2012-01-01

    Electrospun material with bio-inspired ordered architectures and patterns is very interesting,yet remains a challenge.We report here that nanofibrous mats with bird's nest patterned structures can be directly electrospun from chlorinated polypropylene solutions doped with an ionic liquid.The solution viscosity and the ionic liquid content are two dominant factors to influence the lopological morphology of the nanofibrous mats.The patterned structures can be further modulated by the collection time of electrospinning,the humidity of environment and the design of collector.We suggest the electrostatic repulsion between the residual charges of the mat surface and the upcoming nanofibers plays a key role in the formation of the bird's nest patterns.

  10. Optimization and Evaluation of Nested Queries and Procedures

    CERN Document Server

    Guravannavar, Ravindra

    2009-01-01

    Many database applications perform complex data retrieval and update tasks. Nested queries, and queries that invoke user-defined functions, which are written using a mix of procedural and SQL constructs, are often used in such applications. A straight-forward evaluation of such queries involves repeated execution of parameterized sub-queries or blocks containing queries and procedural code. An important problem that arises while optimizing nested queries as well as queries with joins, aggregates and set operations is the problem of finding an optimal sort order from a factorial number of possible sort orders. We show that even a special case of this problem is NP-Hard, and present practical heuristics that are effective and easy to incorporate in existing query optimizers. We also consider iterative execution of queries and updates inside complex procedural blocks such as user-defined functions and stored procedures. Parameter batching is an important means of improving performance as it enables set-orientate...

  11. Towards a streaming model for nested data parallelism

    DEFF Research Database (Denmark)

    Madsen, Frederik Meisner; Filinski, Andrzej

    2013-01-01

    -flattening execution strategy, comes at the price of potentially prohibitive space usage in the common case of computations with an excess of available parallelism, such as dense-matrix multiplication. We present a simple nested data-parallel functional language and associated cost semantics that retains NESL......'s intuitive work--depth model for time complexity, but also allows highly parallel computations to be expressed in a space-efficient way, in the sense that memory usage on a single (or a few) processors is of the same order as for a sequential formulation of the algorithm, and in general scales smoothly......-processable in a streaming fashion. This semantics is directly compatible with previously proposed piecewise execution models for nested data parallelism, but allows the expected space usage to be reasoned about directly at the source-language level. The language definition and implementation are still very much work...

  12. Using Technology-Nested Instructional Strategies to Enhance Student Learning

    Directory of Open Access Journals (Sweden)

    Angela Lumpkin, PhD

    2015-08-01

    Full Text Available Students today expect the use of technology in their classes, rather than have to listen to less-than-engaging lectures. College students are connected electronically and incessant technology consumers. As a result, they may prefer the infusion of technologies to help them learn and enjoy the process of learning, rather than having to listen exclusively to lectures. To investigate this, the authors solicited student perceptions to assess the importance of learning through technology-nested instructional strategies. Student perceptions give direction to and affirm the benefits of instructional strategies that increase student motivation to engage more actively in their learning. Based on quantitative and qualitative responses through action research in multiple courses, students perceive their learning as more engaging and enjoyable when technology-nested instructional strategies are infused into their classes.

  13. The mathematics of non-linear metrics for nested networks

    Science.gov (United States)

    Wu, Rui-Jie; Shi, Gui-Yuan; Zhang, Yi-Cheng; Mariani, Manuel Sebastian

    2016-10-01

    Numerical analysis of data from international trade and ecological networks has shown that the non-linear fitness-complexity metric is the best candidate to rank nodes by importance in bipartite networks that exhibit a nested structure. Despite its relevance for real networks, the mathematical properties of the metric and its variants remain largely unexplored. Here, we perform an analytic and numeric study of the fitness-complexity metric and a new variant, called minimal extremal metric. We rigorously derive exact expressions for node scores for perfectly nested networks and show that these expressions explain the non-trivial convergence properties of the metrics. A comparison between the fitness-complexity metric and the minimal extremal metric on real data reveals that the latter can produce improved rankings if the input data are reliable.

  14. Extraction of Flat and Nested Data Records from Web Pages

    CERN Document Server

    Hiremath, P S

    2010-01-01

    This paper studies the problem of identification and extraction of flat and nested data records from a given web page. With the explosive growth of information sources available on the World Wide Web, it has become increasingly difficult to identify the relevant pieces of information, since web pages are often cluttered with irrelevant content like advertisements, navigation-panels, copyright notices etc., surrounding the main content of the web page. Hence, it is useful to mine such data regions and data records in order to extract information from such web pages to provide value-added services. Currently available automatic techniques to mine data regions and data records from web pages are still unsatisfactory because of their poor performance. In this paper a novel method to identify and extract the flat and nested data records from the web pages automatically is proposed. It comprises of two steps : (1) Identification and Extraction of the data regions based on visual clues information. (2) Identificatio...

  15. Temperature variation in nests of Caiman crocodilus (Crocodylia: Alligatoridae

    Directory of Open Access Journals (Sweden)

    Armando H. Escobedo Galván

    2006-11-01

    Full Text Available Caiman crocodilus is a widely distributed species in the Neotropics; however, studies of incubation temperatures in wildlife are uncommon. Incubation temperature in four nests of Caiman crocodilus were measured with a digital thermometer, in the National Wildlife Refuge Caño Negro, Costa Rica. Average temperatures in these four nests (no. 1-4 were 32.13 + 0.92 °C (no. 1, 32.46 + 0.77 °C (no. 2, 33.60 + 0.95 °C (no. 3, and 31.78 + 2.30 °C (no. 4. Temperature variations recorded showed higher temperatures than those reported from other studies in Caño Negro. The temperatures registered in this study will lead to a higher proportion of males within the caiman population, reducing the number of future reproducing females and, therefore, in the population viability.

  16. PolyChord: next-generation nested sampling

    CERN Document Server

    Handley, W J; Lasenby, A N

    2015-01-01

    PolyChord is a novel nested sampling algorithm tailored for high-dimensional parameter spaces. This paper coincides with the release of PolyChord v1.3, and provides an extensive account of the algorithm. PolyChord utilises slice sampling at each iteration to sample within the hard likelihood constraint of nested sampling. It can identify and evolve separate modes of a posterior semi-independently, and is parallelised using openMPI. It is capable of exploiting a hierarchy of parameter speeds such as those present in CosmoMC and CAMB, and is now in use in the CosmoChord and ModeChord codes. PolyChord is available for download at: http://ccpforge.cse.rl.ac.uk/gf/project/polychord/

  17. DNest4: Diffusive Nested Sampling in C++ and Python

    CERN Document Server

    Brewer, Brendon J

    2016-01-01

    In probabilistic (Bayesian) inferences, we typically want to compute properties of the posterior distribution, describing knowledge of unknown quantities in the context of a particular dataset and the assumed prior information. The marginal likelihood, also known as the "evidence", is a key quantity in Bayesian model selection. The Diffusive Nested Sampling algorithm, a variant of Nested Sampling, is a powerful tool for generating posterior samples and estimating marginal likelihoods. It is effective at solving complex problems including many where the posterior distribution is multimodal or has strong dependencies between variables. DNest4 is an open source (MIT licensed), multi-threaded implementation of this algorithm in C++11, along with associated utilities including: i) RJObject, a class template for finite mixture models, (ii) A Python package allowing basic use without C++ coding, and iii) Experimental support for models implemented in Julia. In this paper we demonstrate DNest4 usage through examples ...

  18. Can hedgerow management mitigate the impacts of predation on songbird nest survival?

    Science.gov (United States)

    Dunn, Jenny C; Gruar, Derek; Stoate, Chris; Szczur, John; Peach, Will J

    2016-12-15

    Nest predators can have significant impacts on songbird reproductive success. These impacts may be amplified by habitat simplification and here we test whether sympathetic management of farmland hedgerows can reduce nest depredation, especially by corvids. We test whether songbirds select nest sites according to structural features of hedgerows (including nest visibility and accessibility), and whether these features influence nest predation risk. Songbirds selected nesting sites affording higher vegetation cover above the nest, increased visibility on the nest-side of the hedgerow and reduced visibility on the far side of the hedge. Nest survival was unrelated to corvid abundance and only weakly related (at the egg stage) to corvid nest proximity. Nest survival at the chick stage was higher where vegetation structure restricted access to corvid-sized predators (averaging 0.78 vs. 0.53), and at nests close to potential vantage points. Overall nest survival was sensitive to hedgerow structure (accessibility) particularly at low exposure to corvid predation, while the overall impact of corvid exposure was dependent on the relationship involving proximity to vantage points. Nest survival over the chick stage was much higher (0.67) in stock-proof, trimmed and mechanically cut hedgerows, (which tended to provide lower side visibility and accessibility) than in recently laid, remnant or leggy hedgerows (0.18). Long-term reductions in the management of British hedgerows may therefore be exposing nesting songbirds to increased predation risk. We recommend regular rotational cutting of hedgerows to maintain a dense woody structure and thereby reduce songbird nest predation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Uncertain nest fates in songbird studies and variation in Mayfield estimation

    Science.gov (United States)

    Manolis, J.C.; Andersen, D.E.; Cuthbert, F.J.

    2000-01-01

    Determining whether nesting attempts are successful can be difficult. Yet, current protocols for estimating nesting success do not address how uncertain nest fates should be handled. We examined the problem of nest-fate uncertainty as it relates to Mayfield estimation of nesting success and in analyses of factors that influence success. We used data from Minnesota to illustrate the potential effect of uncertain fate; 40% of Ovenbird (Seiurus aurocapillus; n = 127) nests and 30% of Least Flycatcher (Empidonax minimus; n = 144) nests had uncertain fates. How this uncertainty is incorporated into Mayfield estimates of success varied widely among researchers. In a survey of researchers who use the Mayfield method, 9 of 22 respondents (of 40 contacted) excluded nests with uncertain fate. Excluding uncertain fates is counter to how Mayfield first described his estimator and can result in severe downward bias. The remaining respondents (59%) included nests with uncertain fate but varied in how they terminated the exposure period. We developed a simulation model that calculated Mayfield estimates using different approaches and compared them with a known rate of nesting success. Magnitude of bias in Mayfield estimates varied considerably in our simulations. The approach with the least bias terminated exposure with the last observed active date for nests with uncertain fate, and with the midpoint between last observed active and first observed inactive dates for nests with known fate. In addition, information necessary to interpret and compare Mayfield estimates often is not reported. These values, including variance estimates and the period lengths used to estimate survival rates, should be reported with Mayfield estimates. Finally, nest fate is commonly used as a categorical variable in studies of factors affecting nesting success. In this approach, however, nests with uncertain fate must be excluded. An alternative approach is Cox regression, which incorporates nests with

  20. Bird predation on nest of a social wasp in Brazilian cerrado

    OpenAIRE

    Barros Henriques, Raimundo Paulo; Torre Palma, Alexandre Ramlo

    2015-01-01

    Birds are rarely observed preying upon wasps' nests (Bertoni 1911, Rau 1941, AIvarez del Toro 1950, Skutch 1959, Windsor 1976). Many of the observations are recorded in tropical forest on nests of Polybia and Metapolybia. In this note we present the first observations on the predation by the curIcrestedjay (Cyanocorax cristatellus) upon the nest of a social wasp (Apoica pallens) in cerrados of Central Brazil. Birds are rarely observed preying upon wasps' nests (Bertoni 1911, Rau 1941, AIva...