Cost effectiveness analysis of the New Jersey rapid testing algorithm for HIV testing in publicly funded testing sites.

PubMed

Stevinson, Kendall; Martin, Eugene G; Marcella, Stephen; Paul, Sindy M

2011-12-01

Before 2009, New Jersey (NJ) publicly funded counseling and testing sites (CTS) tested for HIV using a single rapid test followed, when positive, by a Western Blot (WB) for confirmation. With this strategy, 74.8% of confirmed positive clients returned to receive test results. To improve the client notification rate at these centers, the New Jersey (NJ) Division of HIV, STD and TB Services (DHSTS) implemented a rapid testing algorithm (RTA) which utilizes a second, different, rapid test to verify a preliminary positive. To compare the cost-effectiveness of the two testing algorithms. This was a retrospective cost-effectiveness analysis. New Jersey HIV Rapid Testing Support Program (NJHIV) records, DHSTS grant documents, counseling time estimates from an online survey of site supervisors. Costs included test kits and personnel costs from month of RTA implementation through 11/30 in 2008 and 2009. The incremental cost of the RTA was calculated per additional percent of positive clients who were notified and per day earlier notification. In 2008, 215 of 247 clients with a positive rapid HIV test were confirmed positive by WB. 90.9% of clients were notified a mean of 11.4 days after their initial test. 12 refused confirmatory WB. In 2009, 152 of 170 clients with one positive rapid test had a confirmatory second positive rapid test and were notified on the same day. The incremental cost of the RTA was $20.31 per additional positive person notified and $24.31 per day earlier notification or $3.23 per additional positive person and $3.87 per day earlier notification if the WB were eliminated. The RTA is a cost-effective strategy achieving 100% notification of newly HIV positive clients a mean of 11.4 days earlier compared to standard testing. Copyright © 2011 Elsevier B.V. All rights reserved.

Glyphosate resistance in Ambrosia trifida: Part 2. Rapid response physiology and non-target-site resistance.

PubMed

Moretti, Marcelo L; Van Horn, Christopher R; Robertson, Renae; Segobye, Kabelo; Weller, Stephen C; Young, Bryan G; Johnson, William G; Douglas Sammons, R; Wang, Dafu; Ge, Xia; d' Avignon, André; Gaines, Todd A; Westra, Philip; Green, Amanda C; Jeffery, Taylor; Lespérance, Mackenzie A; Tardif, François J; Sikkema, Peter H; Christopher Hall, J; McLean, Michael D; Lawton, Mark B; Schulz, Burkhard

2018-05-01

The glyphosate-resistant rapid response (GR RR) resistance mechanism in Ambrosia trifida is not due to target-site resistance (TSR) mechanisms. This study explores the physiology of the rapid response and the possibility of reduced translocation and vacuolar sequestration as non-target-site resistance (NTSR) mechanisms. GR RR leaf discs accumulated hydrogen peroxide within minutes of glyphosate exposure, but only in mature leaf tissue. The rapid response required energy either as light or exogenous sucrose. The combination of phenylalanine and tyrosine inhibited the rapid response in a dose-dependent manner. Reduced glyphosate translocation was observed in GR RR, but only when associated with tissue death caused by the rapid response. Nuclear magnetic resonance studies indicated that glyphosate enters the cytoplasm and reaches chloroplasts, and it is not moved into the vacuole of GR RR, GR non-rapid response or glyphosate-susceptible A. trifida. The GR RR mechanism of resistance is not associated with vacuole sequestration of glyphosate, and the observed reduced translocation is likely a consequence of rapid tissue death. Rapid cell death was inhibited by exogenous application of aromatic amino acids phenylalanine and tyrosine. The mechanism by which these amino acids inhibit rapid cell death in the GR RR phenotype remains unknown, and it could involve glyphosate phytotoxicity or other agents generating reactive oxygen species. Implications of these findings are discussed. The GR RR mechanism is distinct from the currently described glyphosate TSR or NTSR mechanisms in other species. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Characteristics of sites and trees affected by rapid white oak mortality as reported by forestry professionals in Missouri

Treesearch

Sharon E. Reed; James T. English; Rose-Marie Muzika; John M. Kabrick; Simeon. Wright

2017-01-01

A new syndrome was named rapid white oak mortality in 2011 to describe the rapid death of white oak trees (Quercus alba L.) within one growing season. A survey with 24 questions about stand and site characteristics, site history, and symptoms was distributed to forestry professionals to gather information about the new syndrome. Sixty-three reports...

Assessment of the serum levels of bone alkaline phosphatase with a new immunoradiometric assay in patients with metabolic bone disease

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

Garnero, P.; Delmas, P.D.

1993-10-01

The authors measured serum bone alkaline phosphatase (B-ALP) with a new immunoradiometric assay (IRMA) in a large sample of healthy controls comprising 173 women and 180 men, 20-88 yr of age, and in patients with metabolic bone disease. Using serum samples from patients with liver disease and patients with Paget's disease with elevated total alkaline phosphatase (T-ALP) as a source of, respectively, liver and bone isoenyzmes, they determined a liver cross-reactivity of the IRMA of 16% that was confirmed by electrophoresis of the circulating alkaline phosphatase isoenzymes. The IRMA was linear for serial sample dilutions, the recovery ranged from 89-110%,more » and the intra- and interassay variations were below 7% and 9%, respectively. B-ALP increased linearly with age in both sexes, and the mean B-ALP serum levels were not significantly different for women and men (11.3 [+-] 4.8 ng/mL for women; 11.0 [+-] 4.0 ng/mL for men). The increase in B-ALP after the menopause was significantly higher than that in T-ALP (+77% vs. +24%; P<0.001). When the values of postmenopausal women were expressed as the SD from the mean of premenopausal women, the mean Z scores were 2.2[+-] 1.8 for B-ALP and 0.9 [+-] 1.3 for T-ALP (P<0.001 between the two).« less

VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.

PubMed

Hocum, Jonah D; Battrell, Logan R; Maynard, Ryan; Adair, Jennifer E; Beard, Brian C; Rawlings, David J; Kiem, Hans-Peter; Miller, Daniel G; Trobridge, Grant D

2015-07-07

Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for retroviral mutagenesis screens. We developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads. VISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of retroviral vector integration sites.

Cost-effectiveness of rapid HCV testing and simultaneous rapid HCV and HIV testing in substance abuse treatment programs

PubMed Central

Schackman, Bruce R.; Leff, Jared A.; Barter, Devra M.; DiLorenzo, Madeline A.; Feaster, Daniel J.; Metsch, Lisa R.; Freedberg, Kenneth A.; Linas, Benjamin P.

2014-01-01

Aims To evaluate the cost-effectiveness of rapid hepatitis C virus (HCV) and simultaneous HCV/HIV antibody testing in substance abuse treatment programs. Design We used a decision analytic model to compare the cost-effectiveness of no HCV testing referral or offer, off-site HCV testing referral, on-site rapid HCV testing offer, and on-site rapid HCV and HIV testing offer. Base case inputs included 11% undetected chronic HCV, 0.4% undetected HIV, 35% HCV co-infection among HIV-infected, 53% linked to HCV care after testing antibody positive, and 67% linked to HIV care. Disease outcomes were estimated from established computer simulation models of HCV (HEP-CE) and HIV (CEPAC). Setting and Participants Data on test acceptance and costs were from a national randomized trial of HIV testing strategies conducted at 12 substance abuse treatment programs in the USA. Measurements Lifetime costs (2011 US dollars) and quality-adjusted life years (QALYs) discounted at 3% annually; incremental cost-effectiveness ratios (ICERs) Findings On-site rapid HCV testing had an ICER of $18,300/QALY compared with no testing, and was more efficient than (dominated) off-site HCV testing referral. On-site rapid HCV and HIV testing had an ICER of $64,500/QALY compared with on-site rapid HCV testing alone. In one and two-way sensitivity analyses, the ICER of on-site rapid HCV and HIV testing remained <$100,000/QALY, except when undetected HIV prevalence was <0.1% or when we assumed frequent HIV testing elsewhere. The ICER remained <$100,000/QALY in approximately 90% of probabilistic sensitivity analyses. Conclusions On-site rapid hepatitis C virus and HIV testing in substance abuse treatment programs is cost-effective at a <$100,000/ quality-adjusted life years threshold. PMID:25291977

A Comparison of two Brunhes Chron Geomagnetic Excursions Recorded by Neighbouring North Atlantic Sites (ODP Sites 1062 and 1063)

NASA Astrophysics Data System (ADS)

Bourne, M.; Mac Niocaill, C.; Knudsen, M. F.; Thomas, A. L.; Henderson, G. M.

2012-04-01

A full picture of geomagnetic field behaviour during the Blake excursion is currently limited by a paucity of robust, high-resolution records of this ambiguous event. Some records seem to point towards a 'double-excursion' character whilst others fail to record the Blake excursion at all. We present here a high-resolution record of the Blake excursion obtained from Ocean Drilling Program (ODP) Site 1062 on the Blake Outer Ridge (ODP Leg 172). Palaeomagnetic measurements in three cores reveal a single excursional feature associated with a broad palaeointensity low, characterised by rapid transitions (less than 500 years) between a stable normal polarity and a fully-reversed, pseudo-stable polarity. A relatively high sedimentation rate (~10 cm kyr-1) allows the determination of transitional field behaviour during the excursion. Rather than assuming a constant sedimentation rate between assigned age tie-points, we employ measurements of 230Thxs concentrations in the sediment to assess variations in the sedimentation rates through the core sections of interest. This allows us to determine an age and duration for the two excursions with greater accuracy and known uncertainty. Our new age model gives an age of 127 ka for the midpoint of the Blake event at Site 1062. The age model also gives a duration for the directional excursion of 7.1±1.6 kyr. This duration is similar to that previously reported for the Iceland Basin Excursion (~185 ka) from the nearby Bermuda Rise (ODP Site 1063), which recorded a ~7-8 kyr event. Similarly, a high sedimentation rate (10-15 cm kyr-1) at this site allows a high-resolution reconstruction of the geomagnetic field behaviour during the Iceland Basin Excursion. The Site 1063 palaeomagnetic record suggests more complicated behaviour than that of the Blake excursion at Site 1062. Instead, transitional VGP paths are characterised by stop-and-go behaviour between VGP clusters that may be related to long-standing thermo-dynamic features of the

On the Rapid Rise of Social Networking Sites: New Findings and Policy Implications

ERIC Educational Resources Information Center

Livingstone, Sonia; Brake, David R

2010-01-01

Social networking sites have been rapidly adopted by children and, especially, teenagers and young people worldwide, enabling new opportunities for the presentation of the self, learning, construction of a wide circle of relationships, and the management of privacy and intimacy. On the other hand, there are also concerns that social networking…

Differences in serum thyroglobulin measurements by 3 commercial immunoradiometric assay kits and laboratory standardization using Certified Reference Material 457 (CRM-457).

PubMed

Lee, Ji In; Kim, Ji Young; Choi, Joon Young; Kim, Hee Kyung; Jang, Hye Won; Hur, Kyu Yeon; Kim, Jae Hyeon; Kim, Kwang-Won; Chung, Jae Hoon; Kim, Sun Wook

2010-09-01

Serum thyroglobulin (Tg) is essential in the follow-up of patients with differentiated thyroid carcinoma (DTC). However, interchangeability and standardization between Tg assays have not yet been achieved, even with the development of an international Tg standard (Certified Reference Material 457 [CRM-457]). Serum Tg from 30 DTC patients and serially diluted CRM-457 were measured using 3 different immunoradiometric assays (IRMA-1, IRMA-2, IRMA-3). The intraclass correlation coefficient (ICC) method was used to describe the concordance of each IRMA to CRM-457. The serum Tg measured by 3 different IRMAs correlated well (r > .85, p < .0001), but clinically relevant discrepancies were found in 13.3% of patients. IRMA-3, which claims to be standardized to CRM-457, showed the best ICC (p(1) = .98) for the CRM-457. Hospitals caring for patients with DTC should either set their own cutoffs for IRMAs for Tg based on their patient pools, or adopt IRMAs standardized to CRM-457 and calibrate their laboratory using CRM-457.

Surgical site infections due to rapidly growing mycobacteria in puducherry, India.

PubMed

Kannaiyan, Kavitha; Ragunathan, Latha; Sakthivel, Sulochana; Sasidar, A R; Muralidaran; Venkatachalam, G K

2015-03-01

Rapidly growing Mycobacteria are increasingly recognized, nowadays as an important pathogen that can cause wide range of clinical syndromes in humans. We herein describe unrelated cases of surgical site infection caused by Rapidly growing Mycobacteria (RGM), seen during a period of 12 months. Nineteen patients underwent operations by different surgical teams located in diverse sections of Tamil Nadu, Pondicherry, Karnataka, India. All patients presented with painful, draining subcutaneous nodules at the infection sites. Purulent material specimens were sent to the microbiology laboratory. Gram stain and Ziehl-Neelsen staining methods were used for direct examination. Culture media included blood agar, chocolate agar, MacConkey agar, Sabourauds agar and Lowenstein-Jensen medium for Mycobacteria. Isolated microorganisms were identified and further tested for antimicrobial susceptibility by standard microbiologic procedures. Mycobacterium fortuitum and M.chelonae were isolated from the purulent drainage obtained from wounds by routine microbiological techniques from all the specimens. All isolates analyzed for antimicrobial susceptibility pattern were sensitive to clarithromycin, linezolid and amikacin but were variable to ciprofloxacin, rifampicin and tobramycin. Our case series highlights that a high level of clinical suspicion should be maintained for patients presenting with protracted soft tissue lesions with a history of trauma or surgery as these infections not only cause physical but also emotional distress that affects both the patients and the surgeon.

WRNIP1 accumulates at laser light irradiated sites rapidly via its ubiquitin-binding zinc finger domain and independently from its ATPase domain

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

Nomura, Hironoshin; Yoshimura, Akari, E-mail: akari_yo@musashino-u.ac.jp; Edo, Takato

2012-01-27

Highlights: Black-Right-Pointing-Pointer WRNIP1 accumulates in laser light irradiated sites very rapidly via UBZ domain. Black-Right-Pointing-Pointer The ATPase domain of WRNIP1 is dispensable for its accumulation. Black-Right-Pointing-Pointer The accumulation of WRNIP1 seems not to be dependent on the interaction with WRN. -- Abstract: WRNIP1 (Werner helicase-interacting protein 1) was originally identified as a protein that interacts with the Werner syndrome responsible gene product. WRNIP1 contains a ubiquitin-binding zinc-finger (UBZ) domain in the N-terminal region and two leucine zipper motifs in the C-terminal region. In addition, it possesses an ATPase domain in the middle of the molecule and the lysine residues servingmore » as ubiquitin acceptors in the entire of the molecule. Here, we report that WRNIP1 accumulates in laser light irradiated sites very rapidly via its ubiquitin-binding zinc finger domain, which is known to bind polyubiquitin and to be involved in ubiquitination of WRNIP1 itself. The accumulation of WRNIP1 in laser light irradiated sites also required the C-terminal region containing two leucine zippers, which is reportedly involved in the oligomerization of WRNIP1. Mutated WRNIP1 with a deleted ATPase domain or with mutations in lysine residues, which serve as ubiquitin acceptors, accumulated in laser light irradiated sites, suggesting that the ATPase domain of WRNIP1 and ubiquitination of WRNIP1 are dispensable for the accumulation.« less

Testing the applicability of rapid on-site enzymatic activity detection for surface water monitoring

NASA Astrophysics Data System (ADS)

Stadler, Philipp; Vogl, Wolfgang; Juri, Koschelnik; Markus, Epp; Maximilian, Lackner; Markus, Oismüller; Monika, Kumpan; Peter, Strauss; Regina, Sommer; Gabriela, Ryzinska-Paier; Farnleitner Andreas, H.; Matthias, Zessner

2015-04-01

On-site detection of enzymatic activities has been suggested as a rapid surrogate for microbiological pollution monitoring of water resources (e.g. using glucuronidases, galactosidases, esterases). Due to the possible short measuring intervals enzymatic methods have high potential as near-real time water quality monitoring tools. This presentation describes results from a long termed field test. For twelve months, two ColiMinder devices (Vienna Water Monitoring, Austria) for on-site determination of enzymatic activity were tested for stream water monitoring at the experimental catchment HOAL (Hydrological Open Air Laboratory, Center for Water Resource Systems, Vienna University of Technology). The devices were overall able to follow and reflect the diverse hydrological and microbiological conditions of the monitored stream during the test period. Continuous data in high temporal resolution captured the course of enzymatic activity in stream water during diverse rainfall events. The method also proofed sensitive enough to determine diurnal fluctuations of enzymatic activity in stream water during dry periods. The method was able to capture a seasonal trend of enzymatic activity in stream water that matches the results gained from Colilert18 analysis for E. coli and coliform bacteria of monthly grab samples. Furthermore the comparison of ColiMinder data with measurements gained at the same test site with devices using the same method but having different construction design (BACTcontrol, microLAN) showed consistent measuring results. Comparative analysis showed significant differences between measured enzymatic activity (modified fishman units and pmol/min/100ml) and cultivation based analyses (most probable number, colony forming unit). Methods of enzymatic activity measures are capable to detect ideally the enzymatic activity caused by all active target bacteria members, including VBNC (viable but nonculturable) while cultivation based methods cannot detect VBNC

Hydrolysis at One of the Two Nucleotide-binding Sites Drives the Dissociation of ATP-binding Cassette Nucleotide-binding Domain Dimers

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

Zoghbi, M. E.; Altenberg, G. A.

The functional unit of ATP-binding cassette (ABC) transporters consists of two transmembrane domains and two nucleotide-binding domains (NBDs). ATP binding elicits association of the two NBDs, forming a dimer in a head-to-tail arrangement, with two nucleotides “sandwiched” at the dimer interface. Each of the two nucleotide-binding sites is formed by residues from the two NBDs. We recently found that the prototypical NBD MJ0796 from Methanocaldococcus jannaschii dimerizes in response to ATP binding and dissociates completely following ATP hydrolysis. However, it is still unknown whether dissociation of NBD dimers follows ATP hydrolysis at one or both nucleotide-binding sites. Here, we usedmore » luminescence resonance energy transfer to study heterodimers formed by one active (donor-labeled) and one catalytically defective (acceptor-labeled) NBD. Rapid mixing experiments in a stop-flow chamber showed that NBD heterodimers with one functional and one inactive site dissociated at a rate indistinguishable from that of dimers with two hydrolysis-competent sites. Comparison of the rates of NBD dimer dissociation and ATP hydrolysis indicated that dissociation followed hydrolysis of one ATP. We conclude that ATP hydrolysis at one nucleotide-binding site drives NBD dimer dissociation.« less

Rapid movement of wastewater from on-site disposal systems into surface waters in the lower Florida Keys

USGS Publications Warehouse

Paul, John H.; McLaughlin, Molly R.; Griffin, Dale W.; Lipp, Erin K.; Stokes, Rodger; Rose, Joan B.

2000-01-01

Viral tracer studies have been used previously to study the potential for wastewater contamination of surface marine waters in the Upper and Middle Florida Keys. Two bacteriophages, the marine bacteriophage φHSIC and the Salmonella phage PRD1, were used as tracers in injection well and septic tank studies in Saddlebunch Keys of the Lower Florida Keys and in septic tank studies in Boot Key Harbor, Marathon, of the Middle Keys. In Boot Key Harbor, both phages were detected in a canal adjacent to the seeded septic tank within 3 h 15 min of the end of the seed period. The tracer was then detected at all sampling sites in Boot Key Harbor, including one on the opposite side of U. S. Highway 1 in Florida Bay, and at an Atlantic Ocean beach outside Boot Key Harbor. Rates of migration based on first appearance of the phage ranged from 1.7 to 57.5 m h-1. In Saddlebunch Keys, φHSIC and PRD1 were used to seed a residential septic tank and a commercial injection well. The septic tank tracer was not found in any surface water samples. The injection well tracer was first detected at a site most distant from the seed site, a channel that connected Sugarloaf Sound with the Atlantic Ocean. The rate of tracer migration from the injection well to this channel ranged from 66.8 to 141 m h-1. Both tracer studies showed a rapid movement of wastewater from on-site sewage treatment and disposal systems in a southeasterly direction toward the reef tract and Atlantic Ocean, with preferential movement through tidal channels. These studies indicate that wastewater disposal systems currently in widespread use in the Florida Keys can rapidly contaminate the marine environment.

A Methodology to Evaluate Ecological Resources and Risk Using Two Case Studies at the Department of Energy's Hanford Site

NASA Astrophysics Data System (ADS)

Burger, Joanna; Gochfeld, Michael; Bunn, Amoret; Downs, Janelle; Jeitner, Christian; Pittfield, Taryn; Salisbury, Jennifer; Kosson, David

2017-03-01

An assessment of the potential risks to ecological resources from remediation activities or other perturbations should involve a quantitative evaluation of resources on the remediation site and in the surrounding environment. We developed a risk methodology to rapidly evaluate potential impact on ecological resources for the U.S. Department of Energy's Hanford Site in southcentral Washington State. We describe the application of the risk evaluation for two case studies to illustrate its applicability. The ecological assessment involves examining previous sources of information for the site, defining different resource levels from 0 to 5. We also developed a risk rating scale from non-discernable to very high. Field assessment is the critical step to determine resource levels or to determine if current conditions are the same as previously evaluated. We provide a rapid assessment method for current ecological conditions that can be compared to previous site-specific data, or that can be used to assess resource value on other sites where ecological information is not generally available. The method is applicable to other Department of Energy's sites, where its development may involve a range of state regulators, resource trustees, Tribes and other stakeholders. Achieving consistency across Department of Energy's sites for valuation of ecological resources on remediation sites will assure Congress and the public that funds and personnel are being deployed appropriately.

A Methodology to Evaluate Ecological Resources and Risk Using Two Case Studies at the Department of Energy's Hanford Site.

PubMed

Burger, Joanna; Gochfeld, Michael; Bunn, Amoret; Downs, Janelle; Jeitner, Christian; Pittfield, Taryn; Salisbury, Jennifer; Kosson, David

2017-03-01

An assessment of the potential risks to ecological resources from remediation activities or other perturbations should involve a quantitative evaluation of resources on the remediation site and in the surrounding environment. We developed a risk methodology to rapidly evaluate potential impact on ecological resources for the U.S. Department of Energy's Hanford Site in southcentral Washington State. We describe the application of the risk evaluation for two case studies to illustrate its applicability. The ecological assessment involves examining previous sources of information for the site, defining different resource levels from 0 to 5. We also developed a risk rating scale from non-discernable to very high. Field assessment is the critical step to determine resource levels or to determine if current conditions are the same as previously evaluated. We provide a rapid assessment method for current ecological conditions that can be compared to previous site-specific data, or that can be used to assess resource value on other sites where ecological information is not generally available. The method is applicable to other Department of Energy's sites, where its development may involve a range of state regulators, resource trustees, Tribes and other stakeholders. Achieving consistency across Department of Energy's sites for valuation of ecological resources on remediation sites will assure Congress and the public that funds and personnel are being deployed appropriately.

Evaluation of the OnSite (Pf/Pan) rapid diagnostic test for diagnosis of clinical malaria

PubMed Central

2012-01-01

Background Accurate diagnosis of malaria is an essential prerequisite for proper treatment and drug resistance monitoring. Microscopy is considered the gold standard for malaria diagnosis but has limitations. ELISA, PCR, and Real Time PCR are also used to diagnose malaria in reference laboratories, although their application at the field level is currently not feasible. Rapid diagnostic tests (RDTs) however, have been brought into field operation and widely adopted in recent days. This study evaluates OnSite (Pf/Pan) antigen test, a new RDT introduced by CTK Biotech Inc, USA for malaria diagnosis in a reference setting. Methods Blood samples were collected from febrile patients referred for malaria diagnosis by clinicians. Subjects were included in this study from two different Upazila Health Complexes (UHCs) situated in two malaria endemic districts of Bangladesh. Microscopy and nested PCR were considered the gold standard in this study. OnSite (Pf/Pan) RDT was performed on preserved whole blood samples. Results In total, 372 febrile subjects were included in this study. Of these subjects, 229 (61.6%) tested positive for Plasmodium infection detected by microscopy and nested PCR. OnSite (Pf/Pan) RDT was 94.2% sensitive (95% CI, 89.3-97.3) and 99.5% specific (95% CI, 97.4-00.0) for Plasmodium falciparum diagnosis and 97.3% sensitive (95% CI, 90.5-99.7) and 98.7% specific (95% CI, 96.6-99.6) for Plasmodium vivax diagnosis. Sensitivity varied with differential parasite count for both P. falciparum and P. vivax. The highest sensitivity was observed in febrile patients with parasitaemia that ranged from 501–1,000 parasites/μL regardless of the Plasmodium species. Conclusion The new OnSite (Pf/Pan) RDT is both sensitive and specific for symptomatic malaria diagnosis in standard laboratory conditions. PMID:23234579

Evaluation of the OnSite (Pf/Pan) rapid diagnostic test for diagnosis of clinical malaria.

PubMed

Mohon, Abu Naser; Elahi, Rubayet; Podder, Milka Patracia; Mohiuddin, Khaja; Hossain, Mohammad Sharif; Khan, Wasif A; Haque, Rashidul; Alam, Mohammad Shafiul

2012-12-12

Accurate diagnosis of malaria is an essential prerequisite for proper treatment and drug resistance monitoring. Microscopy is considered the gold standard for malaria diagnosis but has limitations. ELISA, PCR, and Real Time PCR are also used to diagnose malaria in reference laboratories, although their application at the field level is currently not feasible. Rapid diagnostic tests (RDTs) however, have been brought into field operation and widely adopted in recent days. This study evaluates OnSite (Pf/Pan) antigen test, a new RDT introduced by CTK Biotech Inc, USA for malaria diagnosis in a reference setting. Blood samples were collected from febrile patients referred for malaria diagnosis by clinicians. Subjects were included in this study from two different Upazila Health Complexes (UHCs) situated in two malaria endemic districts of Bangladesh. Microscopy and nested PCR were considered the gold standard in this study. OnSite (Pf/Pan) RDT was performed on preserved whole blood samples. In total, 372 febrile subjects were included in this study. Of these subjects, 229 (61.6%) tested positive for Plasmodium infection detected by microscopy and nested PCR. OnSite (Pf/Pan) RDT was 94.2% sensitive (95% CI, 89.3-97.3) and 99.5% specific (95% CI, 97.4-00.0) for Plasmodium falciparum diagnosis and 97.3% sensitive (95% CI, 90.5-99.7) and 98.7% specific (95% CI, 96.6-99.6) for Plasmodium vivax diagnosis. Sensitivity varied with differential parasite count for both P. falciparum and P. vivax. The highest sensitivity was observed in febrile patients with parasitaemia that ranged from 501-1,000 parasites/μL regardless of the Plasmodium species. The new OnSite (Pf/Pan) RDT is both sensitive and specific for symptomatic malaria diagnosis in standard laboratory conditions.

Measurements of Turbulence at Two Tidal Energy Sites in Puget Sound, WA

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

Thomson, Jim; Polagye, Brian; Durgesh, Vibhav

2012-06-05

Field measurements of turbulence are pre- sented from two sites in Puget Sound, WA (USA) that are proposed for electrical power generation using tidal current turbines. Rapidly sampled data from multiple acoustic Doppler instruments are analyzed to obtain statistical mea- sures of fluctuations in both the magnitude and direction of the tidal currents. The resulting turbulence intensities (i.e., the turbulent velocity fluctuations normalized by the harmonic tidal currents) are typically 10% at the hub- heights (i.e., the relevant depth bin) of the proposed turbines. Length and time scales of the turbulence are also analyzed. Large-scale, anisotropic eddies dominate the energymore » spectra, which may be the result of proximity to headlands at each site. At small scales, an isotropic turbulent cascade is observed and used to estimate the dissipation rate of turbulent kinetic energy. Data quality and sampling parameters are discussed, with an emphasis on the removal of Doppler noise from turbulence statistics.« less

Two-site Photometry and Spectroscopy of the Rapidly Pulsating sdB Star EC 22221-3152

NASA Astrophysics Data System (ADS)

Barlow, B. N.; Kilkenny, D.; Geier, S.; Dunlap, B. H.; Reichart, D. E.; LaCluyze, A. P.; Ivarsen, K. M.; Haislip, J. B.; Nysewander, M. C.

2017-05-01

We present follow-up photometry and spectroscopy of the rapidly pulsating subdwarf B star EC 22221-3152. Using the SAAO 1.0-m telescope and the 0.4-m Panchromatic Robotic Optical Monitoring and Polarimetry Telescopes (PROMPT) at the Cerro Tololo Inter-American Observatory (CTIO), we monitored the star photometrically for one week. By combining data from both telescopes, we were able to resolve 18 significant periodicities in the light curve. Seven of these signals consist of combination frequencies, a first harmonic, and possible rotational splittings that would be indicative of an 8.2-d rotation period. The remaining 11 periodicities appear to represent independent oscillation modes, including three not originally detected in the discovery work. Time series spectroscopy obtained with the Goodman spectrograph on the 4.1-m SOAR telescope reveals possible velocity variations corresponding to two of the observed pulsation modes. From atmospheric model fits to the spectra, we derive {T}{eff}=35600+/- 600 K, log g = 5.86 ± 0.15, and log N(He)/N(H) = -1.4 ± 0.3 and confirm the star’s status as one of the hottest sdBV r stars currently known. Based on observations at the SOAR telescope, a collaboration between CPNq-Brazil, NOAO, UNC, and MSU.

Method for rapid estimation of scour at highway bridges based on limited site data

USGS Publications Warehouse

Holnbeck, S.R.; Parrett, Charles

1997-01-01

Limited site data were used to develop a method for rapid estimation of scour at highway bridges. The estimates can be obtained in a matter of hours rather than several days as required by more-detailed methods. Such a method is important because scour assessments are needed to identify scour-critical bridges throughout the United States. Using detailed scour-analysis methods and scour-prediction equations recommended by the Federal Highway Administration, the U.S. Geological Survey, in cooperation with the Montana Department of Transportation, obtained contraction, pier, and abutment scour-depth data for sites from 10 States.The data were used to develop relations between scour depth and hydraulic variables that can be rapidly measured in the field. Relations between scour depth and hydraulic variables, in the form of envelope curves, were based on simpler forms of detailed scour-prediction equations. To apply the rapid-estimation method, a 100-year recurrence interval peak discharge is determined, and bridge- length data are used in the field with graphs relating unit discharge to velocity and velocity to bridge backwater as a basis for estimating flow depths and other hydraulic variables that can then be applied using the envelope curves. The method was tested in the field. Results showed good agreement among individuals involved and with results from more-detailed methods. Although useful for identifying potentially scour-critical bridges, themethod does not replace more-detailed methods used for design purposes. Use of the rapid- estimation method should be limited to individuals having experience in bridge scour, hydraulics, and flood hydrology, and some training in use of the method.

A Methodology to Evaluate Ecological Resources and Risk Using Two Case Studies at the Department of Energy’s Hanford Site

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

Burger, Joanna; Gochfeld, Michael; Bunn, Amoret

An assessment of the potential risks to ecological resources from remediation activities or other perturbations should involve a quantitative evaluation of resources on the remediation site and in the surrounding environment. We developed a risk methodology to rapidly evaluate potential impact on ecological resources for the U.S. Department of Energy’s Hanford Site in southcentral Washington State. We describe the application of the risk evaluation for two case studies to illustrate its applicability. The ecological assessment involves examining previous sources of information for the site, defining different resource levels from 0 to 5. We also developed a risk rating scale frommore » nondiscernable to very high. Field assessment is the critical step to determine resource levels or to determine if current conditions are the same as previously evaluated. We provide a rapid assessment method for current ecological conditions that can be compared to previous site-specific data, or that can be used to assess resource value on other sites where ecological information is not generally available. The method is applicable to other Department of Energy’s sites, where its development may involve a range of state regulators, resource trustees, Tribes and other stakeholders. Achieving consistency across Department of Energy’s sites for valuation of ecological resources on remediation sites will assure Congress and the public that funds and personnel are being deployed appropriately.« less

Active-site-matched fluorescent probes for rapid and direct detection of vicinal-sulfydryl-containing peptides/proteins in living cells.

PubMed

Pan, Xiaohong; Liang, Ziye; Li, Jing; Wang, Shanshan; Kong, Fanpeng; Xu, Kehua; Tang, Bo

2015-01-26

Vicinal-sulfydryl-containing peptides/proteins (VSPPs) play a crucial role in human pathologies. Fluorescent probes that are capable of detecting intracellular VSPPs in vivo would be useful tools to explore the mechanisms of some diseases. In this study, by regulating the spatial separation of two maleimide groups in a fluorescent dye to match that of two active cysteine residues contained in the conserved amino acid sequence (-CGPC-) of human thioredoxin, two active-site-matched fluorescent probes, o-Dm-Ac and m-Dm-Ac, were developed for real-time imaging of VSPPs in living cells. As a result, the two probes can rapidly respond to small peptide models and reduced proteins, such as WCGPCK (W-6), WCGGPCK (W-7), and WCGGGPCK (W-8), reduced bovine serum albumin (rBSA), and reduced thioredoxin (rTrx). Moreover, o-Dm-Ac displays a higher binding sensitivity with the above-mentioned peptides and proteins, especially with W-7 and rTrx. Furthermore, o-Dm-Ac was successfully used to rapidly and directly detect VSPPs both in vitro and in living cells. Thus, a novel probe-design strategy was proposed and the synthesized probe applied successfully in imaging of target proteins in situ. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid on-site monitoring of Legionella pneumophila in cooling tower water using a portable microfluidic system.

PubMed

Yamaguchi, Nobuyasu; Tokunaga, Yusuke; Goto, Satoko; Fujii, Yudai; Banno, Fumiya; Edagawa, Akiko

2017-06-08

Legionnaires' disease, predominantly caused by the bacterium Legionella pneumophila, has increased in prevalence worldwide. The most common mode of transmission of Legionella is inhalation of contaminated aerosols, such as those generated by cooling towers. Simple, rapid and accurate methods to enumerate L. pneumophila are required to prevent the spread of this organism. Here, we applied a microfluidic device for on-chip fluorescent staining and semi-automated counting of L. pneumophila in cooling tower water. We also constructed a portable system for rapid on-site monitoring and used it to enumerate target bacterial cells rapidly flowing in the microchannel. A fluorescently-labelled polyclonal antibody was used for the selective detection of L. pneumophila serogroup 1 in the samples. The counts of L. pneumophila in cooling tower water obtained using the system and fluorescence microscopy were similar. The detection limit of the system was 10 4  cells/ml, but lower numbers of L. pneumophila cells (10 1 to 10 3  cells/ml) could be detected following concentration of 0.5-3 L of the water sample by filtration. Our technique is rapid to perform (1.5 h), semi-automated (on-chip staining and counting), and portable for on-site measurement, and it may therefore be effective in the initial screening of Legionella contamination in freshwater.

Algal and water-quality data for Rapid Creek and Canyon Lake near Rapid City, South Dakota, 2007

USGS Publications Warehouse

Hoogestraat, Galen K.; Putnam, Larry D.; Graham, Jennifer L.

2008-01-01

This report summarizes the results of algae and water-quality sampling on Rapid Creek and Canyon Lake during May and September 2007. The overall purpose of the study was to determine the algal community composition of Rapid Creek and Canyon Lake in relation to organisms that are known producers of unwanted tastes and odors in drinking-water supplies. Algal assemblage structure (phytoplankton and periphyton) was examined at 16 sites on Rapid Creek and Canyon Lake during May and September 2007, and actinomycetes bacteria were sampled at the Rapid City water treatment plant intake in May 2007, to determine if taste-and-odor producing organisms were present. During the May 2007 sampling, 3 Rapid Creek sites and 4 Canyon Lake sites were quantitatively sampled for phytoplankton in the water column, 7 Rapid Creek sites were quantitatively sampled for attached periphyton, and 4 lake and retention pond sites were qualitatively sampled for periphyton. Five Rapid Creek sites were sampled for geosmin and 2-methylisoborneol, two common taste-and-odor causing compounds known to affect water supplies. During the September 2007 sampling, 4 Rapid Creek sites were quantitatively sampled for attached periphyton, and 3 Canyon Lake sites were qualitatively sampled for periphyton. Water temperature, dissolved oxygen, pH, and specific conductance were measured during each sampling event. Methods of collection and sample analysis are presented for the various types of biological and chemical constituent samples. Diatoms comprised 91-100 percent of the total algal biovolume in periphyton samples collected during May and September. Cyanobacteria (also called blue-green algae) were detected in 7 of the 11 quantitative periphyton samples and ranged from 0.01 to 2.0 percent of the total biovolume. Cyanobacteria were present in 3 of the 7 phytoplankton samples collected in May, but the relative biovolumes were small (0.01-0.2 percent). Six of seven qualitative samples collected from Canyon Lake

Response of canopy nitrogen uptake to a rapid decrease in bulk nitrate deposition in two eastern Canadian boreal forests.

PubMed

Houle, D; Marty, C; Duchesne, L

2015-01-01

A few studies have reported a recent and rapid decline in NO3(-) deposition in eastern North America. Whether this trend can be observed at remote boreal sites with low rates of N deposition and how it could impact canopy uptake (CU) of N remain unknown. Here we report trends between 1997/1999 and 2012 for precipitation, throughfall N deposition as well as inorganic N CU for two boreal forest sites of Quebec, Canada, with contrasted N deposition rates and tree species composition. NO3(-) bulk deposition declined by approximately 50% at both sites over the studied period while no change was observed for NH4(+). As a result, the contribution of NH4(+) to inorganic N deposition changed from ~33% to more than 50% during the study period. On average, 52-59% of N deposition was intercepted by the canopy, the retention being higher for NH4(+) (60-67%) than for NO3(-) (45-54%). The decrease in NO3(-) bulk deposition and the increase in the NH4(+):NO3(-) ratio had important impacts on N-canopy interactions. The contribution of NH4(+) CU to that of total inorganic N CU increased at both sites but the trend was significant only at Tirasse (lowest N deposition). At this site, absolute NO3(-) CU significantly decreased (as did total N CU) during the study period, a consequence of the strong relationship (r(2) = 0.88) between NO3(-) bulk deposition and NO3(-) CU. Our data suggest that N interactions with forest canopies may change rapidly with changes in N deposition as well as with tree species composition.

Rapid Assessment of Ecosystem Services Provided by Two Mineral Extraction Sites Restored for Nature Conservation in an Agricultural Landscape in Eastern England

PubMed Central

Blaen, Phillip J.; Jia, Li; Peh, Kelvin S.-H.; Field, Rob H.; Balmford, Andrew; MacDonald, Michael A.; Bradbury, Richard B.

2015-01-01

Despite growing recognition that mineral sites restored for nature conservation can enhance local biodiversity, the wider societal benefits provided by this type of restoration relative to alternative options are not well understood. This study addresses this research gap by quantifying differences in ecosystem services provision under two common mineral site after-uses: nature conservation and agriculture. Using a combination of site-specific primary field data, benefits transfer and modelling, we show that for our sites restoration for nature conservation provides a more diverse array of ecosystem services than would be delivered under an agricultural restoration scenario. We also explore the effects of addressing different conservation targets, which we find alter the provision of ecosystem services on a service-specific basis. Highly species-focused intervention areas are associated with increased carbon storage and livestock grazing provision, whereas non-intervention areas are important for carbon sequestration, fishing, recreation and flood risk mitigation. The results of this study highlight the wider societal importance of restored mineral sites and may help conservation managers and planners to develop future restoration strategies that provide benefits for both biodiversity and human well-being. PMID:25894293

Rapid assessment of ecosystem services provided by two mineral extraction sites restored for nature conservation in an agricultural landscape in eastern England.

PubMed

Blaen, Phillip J; Jia, Li; Peh, Kelvin S-H; Field, Rob H; Balmford, Andrew; MacDonald, Michael A; Bradbury, Richard B

2015-01-01

Despite growing recognition that mineral sites restored for nature conservation can enhance local biodiversity, the wider societal benefits provided by this type of restoration relative to alternative options are not well understood. This study addresses this research gap by quantifying differences in ecosystem services provision under two common mineral site after-uses: nature conservation and agriculture. Using a combination of site-specific primary field data, benefits transfer and modelling, we show that for our sites restoration for nature conservation provides a more diverse array of ecosystem services than would be delivered under an agricultural restoration scenario. We also explore the effects of addressing different conservation targets, which we find alter the provision of ecosystem services on a service-specific basis. Highly species-focused intervention areas are associated with increased carbon storage and livestock grazing provision, whereas non-intervention areas are important for carbon sequestration, fishing, recreation and flood risk mitigation. The results of this study highlight the wider societal importance of restored mineral sites and may help conservation managers and planners to develop future restoration strategies that provide benefits for both biodiversity and human well-being.

SITE CHARACTERIZATION AND THERMAL REMEDIATION TREATABILITY STUDIES FOR TWO WOOD TREATER SITES

EPA Science Inventory

Assessment of the applicability of thermal remediation at two wood treater sites is ongoing. The two wood treaters had been in operation for 50 to 80 years, and a variety of wood treating chemicals had been employed, including creosote, pentachlorophenol, and various metal prepa...

Mineral precipitation and dissolution at two slag-disposal sites in northwestern Indiana, USA

USGS Publications Warehouse

Bayless, E.R.; Schulz, M.S.

2003-01-01

Slag is a ubiquitous byproduct of the iron- and steel-refining industries. In northwestern Indiana and northeastern Illinois, slag has been deposited over more than 52 km2 of land surface. Despite the widespread use of slag for fill and construction purposes, little is known about its chemical effects on the environment. Two slagdisposal sites were examined in northwestern Indiana where slag was deposited over the native glacial deposits. At a third site, where slag was not present, background conditions were defined. Samples were collected from cores and drill cuttings and described with scanning electron microscopy and electron microprobe analysis. Ground-water samples were collected and used to assess thermodynamic equilibria between authigenic minerals and existing conditions. Differences in the mineralogy at background and slag-affected sites were apparent. Calcite, dolomite, gypsum, iron oxides, and clay minerals were abundant in native sediments immediately beneath the slag. Mineral features indicated that these minerals precipitated rapidly from slag drainage and co-precipitated minor amounts of non-calcium metals and trace elements. Quartz fragments immediately beneath the slag showed extensive pitting that was not apparent in sediments from the background site, indicating chemical weathering by the hyperalkaline slag drainage. The environmental impacts of slag-related mineral precipitation include disruption of natural ground-water flow patterns and bed-sediment armoring in adjacent surface-water systems. Dissolution of native quartz by the hyperalkaline drainage may cause instability in structures situated over slag fill or in roadways comprised of slag aggregates.

Rapid, On-Site, Ultrasensitive Melamine Quantitation Method for Protein Beverages Using Time-Resolved Fluorescence Detection Paper.

PubMed

Li, Guanghua; Wang, Du; Zhou, Aijun; Sun, Yimin; Zhang, Qi; Poapolathep, Amnart; Zhang, Li; Fan, Zhiyong; Zhang, Zhaowei; Li, Peiwu

2018-06-06

To ensure protein beverage safety and prevent illegal melamine use to artificially increase protein content, a rapid, on-site, ultrasensitive detection method for melamine must be developed because melamine is detrimental to human health. Herein, an ultrasensitive time-resolved fluorescence detection paper (TFDP) was developed to detect melamine in protein beverages within 15 min using a one-step sample preparation. The lower limits of detection were 0.89, 0.94, and 1.05 ng/mL, and the linear ranges were 2.67-150, 2.82-150, and 3.15-150 ng/mL (R 2 > 0.982) for peanut, walnut, and coconut beverages, respectively. The recovery rates were 85.86-110.60% with a coefficient of variation <7.80% in the spiking experiment. A high specificity was observed in the interferent experiment. When detecting real protein beverage samples, the TFDP and ultraperformance liquid chromatography-tandem mass spectrometer (UPLC-MS/MS) results were consistent. This method is a promising alternative for rapid, on-site detection of melamine in beverages.

Rapid Reconnaissance Mapping of Volatile Organic Compounds by Photoionization Detection at the USGS Amargosa Desert Research Site

NASA Astrophysics Data System (ADS)

Thordsen, J. J.; Stonestrom, D. A.; Conaway, C. H.; Luo, W.; Baker, R. J.; Andraski, B. J.

2015-12-01

Two types of handheld photoionization detectors were evaluated in April 2015 for reconnaissance mapping of volatile organic compounds (VOCs) in the unsaturated zone surrounding legacy disposal trenches for commercial low-level radioactive waste near Beatty, Nevada (USA). This method is rapid and cost effective when compared to the more conventional procedure used ate the site, where VOCs are collected on sorbent cartridges in the field followed by thermal desorption, gas chromatographic separation, and quantitation by mass spectroscopy in the laboratory (TD-GC-MS analysis). Using the conventional method, more than sixty distinct compounds have been identified in the 110-m deep unsaturated zone vapor phase, and the changing nature of the VOC mix over a 15-yr timeframe has been recorded. Analyses to date have identified chlorofluorocarbons (CFCs), chlorinated ethenes, chlorinated ethanes, gasoline-range hydrocarbons, chloroform, and carbon tetrachloride as the main classes of VOCs present. The VOC plumes emanating from the various subgroups of trenches are characterized by different relative abundances of the compound classes, and total VOC concentrations that cover several orders of magnitude. One of the photoionization detectors, designed for industrial compliance testing, lacked sufficient dynamic range and sensitivity to be useful. The other, a wide range (1 ppb-20,000 ppm) research-grade instrument with a 10.6 eV photoionization detector (PID) lamp, produced promising results, detecting roughly half of the non-CFC VOCs present. The rapid and inexpensive photoionization method is envisioned as a screening tool to supplement, expedite, and direct the collection of additional samples for TD-GC-MS analyses at this and other VOC-contaminated sites.

Two-Site Comparison of Transpiration by Larrea Tridentata

NASA Astrophysics Data System (ADS)

Cavanaugh, M. L.; Kurc, S. A.; Scott, R. L.; Bryant, R. B.

2008-12-01

As a result of landscape changes within the desert southwestern U.S. such as increased grazing, reduced wildfire frequency, and changes in atmospheric conditions, the native creosotebush (Larrea tridentata) has encroached upon historically grass-dominated ecosystems, expanding in range and land cover density. To understand how creosotebush influences the water budget of ecosystems, heat balance sap flow sensors were employed on creosotebush stems at both the Santa Rita Experimental Range (SRER) and Walnut Gulch Experimental Watershed (WGEW). Additionally, both sites are equipped with eddy covariance towers, associated micrometeorological measurements, and profiles of water content reflectometers for soil moisture. The differences found between the two sites, including soil type and precipitation regime, are the basis of the following hypotheses. Firstly, we hypothesize that we will not see transpiration (T) responses following storms less than 5 mm at both sites. Secondly, we hypothesize that at both sites we will see a lagged response of T to large precipitation events, with evaporation being the dominate component in the partitioning of evapotranspiration (ET) for the first two days. Thirdly, we hypothesize that the ratio of plant transpiration to total evapotranspiration (T/ET) will be less at SRER due to the larger amount of bare soil exposed at this site. In this study, we show data from one summer at both sites and show how these relate to different precipitation events and soil moisture reservoirs.

Immunoassay of serum polypeptide hormones by using 125I-labelled anti(-immunoglobulin G) antibodies.

PubMed

Beck, P; Nicholas, H

1975-03-01

1. A technique for indirectly labelling antibodies to polypeptide hormones, by combining them with radioactively labelled anti-(immunoglobulin G) is described. (a) 125I-labelled anti-(rabbit immunoglobulin G) and anti-(guinea-pig immunoglobulin G) antibodies with high specific radioactivity were prepared after purification of the antibodies on immunoadsorbents containing the respective antigens. (b) Rabbit immunoglobulin G antibodies to human growth hormone, porcine glucagon and guinea-pig immunoglobulin G antibodies to bovine insulin and bovine parathyroid hormone were combined with immunoadsorbents containing the respective polypeptide hormone antigen. (c) The immunoglobulin G antibodies to the polypeptide hormones were reacted with 125-I-labelled anti-(immunoglobulin G) antibodies directed against the appropriate species of immunoglobulin G,and the anti-hormone antibodies were combined with the hormone-containing immunoadsorbent. (d) 125I-labelled anti-(immunoglobulin G) antibodies and anti-hormone antibodies were simultaneously eluted from the hormone-containing immunoadsorbent by dilute HCl, pH 2.0. After elution the anti-(immunoglobulin G) antibodies and antihormone antibodies were allowed to recombine at pH 8.0 and 4 degrees C. 2. The resultant immunoglobulin G-anti-immunoglobulin G complex was used in immunoradiometric (labelled antibody) and two-site assays of the respective polypeptide hormone. 3. By using these immunoassays, concentrations down to 90pg of human growth hormone/ml, 100 pg of bovine insulin/ml, 80 pg of bovine parathyroid hormone/ml and 150 pg of glucagon/ml were readily detected. Assays of human plasma for growth hormone and insulin by these methods showed good agreement with results obtained by using a directly 125I-labelled anti-hormone antibody in an immunoradiometric assay of human growth hormone or by radioimmunoassay of human insulin. 4. The method described allows immunoradiometric or two-site assays to be performed starting with as

Are rapid population estimates accurate? A field trial of two different assessment methods.

PubMed

Grais, Rebecca F; Coulombier, Denis; Ampuero, Julia; Lucas, Marcelino E S; Barretto, Avertino T; Jacquier, Guy; Diaz, Francisco; Balandine, Serge; Mahoudeau, Claude; Brown, Vincent

2006-09-01

Emergencies resulting in large-scale displacement often lead to populations resettling in areas where basic health services and sanitation are unavailable. To plan relief-related activities quickly, rapid population size estimates are needed. The currently recommended Quadrat method estimates total population by extrapolating the average population size living in square blocks of known area to the total site surface. An alternative approach, the T-Square, provides a population estimate based on analysis of the spatial distribution of housing units taken throughout a site. We field tested both methods and validated the results against a census in Esturro Bairro, Beira, Mozambique. Compared to the census (population: 9,479), the T-Square yielded a better population estimate (9,523) than the Quadrat method (7,681; 95% confidence interval: 6,160-9,201), but was more difficult for field survey teams to implement. Although applicable only to similar sites, several general conclusions can be drawn for emergency planning.

Application of the dengue virus NS1 antigen rapid test for on-site detection of imported dengue cases at airports.

PubMed

Shu, Pei-Yun; Yang, Cheng-Fen; Kao, Jeng-Fong; Su, Chien-Ling; Chang, Shu-Fen; Lin, Chien-Chou; Yang, Wen-Chih; Shih, Hsiu; Yang, Shih-Yan; Wu, Ping-Fuai; Wu, Ho-Sheng; Huang, Jyh-Hsiung

2009-04-01

We used the dengue virus NS1 antigen (Ag) rapid test for on-site detection of imported dengue cases at airports. Among 22 positive cases of dengue identified from 850 patients with a fever suspected to have dengue, 17 were NS1 Ag test positive. These findings demonstrate the usefulness of the NS1 Ag rapid test in screening imported dengue cases at airports.

Application of the Dengue Virus NS1 Antigen Rapid Test for On-Site Detection of Imported Dengue Cases at Airports▿

PubMed Central

Shu, Pei-Yun; Yang, Cheng-Fen; Kao, Jeng-Fong; Su, Chien-Ling; Chang, Shu-Fen; Lin, Chien-Chou; Yang, Wen-Chih; Shih, Hsiu; Yang, Shih-Yan; Wu, Ping-Fuai; Wu, Ho-Sheng; Huang, Jyh-Hsiung

2009-01-01

We used the dengue virus NS1 antigen (Ag) rapid test for on-site detection of imported dengue cases at airports. Among 22 positive cases of dengue identified from 850 patients with a fever suspected to have dengue, 17 were NS1 Ag test positive. These findings demonstrate the usefulness of the NS1 Ag rapid test in screening imported dengue cases at airports. PMID:19193828

Control of Ion Selectivity in LeuT: Two Na+ Binding Sites with two different mechanisms

PubMed Central

Noskov, Sergei Y.; Roux, Benoît

2016-01-01

The x-ray structure of LeuT, a bacterial homologue of Na+/Cl−-dependent neurotransmitter transporter, provides a great opportunity to better understand the molecular basis of monovalent cation selectivity in ion-coupled transporters. LeuT possesses two ion-binding sites, NA1 and NA2, which are highly selective for Na+. Extensive all-atom free energy molecular dynamics simulations of LeuT embedded in an explicit membrane are performed at different temperatures and various occupancy states of the binding sites to dissect the molecular mechanism of ion selectivity. The results show that the two binding sites display robust selectivity for Na+ over K+ or Li+, the competing ions of most similar radii. Of particular interest, the mechanism primarily responsible for selectivity for each of the two binding sites appears to be different. In site NA1, selectivity for Na+ over K+ arises predominantly from the strong electrostatic field arising from the negatively charged carboxylate group of the leucine substrate coordinating the ion directly. In site NA2, which comprises only neutral ligands, selectivity for Na+ is enforced by the local structural restraints arising from the hydrogen-bonding network and the covalent connectivity of the poly-peptide chain surrounding the ion according to a snug-fit mechanism. PMID:18280500

Concealed Accessory Pathways with a Single Ventricular and Two Discrete Atrial Insertion Sites.

PubMed

Kipp, Ryan T; Abu Sham'a, Raed; Hiroyuki, Ito; Han, Frederick T; Refaat, Marwan; Hsu, Jonathan C; Field, Michael E; Kopp, Douglas E; Marcus, Gregory M; Scheinman, Melvin M; Hoffmayer, Kurt S

2017-03-01

Atrioventricular reciprocating tachycardia (AVRT) utilizing a concealed accessory pathway is common. It is well appreciated that some patients may have multiple accessory pathways with separate atrial and ventricular insertion sites. We present three cases of AVRT utilizing concealed pathways with evidence that each utilizing a single ventricular insertion and two discrete atrial insertion sites. In case one, two discrete atrial insertion sites were mapped in two separate procedures, and only during the second ablation was the Kent potential identified. Ablation of the Kent potential at this site remote from the two atrial insertion sites resulted in the termination of the retrograde conduction in both pathways. Case two presented with supraventricular tachycardia (SVT) with alternating eccentric atrial activation patterns without alteration in the tachycardia cycle length. The two distinct atrial insertion sites during orthodromic AVRT and ventricular pacing were targeted and each of the two atrial insertion sites were successfully mapped and ablated. In case three, retrograde decremental conduction utilizing both atrial insertion sites was identified prior to ablation. After mapping and ablation of the first discrete atrial insertion site, tachycardia persisted utilizing the second atrial insertion site. Only after ablation of the second atrial insertion site was SVT noninducible, and VA conduction was no longer present. Concealed retrograde accessory pathways with discrete atrial insertion sites may have a common ventricular insertion site. Identification and ablation of the ventricular insertion site or the separate discrete atrial insertion sites result in successful treatment. © 2017 Wiley Periodicals, Inc.

Genetic Encoding of bicyclononynes and trans-cyclooctenes for site-specific protein labeling in vitro and in live mammalian cells via rapid fluorogenic Diels-Alder reactions.

PubMed

Lang, Kathrin; Davis, Lloyd; Wallace, Stephen; Mahesh, Mohan; Cox, Daniel J; Blackman, Melissa L; Fox, Joseph M; Chin, Jason W

2012-06-27

Rapid, site-specific labeling of proteins with diverse probes remains an outstanding challenge for chemical biologists. Enzyme-mediated labeling approaches may be rapid but use protein or peptide fusions that introduce perturbations into the protein under study and may limit the sites that can be labeled, while many "bioorthogonal" reactions for which a component can be genetically encoded are too slow to effect quantitative site-specific labeling of proteins on a time scale that is useful for studying many biological processes. We report a fluorogenic reaction between bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) and tetrazines that is 3-7 orders of magnitude faster than many bioorthogonal reactions. Unlike the reactions of strained alkenes, including trans-cyclooctenes and norbornenes, with tetrazines, the BCN-tetrazine reaction gives a single product of defined stereochemistry. We have discovered aminoacyl-tRNA synthetase/tRNA pairs for the efficient site-specific incorporation of a BCN-containing amino acid, 1, and a trans-cyclooctene-containing amino acid 2 (which also reacts extremely rapidly with tetrazines) into proteins expressed in Escherichia coli and mammalian cells. We demonstrate the rapid fluorogenic labeling of proteins containing 1 and 2 in vitro, in E. coli , and in live mammalian cells. These approaches may be extended to site-specific protein labeling in animals, and we anticipate that they will have a broad impact on labeling and imaging studies.

Two-loop beam and soft functions for rapidity-dependent jet vetoes

NASA Astrophysics Data System (ADS)

Gangal, Shireen; Gaunt, Jonathan R.; Stahlhofen, Maximilian; Tackmann, Frank J.

2017-02-01

Jet vetoes play an important role in many analyses at the LHC. Traditionally, jet vetoes have been imposed using a restriction on the transverse momentum p Tj of jets. Alternatively, one can also consider jet observables for which p Tj is weighted by a smooth function of the jet rapidity y j that vanishes as | y j | → ∞. Such observables are useful as they provide a natural way to impose a tight veto on central jets but a looser one at forward rapidities. We consider two such rapidity-dependent jet veto observables, T_{Bj} and {T_{Cj} , and compute the required beam and dijet soft functions for the jet-vetoed color-singlet production cross section at two loops. At this order, clustering effects from the jet algorithm become important. The dominant contributions are computed fully analytically while corrections that are subleading in the limit of small jet radii are expressed in terms of finite numerical integrals. Our results enable the full NNLL' resummation and are an important step towards N3LL resummation for cross sections with a T_{Bj} or T_{Cj} jet veto.

Assessment of compost application to coal ash disposal sites to promote the rapid vegetation establishment

NASA Astrophysics Data System (ADS)

Repmann, F.; Slazak, A.; Babic, M.; Schneider, B. U.; Schaaf, W.; Hüttl, R. F.

2009-04-01

In the city of Tuzla, located in Bosnia and Herzegovina, a coal fired thermo electric power plant is operated by the company JP ELEKTROPRIVERDA BIH TERMOELEKTRANA "TUZLA". High amounts of ash are produced by the power plant, which are currently disposed into settlement ponds bordered by dams in natural valleys. A total of four ash disposal sites covering an area of approx. 170 ha have been established during the last decades. Due to the fact that residual ash from coal combustion was found to contain a variety of trace elements (Ni, Cr, As, B), it must be assumed that ash disposal of that magnitude constitutes an environmental problem which is investigated within the EU-FP6 / STREP project "Reintegration of Coal Ash Disposal Sites and Mitigation of Pollution in the West Balkan Area" RECOAL. The main hazards relate to soil and groundwater contamination due to leaching toxins, dust dispersion, and toxins entering the food chain as these disposal sites are used for agricultural purposes. In order to rapidly establish a vegetation cover on barren ash dumps that particularly would prevent dust erosion we assessed the applicability of compost, produced from locally available municipal and industrial organic residues as an amendment to ash to improve substrate fertility. The envisaged remediation technology was considered to be a low cost, easy applicable and rapid method capable of substantially enhancing living conditions of residents in the vicinity of the abandoned disposal sites. Various compost application rates were evaluated in the field on experimental site Divkovici I in Tuzla and additionally in the greenhouse environment at Brandenburg Technical University Cottbus. Field and laboratory tests revealed that plant growth and cover rate can substantially be improved by mixing compost into the upper ash layer to a maximum depth of approx. 20 cm. Besides direct growth observations in the field analysis of soil parameters gave evidence that the fertility of ashy

Rapid on-site sensing aflatoxin B1 in food and feed via a chromatographic time-resolved fluoroimmunoassay.

PubMed

Zhang, Zhaowei; Tang, Xiaoqian; Wang, Du; Zhang, Qi; Li, Peiwu; Ding, Xiaoxia

2015-01-01

Aflatoxin B1 poses grave threats to food and feed safety due to its strong carcinogenesis and toxicity, thus requiring ultrasensitive rapid on-site determination. Herein, a portable immunosensor based on chromatographic time-resolved fluoroimmunoassay was developed for sensitive and on-site determination of aflatoxin B1 in food and feed samples. Chromatographic time-resolved fluoroimmunoassay offered a magnified positive signal and low signal-to-noise ratio in time-resolved mode due to the absence of noise interference caused by excitation light sources. Compared with the immunosensing performance in previous studies, this platform demonstrated a wider dynamic range of 0.2-60 μg/kg, lower limit of detection from 0.06 to 0.12 µg/kg, and considerable recovery from 80.5% to 116.7% for different food and feed sample matrices. It was found to be little cross-reactivity with other aflatoxins (B2, G1, G2, and M1). In the case of determination of aflatoxin B1 in peanuts, corn, soy sauce, vegetable oil, and mouse feed, excellent agreement was found when compared with aflatoxin B1 determination via the conversational high-performance liquid chromatography method. The chromatographic time-resolved fluoroimmunoassay affords a powerful alternative for rapid on-site determination of aflatoxin B1 and holds a promise for food safety in consideration of practical food safety and environmental monitoring.

Rapid On-Site Sensing Aflatoxin B1 in Food and Feed via a Chromatographic Time-Resolved Fluoroimmunoassay

PubMed Central

Wang, Du; Zhang, Qi; Li, Peiwu; Ding, Xiaoxia

2015-01-01

Aflatoxin B1 poses grave threats to food and feed safety due to its strong carcinogenesis and toxicity, thus requiring ultrasensitive rapid on-site determination. Herein, a portable immunosensor based on chromatographic time-resolved fluoroimmunoassay was developed for sensitive and on-site determination of aflatoxin B1 in food and feed samples. Chromatographic time-resolved fluoroimmunoassay offered a magnified positive signal and low signal-to-noise ratio in time-resolved mode due to the absence of noise interference caused by excitation light sources. Compared with the immunosensing performance in previous studies, this platform demonstrated a wider dynamic range of 0.2-60 μg/kg, lower limit of detection from 0.06 to 0.12 µg/kg, and considerable recovery from 80.5% to 116.7% for different food and feed sample matrices. It was found to be little cross-reactivity with other aflatoxins (B2, G1, G2, and M1). In the case of determination of aflatoxin B1 in peanuts, corn, soy sauce, vegetable oil, and mouse feed, excellent agreement was found when compared with aflatoxin B1 determination via the conversational high-performance liquid chromatography method. The chromatographic time-resolved fluoroimmunoassay affords a powerful alternative for rapid on-site determination of aflatoxin B1 and holds a promise for food safety in consideration of practical food safety and environmental monitoring. PMID:25874803

Fine-scale characteristics of fluvial bull trout redds and adjacent sites in Rapid River, Idaho, 1993-2007

Treesearch

John W. Guzevich; Russell F. Thurow

2017-01-01

From 1993 to 2007, we used single pass, September surveys to locate and measure fluvial bull trout (Salvelinus confluentus) redds in Rapid River, Idaho. Here we describe substrate sizes, redd dimensions, and water depths, velocities, and temperatures within and adjacent to 337 redds. Most (79%) spawning sites had fewer than 20% surface fines (< 2 mm) and mean,...

Invasion percolation between two sites in two, three, and four dimensions

NASA Astrophysics Data System (ADS)

Lee, Sang Bub

2009-06-01

The mass distribution of invaded clusters in non-trapping invasion percolation between an injection site and an extraction site has been studied, in two, three, and four dimensions. This study is an extension of the recent study focused on two dimensions by Araújo et al. [A.D. Araújo, T.F. Vasconcelos, A.A. Moreira, L.S. Lucena, J.S. Andrade Jr., Phys. Rev. E 72 (2005) 041404] with respect to higher dimensions. The mass distribution exhibits a power-law behavior, P(m)∝m. It has been found that the index α for pe

RAPID ON-SITE METHODS OF CHEMICAL ANALYSIS

EPA Science Inventory

The analysis of potentially hazardous air, water and soil samples collected and shipped to service laboratories off-site is time consuming and expensive. This Chapter addresses the practical alternative of performing the requisite analytical services on-site. The most significant...

Two Years of Site Diversity Measurements in Guam, USA

NASA Technical Reports Server (NTRS)

Acosta, Roberto J.; Morse, J.; Zemba, M.; Nessel, J.

2012-01-01

As NASA communication networks upgrade to higher frequencies, such as Ka-Band, atmospherically induced attenuation can become significant. This attenuation is caused by rain, clouds and atmospheric gases (oxygen and water vapor), with rain having the most noticeable effects. One technique to circumvent the increase in attenuation is to operate two terminals separated by a distance that exceeds the average rain cell size. The fact that rain cells are of finite size can then be exploited by rerouting the signal to the terminal with the strongest link. This technique, known as site diversity, is best suited for climates that have compact (less than 2km) and intense rain cells such as in Guam. In order to study the potential diversity gain at the Tracking and Data Relay Satellite (TDRS) Remote Ground Terminal (GRGT) complex in Guam a site test interferometer (STI) was installed in May of 2010. The STI is composed of two terminals with a 900m baseline that observe the same unmodulated beacon signal broadcast from a geostationary satellite (e.g., UFO 8). The potential site diversity gain is calculated by measuring the difference in signal attenuation seen at each terminal. Over the two years of data collection the cumulative distribution function (CDF) of the site diversity gain shows a better than 3 dB improvement for 90% of the time over standard operation. These results show that the use of site diversity in Guam can be very effective in combating rain fades.

Rapid in vitro labeling procedures for two-dimensional gel fingerprinting

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

Lee, Y.F.; Fowlks, E.R.

1982-01-15

Improvements of existing in vitro procedures for labeling RNA radioactively, and modifications of the two-dimensional polyacrylamide gel electrophoresis system for making RNA fingerprints are described. These improvements are (a) inactivation of phosphatase with nitric acid at pH 2.0 eliminated the phenol-cholorform extraction step during 5'-end labeling with polynucleotide kinase and (..gamma..-/sup 32/P)ATP; (b) ZnSO/sub 4/ inactivation of R Nase T/sub 1/ results in a highly efficient procedure for 3'-end labeling with T4 ligase and (5'-/sup 32/P)pCp; and (c) a rapid 4-min procedure for variable quantity range of /sup 125/I and RNA results in a qualitative and quantitative sample for high-molecularmore » weight RNA fingerprinting. Thus, these in vitro procedures become rapid and reproducible when combined with two-dimensional gel electrophoresis which eliminates simultaneously labeled impurities. Each labeling procedure is compared, using tobacco mosaic virus, Brome mosaic virus, and polio RNA. A series of Ap-rich oligonucleotides was discovered in the inner genome of Brome mosaic Virus RNA-3.« less

A COMPARISON OF TWO RAPID BIOLOGICAL ASSESSMENT SAMPLING METHODS FOR MACROINVERTEBRATES

EPA Science Inventory

In 2003, the Office of Research and Developments (ORD's) National Exposure Research Laboratory initiated a collaborative research effort with U.S. EPA Region 3 to conduct a study comparing two rapid biological assessment methods for collecting stream macroinvertebrates. One metho...

A rapid, controlled-environment seedling root screen for wheat correlates well with rooting depths at vegetative, but not reproductive, stages at two field sites

PubMed Central

Watt, M.; Moosavi, S.; Cunningham, S. C.; Kirkegaard, J. A.; Rebetzke, G. J.; Richards, R. A.

2013-01-01

Background and Aims Root length and depth determine capture of water and nutrients by plants, and are targets for crop improvement. Here we assess a controlled-environment wheat seedling screen to determine speed, repeatability and relatedness to performance of young and adult plants in the field. Methods Recombinant inbred lines (RILs) and diverse genotypes were grown in rolled, moist germination paper in growth cabinets, and primary root number and length were measured when leaf 1 or 2 were fully expanded. For comparison, plants were grown in the field and root systems were harvested at the two-leaf stage with either a shovel or a soil core. From about the four-leaf stage, roots were extracted with a steel coring tube only, placed directly over the plant and pushed to the required depth with a hydraulic ram attached to a tractor. Key Results In growth cabinets, repeatability was greatest (r = 0·8, P < 0·01) when the paper was maintained moist and seed weight, pathogens and germination times were controlled. Scanned total root length (slow) was strongly correlated (r = 0·7, P < 0·01) with length of the two longest seminal axile roots measured with a ruler (fast), such that 100–200 genotypes were measured per day. Correlation to field-grown roots at two sites at two leaves was positive and significant within the RILs and cultivars (r = 0·6, P = 0·01), and at one of the two sites at the five-leaf stage within the RILs (r = 0·8, P = 0·05). Measurements made in the field with a shovel or extracted soil cores were fast (5 min per core) and had significant positive correlations to scanner measurements after root washing and cleaning (>2 h per core). Field measurements at two- and five-leaf stages did not correlate with root depth at flowering. Conclusions The seedling screen was fast, repeatable and reliable for selecting lines with greater total root length in the young vegetative phase in the field. Lack of significant correlation with reproductive stage

The long-term fate of permafrost peatlands under rapid climate warming

PubMed Central

Swindles, Graeme T.; Morris, Paul J.; Mullan, Donal; Watson, Elizabeth J.; Turner, T. Edward; Roland, Thomas P.; Amesbury, Matthew J.; Kokfelt, Ulla; Schoning, Kristian; Pratte, Steve; Gallego-Sala, Angela; Charman, Dan J.; Sanderson, Nicole; Garneau, Michelle; Carrivick, Jonathan L.; Woulds, Clare; Holden, Joseph; Parry, Lauren; Galloway, Jennifer M.

2015-01-01

Permafrost peatlands contain globally important amounts of soil organic carbon, owing to cold conditions which suppress anaerobic decomposition. However, climate warming and permafrost thaw threaten the stability of this carbon store. The ultimate fate of permafrost peatlands and their carbon stores is unclear because of complex feedbacks between peat accumulation, hydrology and vegetation. Field monitoring campaigns only span the last few decades and therefore provide an incomplete picture of permafrost peatland response to recent rapid warming. Here we use a high-resolution palaeoecological approach to understand the longer-term response of peatlands in contrasting states of permafrost degradation to recent rapid warming. At all sites we identify a drying trend until the late-twentieth century; however, two sites subsequently experienced a rapid shift to wetter conditions as permafrost thawed in response to climatic warming, culminating in collapse of the peat domes. Commonalities between study sites lead us to propose a five-phase model for permafrost peatland response to climatic warming. This model suggests a shared ecohydrological trajectory towards a common end point: inundated Arctic fen. Although carbon accumulation is rapid in such sites, saturated soil conditions are likely to cause elevated methane emissions that have implications for climate-feedback mechanisms. PMID:26647837

Rapid Bioassessment Methods for Assessing Stream Macroinvertebrate Community on the Savannah River Site

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

Specht, W.L.

Macroinvertebrate sampling was performed at 16 locations in the Savannah River Site (SRS) streams using Hester-Dendy multiplate samplers and EPA Rapid Bioassessment Protocols (RBP). Some of the sampling locations were unimpacted, while other locations had been subject to various forms of perturbation by SRS activities. In general, the data from the Hester-Dendy multiplate samplers were more sensitive at detecting impacts than were the RBP data. We developed a Biotic Index for the Hester-Dendy data which incorporated eight community structure, function, and balance parameters. when tested using a data set that was unrelated to the data set that was used inmore » developing the Biotic Index, the index was very successful at detecting impact.« less

Rapid diagnostic tests for malaria at sites of varying transmission intensity in Uganda.

PubMed

Hopkins, Heidi; Bebell, Lisa; Kambale, Wilson; Dokomajilar, Christian; Rosenthal, Philip J; Dorsey, Grant

2008-02-15

In Africa, fever is often treated presumptively as malaria, resulting in misdiagnosis and the overuse of antimalarial drugs. Rapid diagnostic tests (RDTs) for malaria may allow improved fever management. We compared RDTs based on histidine-rich protein 2 (HRP2) and RDTs based on Plasmodium lactate dehydrogenase (pLDH) with expert microscopy and PCR-corrected microscopy for 7000 patients at sites of varying malaria transmission intensity across Uganda. When all sites were considered, the sensitivity of the HRP2-based test was 97% when compared with microscopy and 98% when corrected by PCR; the sensitivity of the pLDH-based test was 88% when compared with microscopy and 77% when corrected by PCR. The specificity of the HRP2-based test was 71% when compared with microscopy and 88% when corrected by PCR; the specificity of the pLDH-based test was 92% when compared with microscopy and >98% when corrected by PCR. Based on Plasmodium falciparum PCR-corrected microscopy, the positive predictive value (PPV) of the HRP2-based test was high (93%) at all but the site with the lowest transmission rate; the pLDH-based test and expert microscopy offered excellent PPVs (98%) for all sites. The negative predictive value (NPV) of the HRP2-based test was consistently high (>97%); in contrast, the NPV for the pLDH-based test dropped significantly (from 98% to 66%) as transmission intensity increased, and the NPV for expert microscopy decreased significantly (99% to 54%) because of increasing failure to detect subpatent parasitemia. Based on the high PPV and NPV, HRP2-based RDTs are likely to be the best diagnostic choice for areas with medium-to-high malaria transmission rates in Africa.

Cloning of novel rice blast resistance genes from two rapidly evolving NBS-LRR gene families in rice.

PubMed

Guo, Changjiang; Sun, Xiaoguang; Chen, Xiao; Yang, Sihai; Li, Jing; Wang, Long; Zhang, Xiaohui

2016-01-01

Most rice blast resistance genes (R-genes) encode proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. Our previous study has shown that more rice blast R-genes can be cloned in rapidly evolving NBS-LRR gene families. In the present study, two rapidly evolving R-gene families in rice were selected for cloning a subset of genes from their paralogs in three resistant rice lines. A total of eight functional blast R-genes were identified among nine NBS-LRR genes, and some of these showed resistance to three or more blast strains. Evolutionary analysis indicated that high nucleotide diversity of coding regions served as important parameters in the determination of gene resistance. We also observed that amino-acid variants (nonsynonymous mutations, insertions, or deletions) in essential motifs of the NBS domain contribute to the blast resistance capacity of NBS-LRR genes. These results suggested that the NBS regions might also play an important role in resistance specificity determination. On the other hand, different splicing patterns of introns were commonly observed in R-genes. The results of the present study contribute to improving the effectiveness of R-gene identification by using evolutionary analysis method and acquisition of novel blast resistance genes.

Potential of cross-priming amplification and DNA-based lateral-flow strip biosensor for rapid on-site GMO screening.

PubMed

Huang, Xin; Zhai, Congcong; You, Qimin; Chen, Hongjun

2014-07-01

The requirement to monitor the presence of genetically modified organisms (GMO) in a variety of marked products has generated an increasing demand for reliable, rapid, and time and cost-effective analytical methods. Here we report an on-site method for rapid detection of cauliflower mosaic virus promoter (CaMV 35S), a common element present in most GMO, using cross-priming amplification (CPA) technology. Detection was achieved using a DNA-based contamination-proof strip biosensor. The limit of detection was 30 copies for the pBI121 plasmid containing the CaMV 35S gene. The certified reference sample of GM maize line MON810 was detectable even at the low relative mass concentration of 0.05%. The developed CPA method had high specificity for the CaMV 35S gene, as compared with other GM lines not containing this gene and non-GM products. The method was further validated using nine real-world samples, and the results were confirmed by real-time PCR analysis. Because of its simplicity, rapidity, and high sensitivity, this method of detecting the CaMV 35S gene has great commercial prospects for rapid GMO screening of high-consumption food and agriculture products.

Autonomous multispecies reaction-diffusion systems with more-than-two-site interactions

NASA Astrophysics Data System (ADS)

Shariati, Ahmad; Aghamohammadi, Amir; Khorrami, Mohammad

2001-12-01

Autonomous multispecies systems with more-than-two-neighbor interactions are studied. Conditions necessary and sufficient for the closedness of the evolution equations of the n-point functions are obtained. The average numbers of the particles at each site for one species and three-site interactions, and its generalization to the more-than-three-site interactions, are explicitly obtained. Generalizations of the Glauber model in different directions, using generalized rates, generalized numbers of states at each site, and generalized numbers of interacting sites, are also investigated.

On-site bundled rapid HIV/HCV testing in substance use disorder treatment programs: study protocol for a hybrid design randomized controlled trial.

PubMed

Frimpong, Jemima A; D'Aunno, Thomas; Perlman, David C; Strauss, Shiela M; Mallow, Alissa; Hernandez, Diana; Schackman, Bruce R; Feaster, Daniel J; Metsch, Lisa R

2016-03-03

More than 1.2 million people in the United States are living with human immunodeficiency virus (HIV), and 3.2 million are living with hepatitis C virus (HCV). An estimated 25 % of persons living with HIV also have HCV. It is therefore of great public health importance to ensure the prompt diagnosis of both HIV and HCV in populations that have the highest prevalence of both infections, including individuals with substance use disorders (SUD). In this theory-driven, efficacy-effectiveness-implementation hybrid study, we will develop and test an on-site bundled rapid HIV/HCV testing intervention for SUD treatment programs. Its aim is to increase the receipt of HIV and HCV test results among SUD treatment patients. Using a rigorous process involving patients, providers, and program managers, we will incorporate rapid HCV testing into evidence-based HIV testing and linkage to care interventions. We will then test, in a randomized controlled trial, the extent to which this bundled rapid HIV/HCV testing approach increases receipt of HIV and HCV test results. Lastly, we will conduct formative research to understand the barriers to, and facilitators of, the adoption, implementation, and sustainability of the bundled rapid testing strategy in SUD treatment programs. Novel approaches that effectively integrate on-site rapid HIV and rapid HCV testing are needed to address both the HIV and HCV epidemics. If feasible and efficacious, bundled rapid HIV/HCV testing may offer a scalable, potentially cost-effective approach to testing high-risk populations, such as patients of SUD treatment programs. It may ultimately lead to improved linkage to care and progress through the HIV and HCV care and treatment cascades. ClinicalTrials.gov: NCT02355080 . (30 January 2015).

Comparative evaluation of two rapid field tests for malaria diagnosis: Partec Rapid Malaria Test® and Binax Now® Malaria Rapid Diagnostic Test.

PubMed

Nkrumah, Bernard; Acquah, Samuel Ek; Ibrahim, Lukeman; May, Juergen; Brattig, Norbert; Tannich, Egbert; Nguah, Samuel Blay; Adu-Sarkodie, Yaw; Huenger, Frank

2011-05-23

About 90% of all malaria deaths in sub-Saharan Africa occur in children under five years. Fast and reliable diagnosis of malaria requires confirmation of the presence of malaria parasites in the blood of patients with fever or history suggestive of malaria; hence a prompt and accurate diagnosis of malaria is the key to effective disease management. Confirmation of malaria infection requires the availability of a rapid, sensitive, and specific testing at an affordable cost. We compared two recent methods (the novel Partec Rapid Malaria Test® (PT) and the Binax Now® Malaria Rapid Diagnostic Test (BN RDT) with the conventional Giemsa stain microscopy (GM) for the diagnosis of malaria among children in a clinical laboratory of a hospital in a rural endemic area of Ghana. Blood samples were collected from 263 children admitted with fever or a history of fever to the pediatric clinic of the Agogo Presbyterian Hospital. The three different test methods PT, BN RDT and GM were performed independently by well trained and competent laboratory staff to assess the presence of malaria parasites. Results were analyzed and compared using GM as the reference standard. In 107 (40.7%) of 263 study participants, Plasmodium sp. was detected by GM. PT and BN RDT showed positive results in 111 (42.2%) and 114 (43.4%), respectively. Compared to GM reference standard, the sensitivities of the PT and BN RDT were 100% (95% CI: 96.6-100) and 97.2% (95% CI: 92.0-99.4), respectively, specificities were 97.4% (95% CI: 93.6-99.3) and 93.6% (95% CI: 88.5-96.9), respectively. There was a strong agreement (kappa) between the applied test methods (GM vs PT: 0.97; p < 0.001 and GM vs BN RDT: 0.90; p < 0.001). The average turnaround time per tests was 17 minutes. In this study two rapid malaria tests, PT and BN RDT, demonstrated a good quality of their performance compared to conventional GM. Both methods require little training, have short turnaround times, are applicable as well as affordable and

Comparative evaluation of two rapid field tests for malaria diagnosis: Partec Rapid Malaria Test® and Binax Now® Malaria Rapid Diagnostic Test

PubMed Central

2011-01-01

Background About 90% of all malaria deaths in sub-Saharan Africa occur in children under five years. Fast and reliable diagnosis of malaria requires confirmation of the presence of malaria parasites in the blood of patients with fever or history suggestive of malaria; hence a prompt and accurate diagnosis of malaria is the key to effective disease management. Confirmation of malaria infection requires the availability of a rapid, sensitive, and specific testing at an affordable cost. We compared two recent methods (the novel Partec Rapid Malaria Test® (PT) and the Binax Now® Malaria Rapid Diagnostic Test (BN RDT) with the conventional Giemsa stain microscopy (GM) for the diagnosis of malaria among children in a clinical laboratory of a hospital in a rural endemic area of Ghana. Methods Blood samples were collected from 263 children admitted with fever or a history of fever to the pediatric clinic of the Agogo Presbyterian Hospital. The three different test methods PT, BN RDT and GM were performed independently by well trained and competent laboratory staff to assess the presence of malaria parasites. Results were analyzed and compared using GM as the reference standard. Results In 107 (40.7%) of 263 study participants, Plasmodium sp. was detected by GM. PT and BN RDT showed positive results in 111 (42.2%) and 114 (43.4%), respectively. Compared to GM reference standard, the sensitivities of the PT and BN RDT were 100% (95% CI: 96.6-100) and 97.2% (95% CI: 92.0-99.4), respectively, specificities were 97.4% (95% CI: 93.6-99.3) and 93.6% (95% CI: 88.5-96.9), respectively. There was a strong agreement (kappa) between the applied test methods (GM vs PT: 0.97; p < 0.001 and GM vs BN RDT: 0.90; p < 0.001). The average turnaround time per tests was 17 minutes. Conclusion In this study two rapid malaria tests, PT and BN RDT, demonstrated a good quality of their performance compared to conventional GM. Both methods require little training, have short turnaround times, are

Rapid Recovery of an Urban Remnant Reptile Community following Summer Wildfire.

PubMed

Davis, Robert A; Doherty, Tim S

2015-01-01

Reptiles in urban remnants are threatened with extinction by increased fire frequency, habitat fragmentation caused by urban development, and competition and predation from exotic species. Understanding how urban reptiles respond to and recover from such disturbances is key to their conservation. We monitored the recovery of an urban reptile community for five years following a summer wildfire at Kings Park in Perth, Western Australia, using pitfall trapping at five burnt and five unburnt sites. The reptile community recovered rapidly following the fire. Unburnt sites initially had higher species richness and total abundance, but burnt sites rapidly converged, recording a similar total abundance to unburnt areas within two years, and a similar richness within three years. The leaf-litter inhabiting skink Hemiergis quadrilineata was strongly associated with longer unburnt sites and may be responding to the loss of leaf litter following the fire. Six rarely-captured species were also strongly associated with unburnt areas and were rarely or never recorded at burnt sites, whereas two other rarely-captured species were associated with burnt sites. We also found that one lizard species, Ctenotus fallens, had a smaller average body length in burnt sites compared to unburnt sites for four out of the five years of monitoring. Our study indicates that fire management that homogenises large areas of habitat through frequent burning may threaten some species due to their preference for longer unburnt habitat. Careful management of fire may be needed to maximise habitat suitability within the urban landscape.

GAS HYDRATES AT TWO SITES OF AN ACTIVE CONTINENTAL MARGIN.

USGS Publications Warehouse

Kvenvolden, K.A.

1985-01-01

Sediment containing gas hydrates from two distant Deep Sea Drilling Project sites (565 and 568), located about 670 km apart on the landward flank of the Middle America Trench, was studied to determine the geochemical conditions that characterize the occurrence of gas hydrates. Site 565 was located in the Pacific Ocean offshore the Nicoya Peninsula of Costa Rica in 3,111 m of water. The depth of the hole at this site was 328 m, and gas hydrates were recovered from 285 and 319 m. Site 568 was located about 670 km to the northwest offshore Guatemala in 2,031 m of water. At this site the hole penetrated to 418 m, and gas hydrates were encountered at 404 m.

Rapid identification of fluorochrome modification sites in proteins by LC ESI-Q-TOF mass spectrometry.

PubMed

Manikwar, Prakash; Zimmerman, Tahl; Blanco, Francisco J; Williams, Todd D; Siahaan, Teruna J

2011-07-20

Conjugation of either a fluorescent dye or a drug molecule to the ε-amino groups of lysine residues of proteins has many applications in biology and medicine. However, this type of conjugation produces a heterogeneous population of protein conjugates. Because conjugation of fluorochrome or drug molecule to a protein may have deleterious effects on protein function, the identification of conjugation sites is necessary. Unfortunately, the identification process can be time-consuming and laborious; therefore, there is a need to develop a rapid and reliable way to determine the conjugation sites of the fluorescent label or drug molecule. In this study, the sites of conjugation of fluorescein-5'-isothiocyanate and rhodamine-B-isothiocyanate to free amino groups on the insert-domain (I-domain) protein derived from the α-subunit of lymphocyte function-associated antigen-1 (LFA-1) were determined by electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-Q-TOF MS) along with peptide mapping using trypsin digestion. A reporter fragment of the fluorochrome moiety that is generated in the collision cell of the Q-TOF without explicit MS/MS precursor selection was used to identify the conjugation site. Selected ion plots of the reporter ion readily mark modified peptides in chromatograms of the complex digest. Interrogation of theses spectra reveals a neutral loss/precursor pair that identifies the modified peptide. The results show that one to seven fluorescein molecules or one to four rhodamine molecules were attached to the lysine residue(s) of the I-domain protein. No modifications were found in the metal ion-dependent adhesion site (MIDAS), which is an important binding region of the I-domain.

A two-site ELISA can quantify upregulation of SMN protein by drugs for spinal muscular atrophy.

PubMed

Nguyen thi Man; Humphrey, E; Lam, L T; Fuller, H R; Lynch, T A; Sewry, C A; Goodwin, P R; Mackenzie, A E; Morris, G E

2008-11-25

Spinal muscular atrophy (SMA) is an autosomal recessive disorder characterized by loss of lower motor neurons during early or postnatal development. Severity is variable and is inversely related to the levels of survival of motor neurons (SMN) protein. The aim of this study was to produce a two-site ELISA capable of measuring both the low, basal levels of SMN protein in cell cultures from patients with severe SMA and small increases in these levels after treatment of cells with drugs. A monoclonal antibody against recombinant SMN, MANSMA1, was selected for capture of SMN onto microtiter plates. A selected rabbit antiserum against refolded recombinant SMN was used for detection of the captured SMN. The ratio of SMN levels in control fibroblasts to levels in SMA fibroblasts was greater than 3.0, consistent with Western blot data. The limit of detection was 0.13 ng/mL and SMN could be measured in human NT-2 neuronal precursor cells grown in 96-well culture plates (3 x 10(4) cells per well). Increases in SMN levels of 50% were demonstrable by ELISA after 24 hours treatment of 10(5) SMA fibroblasts with valproate or phenylbutyrate. A rapid and specific two-site, 96-well ELISA assay, available in kit format, can now quantify the effects of drugs on survival of motor neurons protein levels in cell cultures.

Two Oxidation Sites for Low Redox Potential Substrates

PubMed Central

Morales, María; Mate, María J.; Romero, Antonio; Martínez, María Jesús; Martínez, Ángel T.; Ruiz-Dueñas, Francisco J.

2012-01-01

Versatile peroxidase shares with manganese peroxidase and lignin peroxidase the ability to oxidize Mn2+ and high redox potential aromatic compounds, respectively. Moreover, it is also able to oxidize phenols (and low redox potential dyes) at two catalytic sites, as shown by biphasic kinetics. A high efficiency site (with 2,6-dimethoxyphenol and p-hydroquinone catalytic efficiencies of ∼70 and ∼700 s−1 mm−1, respectively) was localized at the same exposed Trp-164 responsible for high redox potential substrate oxidation (as shown by activity loss in the W164S variant). The second site, characterized by low catalytic efficiency (∼3 and ∼50 s−1 mm−1 for 2,6-dimethoxyphenol and p-hydroquinone, respectively) was localized at the main heme access channel. Steady-state and transient-state kinetics for oxidation of phenols and dyes at the latter site were improved when side chains of residues forming the heme channel edge were removed in single and multiple variants. Among them, the E140G/K176G, E140G/P141G/K176G, and E140G/W164S/K176G variants attained catalytic efficiencies for oxidation of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonate) at the heme channel similar to those of the exposed tryptophan site. The heme channel enlargement shown by x-ray diffraction of the E140G, P141G, K176G, and E140G/K176G variants would allow a better substrate accommodation near the heme, as revealed by the up to 26-fold lower Km values (compared with native VP). The resulting interactions were shown by the x-ray structure of the E140G-guaiacol complex, which includes two H-bonds of the substrate with Arg-43 and Pro-139 in the distal heme pocket (at the end of the heme channel) and several hydrophobic interactions with other residues and the heme cofactor. PMID:23071108

Two nucleotide binding sites modulate ( sup 3 H) glyburide binding to rat cortex membranes

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

Johnson, D.E.; Gopalakrishnan, M.; Triggle, D.J.

1991-03-11

The effects of nucleotides on the binding of the ATP-dependent K{sup +}-channel antagonist ({sup 3}H)glyburide (GLB) to rat cortex membranes were examined. Nucleotide triphosphates (NTPs) and nucleotide diphosphate (NDPs) inhibited the binding of GLB. This effect was dependent on the presence of dithiothreitol (DTT). Inhibition of binding by NTPs, with the exception of ATP{gamma}S, was dependent on the presence of Mg{sup 2+}. GLB binding showed a biphasic response to ADP: up to 3 mM, ADP inhibited binding, and above this concentration GLB binding increased rapidly, and was restored to normal levels by 10 mM ADP. In the presence of Mg{supmore » 2+}, ADP did not stimulate binding. Saturation analysis in the presence of Mg{sup 2+} and increasing concentrations of ADP showed that ADP results primarily in a change of the B{sub max} for GLB binding. The differential effects of NTPS and NDPs indicate that two nucleotide binding sites regulate GLB binding.« less

Evaluation of Performance of Two Rapid Tests for Detection of HIV-1 and -2 in High- and Low-Prevalence Populations in Nigeria

PubMed Central

Njoku, Ogbonnaya S.; Shutt, Ashley; Malia, Jennifer; Jagodzinski, Linda L.; Milazzo, Mark; Suleiman, Aminu; Ogundeji, Amos A.; Nelson, Robert; Ayemoba, Ojor R.; O'Connell, Robert J.; Singer, Darrell E.; Michael, Nelson L.; Peel, Sheila A.

2015-01-01

The availability of reliable human immunodeficiency virus types 1 and 2 (HIV-1/2) rapid tests in resource-limited settings represents an important advancement in the accurate diagnosis of HIV infection and presents opportunities for implementation of effective prevention and treatment interventions among vulnerable populations. A study of the potential target populations for future HIV vaccine studies examined the prevalence of HIV infections at six selected sites in Nigeria and evaluated the use of two rapid diagnostic tests (RDTs) for HIV. The populations included market workers at sites adjacent to military installations and workers at highway settlements (truck stops) who may have a heightened risk of HIV exposure. Samples from 3,187 individuals who provided informed consent were tested in parallel using the Determine (DT) and Stat-Pak (SP) RDTs; discordant results were subjected to the Uni-Gold (UG) RDT as a tiebreaker. The results were compared to those of a third-generation enzyme immunoassay screen with confirmation of repeat reactive samples by HIV-1 Western blotting. One participant was HIV-2 infected, yielding positive results on both RDTs. Using the laboratory algorithm as a gold standard, we calculated sensitivities of 98.5% (confidence interval [CI], 97.1 to 99.8%) for DT and 98.1% (CI, 96.7 to 99.6%) for SP and specificities of 98.7% (CI, 98.3 −99.1%) for DT and 99.8% (CI, 99.6 to 100%) for SP. Similar results were obtained when the sites were stratified into those of higher HIV prevalence (9.4% to 22.8%) versus those of lower prevalence (3.2% to 7.3%). A parallel two-test algorithm requiring both DT and SP to be positive resulted in the highest sensitivity (98.1%; CI, 96.7 to 99.6%) and specificity (99.97%; CI, 99.9 to 100%) relative to those for the reference laboratory algorithm. PMID:26311857

Evaluation of Performance of Two Rapid Tests for Detection of HIV-1 and -2 in High- and Low-Prevalence Populations in Nigeria.

PubMed

Manak, Mark M; Njoku, Ogbonnaya S; Shutt, Ashley; Malia, Jennifer; Jagodzinski, Linda L; Milazzo, Mark; Suleiman, Aminu; Ogundeji, Amos A; Nelson, Robert; Ayemoba, Ojor R; O'Connell, Robert J; Singer, Darrell E; Michael, Nelson L; Peel, Sheila A

2015-11-01

The availability of reliable human immunodeficiency virus types 1 and 2 (HIV-1/2) rapid tests in resource-limited settings represents an important advancement in the accurate diagnosis of HIV infection and presents opportunities for implementation of effective prevention and treatment interventions among vulnerable populations. A study of the potential target populations for future HIV vaccine studies examined the prevalence of HIV infections at six selected sites in Nigeria and evaluated the use of two rapid diagnostic tests (RDTs) for HIV. The populations included market workers at sites adjacent to military installations and workers at highway settlements (truck stops) who may have a heightened risk of HIV exposure. Samples from 3,187 individuals who provided informed consent were tested in parallel using the Determine (DT) and Stat-Pak (SP) RDTs; discordant results were subjected to the Uni-Gold (UG) RDT as a tiebreaker. The results were compared to those of a third-generation enzyme immunoassay screen with confirmation of repeat reactive samples by HIV-1 Western blotting. One participant was HIV-2 infected, yielding positive results on both RDTs. Using the laboratory algorithm as a gold standard, we calculated sensitivities of 98.5% (confidence interval [CI], 97.1 to 99.8%) for DT and 98.1% (CI, 96.7 to 99.6%) for SP and specificities of 98.7% (CI, 98.3 -99.1%) for DT and 99.8% (CI, 99.6 to 100%) for SP. Similar results were obtained when the sites were stratified into those of higher HIV prevalence (9.4% to 22.8%) versus those of lower prevalence (3.2% to 7.3%). A parallel two-test algorithm requiring both DT and SP to be positive resulted in the highest sensitivity (98.1%; CI, 96.7 to 99.6%) and specificity (99.97%; CI, 99.9 to 100%) relative to those for the reference laboratory algorithm. Copyright © 2015, Manak et al.

Large-volume constant-concentration sampling technique coupling with surface-enhanced Raman spectroscopy for rapid on-site gas analysis

NASA Astrophysics Data System (ADS)

Zhang, Zhuomin; Zhan, Yisen; Huang, Yichun; Li, Gongke

2017-08-01

In this work, a portable large-volume constant-concentration (LVCC) sampling technique coupling with surface-enhanced Raman spectroscopy (SERS) was developed for the rapid on-site gas analysis based on suitable derivatization methods. LVCC sampling technique mainly consisted of a specially designed sampling cell including the rigid sample container and flexible sampling bag, and an absorption-derivatization module with a portable pump and a gas flowmeter. LVCC sampling technique allowed large, alterable and well-controlled sampling volume, which kept the concentration of gas target in headspace phase constant during the entire sampling process and made the sampling result more representative. Moreover, absorption and derivatization of gas target during LVCC sampling process were efficiently merged in one step using bromine-thiourea and OPA-NH4+ strategy for ethylene and SO2 respectively, which made LVCC sampling technique conveniently adapted to consequent SERS analysis. Finally, a new LVCC sampling-SERS method was developed and successfully applied for rapid analysis of trace ethylene and SO2 from fruits. It was satisfied that trace ethylene and SO2 from real fruit samples could be actually and accurately quantified by this method. The minor concentration fluctuations of ethylene and SO2 during the entire LVCC sampling process were proved to be < 4.3% and 2.1% respectively. Good recoveries for ethylene and sulfur dioxide from fruit samples were achieved in range of 95.0-101% and 97.0-104% respectively. It is expected that portable LVCC sampling technique would pave the way for rapid on-site analysis of accurate concentrations of trace gas targets from real samples by SERS.

Large-volume constant-concentration sampling technique coupling with surface-enhanced Raman spectroscopy for rapid on-site gas analysis.

PubMed

Zhang, Zhuomin; Zhan, Yisen; Huang, Yichun; Li, Gongke

2017-08-05

In this work, a portable large-volume constant-concentration (LVCC) sampling technique coupling with surface-enhanced Raman spectroscopy (SERS) was developed for the rapid on-site gas analysis based on suitable derivatization methods. LVCC sampling technique mainly consisted of a specially designed sampling cell including the rigid sample container and flexible sampling bag, and an absorption-derivatization module with a portable pump and a gas flowmeter. LVCC sampling technique allowed large, alterable and well-controlled sampling volume, which kept the concentration of gas target in headspace phase constant during the entire sampling process and made the sampling result more representative. Moreover, absorption and derivatization of gas target during LVCC sampling process were efficiently merged in one step using bromine-thiourea and OPA-NH 4 + strategy for ethylene and SO 2 respectively, which made LVCC sampling technique conveniently adapted to consequent SERS analysis. Finally, a new LVCC sampling-SERS method was developed and successfully applied for rapid analysis of trace ethylene and SO 2 from fruits. It was satisfied that trace ethylene and SO 2 from real fruit samples could be actually and accurately quantified by this method. The minor concentration fluctuations of ethylene and SO 2 during the entire LVCC sampling process were proved to be <4.3% and 2.1% respectively. Good recoveries for ethylene and sulfur dioxide from fruit samples were achieved in range of 95.0-101% and 97.0-104% respectively. It is expected that portable LVCC sampling technique would pave the way for rapid on-site analysis of accurate concentrations of trace gas targets from real samples by SERS. Copyright © 2017 Elsevier B.V. All rights reserved.

Rapid Recovery of an Urban Remnant Reptile Community following Summer Wildfire

PubMed Central

2015-01-01

Reptiles in urban remnants are threatened with extinction by increased fire frequency, habitat fragmentation caused by urban development, and competition and predation from exotic species. Understanding how urban reptiles respond to and recover from such disturbances is key to their conservation. We monitored the recovery of an urban reptile community for five years following a summer wildfire at Kings Park in Perth, Western Australia, using pitfall trapping at five burnt and five unburnt sites. The reptile community recovered rapidly following the fire. Unburnt sites initially had higher species richness and total abundance, but burnt sites rapidly converged, recording a similar total abundance to unburnt areas within two years, and a similar richness within three years. The leaf-litter inhabiting skink Hemiergis quadrilineata was strongly associated with longer unburnt sites and may be responding to the loss of leaf litter following the fire. Six rarely-captured species were also strongly associated with unburnt areas and were rarely or never recorded at burnt sites, whereas two other rarely-captured species were associated with burnt sites. We also found that one lizard species, Ctenotus fallens, had a smaller average body length in burnt sites compared to unburnt sites for four out of the five years of monitoring. Our study indicates that fire management that homogenises large areas of habitat through frequent burning may threaten some species due to their preference for longer unburnt habitat. Careful management of fire may be needed to maximise habitat suitability within the urban landscape. PMID:25992802

Rapid on-site/in-situ detection of heavy metal ions in environmental water using a structure-switching DNA optical biosensor.

PubMed

Long, Feng; Zhu, Anna; Shi, Hanchang; Wang, Hongchen; Liu, Jingquan

2013-01-01

A structure-switching DNA optical biosensor for rapid on-site/in situ detection of heavy metal ions is reported. Mercury ions (Hg²⁺), highly toxic and ubiquitous pollutants, were selected as model target. In this system, fluorescence-labeled DNA containing T-T mismatch structure was introduced to bind with DNA probes immobilized onto the sensor surface. In the presence of Hg²⁺, some of the fluorescence-labeled DNAs bind with Hg²⁺ to form T-Hg²⁺-T complexes through the folding of themselves into a hairpin structure and dehybridization from the sensor surface, which leads to decrease in fluorescence signal. The total analysis time for a single sample was less than 10 min with detection limit of 1.2 nM. The rapid on-site/in situ determination of Hg²⁺ was readily performed in natural water. This sensing strategy can be extended in principle to other metal ions by substituting the T-Hg²⁺-T complexes with other specificity structures that selectively bind to other analytes.

Ability of a rapid HIV testing site to attract and test vulnerable populations: a cross-sectional study on Actuel sur Rue.

PubMed

Engler, Kim; Rollet, Kathleen; Lessard, David; Thomas, Réjean; Lebouché, Bertrand

2016-10-01

Quebec's HIV epidemic persists, particularly among men who have sex with men (MSM) and in Montreal. Increasing access to HIV testing is necessary and community-based rapid testing offers one strategy. This paper examines the clienteles and activities of a rapid HIV testing site in Montreal, the pilot project Actuel sur Rue. Comparative analyses were conducted with 1357 MSM, 147 heterosexual men and 64 women who visited Actuel sur Rue between July 2012 and November 2013 on socio-demographics, health, drug use, sexual practices/infection and HIV testing/prevention. Significant group differences were observed in each category. Actuel sur Rue received 1901 clients, conducted 1417 rapid HIV tests and tested 77 never-tested individuals. Rapid testing produced a high reactive rate (2%). Only 1/28 of those with reactive tests had no previous HIV testing, and 36% had used post-exposure prophylaxis, suggesting missed opportunities for prevention. Findings highlight diverse client vulnerability profiles and the relevance of checkpoints and further prevention efforts. © The Author(s) 2016.

Chemical and biological assessment of two offshore drilling sites in the Alaskan Arctic.

PubMed

Trefry, John H; Dunton, Kenneth H; Trocine, Robert P; Schonberg, Susan V; McTigue, Nathan D; Hersh, Eric S; McDonald, Thomas J

2013-05-01

A retrospective chemical and biological study was carried out in Camden Bay, Alaskan Beaufort Sea, where single exploratory oil wells were drilled at two sites more than two decades ago. Barium from discharged drilling mud was present in sediments at concentrations as high as 14%, ~200 times above background, with significantly higher concentrations of Ba, but not other metals, within 250 m of the drilling site versus reference stations. Elevated concentrations of Cr, Cu, Hg and Pb were found only at two stations within 25 m of one drilling site. Concentrations of total polycyclic aromatic hydrocarbons (TPAH) were not significantly different at reference versus drilling-site stations; however, TPAH were elevated in Ba-rich layers from naturally occurring perylene in ancient formation cuttings. Infaunal biomass and species abundance were not significantly different at reference versus drilling-site stations; infauna were less diverse at drilling-site stations. Our assessment showed that discharges from single wells within large areas caused minimal long-term, adverse impacts to the benthic ecosystem. Copyright © 2013 Elsevier Ltd. All rights reserved.

Integrated one- and two-photon scanned oblique plane illumination (SOPi) microscopy for rapid volumetric imaging

NASA Astrophysics Data System (ADS)

Kumar, Manish; Kishore, Sandeep; Nasenbeny, Jordan; McLean, David L.; Kozorovitskiy, Yevgenia

2018-05-01

Versatile, sterically accessible imaging systems capable of in vivo rapid volumetric functional and structural imaging deep in the brain continue to be a limiting factor in neuroscience research. Towards overcoming this obstacle, we present integrated one- and two-photon scanned oblique plane illumination (SOPi) microscopy which uses a single front-facing microscope objective to provide light-sheet scanning based rapid volumetric imaging capability at subcellular resolution. Our planar scan-mirror based optimized light-sheet architecture allows for non-distorted scanning of volume samples, simplifying accurate reconstruction of the imaged volume. Integration of both one-photon (1P) and two-photon (2P) light-sheet microscopy in the same system allows for easy selection between rapid volumetric imaging and higher resolution imaging in scattering media. Using SOPi, we demonstrate deep, large volume imaging capability inside scattering mouse brain sections and rapid imaging speeds up to 10 volumes per second in zebrafish larvae expressing genetically encoded fluorescent proteins GFP or GCaMP6s. SOPi flexibility and steric access makes it adaptable for numerous imaging applications and broadly compatible with orthogonal techniques for actuating or interrogating neuronal structure and activity.

Integrated one- and two-photon scanned oblique plane illumination (SOPi) microscopy for rapid volumetric imaging.

PubMed

Kumar, Manish; Kishore, Sandeep; Nasenbeny, Jordan; McLean, David L; Kozorovitskiy, Yevgenia

2018-05-14

Versatile, sterically accessible imaging systems capable of in vivo rapid volumetric functional and structural imaging deep in the brain continue to be a limiting factor in neuroscience research. Towards overcoming this obstacle, we present integrated one- and two-photon scanned oblique plane illumination (SOPi, /sōpī/) microscopy which uses a single front-facing microscope objective to provide light-sheet scanning based rapid volumetric imaging capability at subcellular resolution. Our planar scan-mirror based optimized light-sheet architecture allows for non-distorted scanning of volume samples, simplifying accurate reconstruction of the imaged volume. Integration of both one-photon (1P) and two-photon (2P) light-sheet microscopy in the same system allows for easy selection between rapid volumetric imaging and higher resolution imaging in scattering media. Using SOPi, we demonstrate deep, large volume imaging capability inside scattering mouse brain sections and rapid imaging speeds up to 10 volumes per second in zebrafish larvae expressing genetically encoded fluorescent proteins GFP or GCaMP6s. SOPi's flexibility and steric access makes it adaptable for numerous imaging applications and broadly compatible with orthogonal techniques for actuating or interrogating neuronal structure and activity.

Comparison of two trajectory based models for locating particle sources for two rural New York sites

NASA Astrophysics Data System (ADS)

Zhou, Liming; Hopke, Philip K.; Liu, Wei

Two back trajectory-based statistical models, simplified quantitative transport bias analysis and residence-time weighted concentrations (RTWC) have been compared for their capabilities of identifying likely locations of source emissions contributing to observed particle concentrations at Potsdam and Stockton, New York. Quantitative transport bias analysis (QTBA) attempts to take into account the distribution of concentrations around the directions of the back trajectories. In full QTBA approach, deposition processes (wet and dry) are also considered. Simplified QTBA omits the consideration of deposition. It is best used with multiple site data. Similarly the RTWC approach uses concentrations measured at different sites along with the back trajectories to distribute the concentration contributions across the spatial domain of the trajectories. In this study, these models are used in combination with the source contribution values obtained by the previous positive matrix factorization analysis of particle composition data from Potsdam and Stockton. The six common sources for the two sites, sulfate, soil, zinc smelter, nitrate, wood smoke and copper smelter were analyzed. The results of the two methods are consistent and locate large and clearly defined sources well. RTWC approach can find more minor sources but may also give unrealistic estimations of the source locations.

Rapid Benefit Indicator (RBI) Checklist Tool - Quick Start ...

EPA Pesticide Factsheets

The Rapid Benefits Indicators (RBI) approach consists of five steps and is outlined in Assessing the Benefits of Wetland Restoration – A Rapid Benefits Indicators Approach for Decision Makers. This checklist tool is intended to be used to record information as you answer the questions in that guide. When performing a Rapid Benefits Indicator (RBI) assessment on wetlands restoration site(s) results can be recorded and reviewed using this VBA enabled MS Excel Checklist Tool.

Efficient multi-site two-photon functional imaging of neuronal circuits.

PubMed

Castanares, Michael Lawrence; Gautam, Vini; Drury, Jack; Bachor, Hans; Daria, Vincent R

2016-12-01

Two-photon imaging using high-speed multi-channel detectors is a promising approach for optical recording of cellular membrane dynamics at multiple sites. A main bottleneck of this technique is the limited number of photons captured within a short exposure time (~1ms). Here, we implement temporal gating to improve the two-photon fluorescence yield from holographically projected multiple foci whilst maintaining a biologically safe incident average power. We observed up to 6x improvement in the signal-to-noise ratio (SNR) in Fluorescein and cultured hippocampal neurons showing evoked calcium transients. With improved SNR, we could pave the way to achieving multi-site optical recording of fluorogenic probes with response times in the order of ~1ms.

The Rapid Distortion of Two-Way Coupled Particle-Laden Turbulence

NASA Astrophysics Data System (ADS)

Kasbaoui, Mohamed; Koch, Donald; Desjardins, Olivier

2017-11-01

The modulation of sheared turbulence by dispersed particles is addressed in the two-way coupling regime. The preferential sampling of the straining regions of the flow by inertial particles in turbulence leads to the formation of clusters. These fast sedimenting particle structures cause the anisotropic alteration of turbulence at small scales in the direction of gravity. These effects are investigated in a revisited Rapid Distortion Theory (RDT), extended for two-way coupled particle-laden flows. To make the analysis tractable, we assume that particles have small but non-zero inertia. In the classical results for single-phase flows, the RDT assumption of fast shearing compared to the turbulence time scales leads to the distortion of ``frozen'' turbulence. In particle-laden turbulence, the coupling between the two phases remains strong even under fast shearing and leads to a dynamic modulation of the turbulence spectrum. Turbulence statistics obtained from RDT are compared with Euler-Lagrange simulations of homogeneously sheared particle-laden turbulence.

Crude oil metabolites in groundwater at two spill sites

USGS Publications Warehouse

Bekins, Barbara A.; Cozzarelli, Isabelle M.; Erickson, Melinda L.; Steenson, Ross; Thorn, Kevin A.

2016-01-01

Two groundwater plumes in north central Minnesota with residual crude oil sources have 20 to 50 mg/L of nonvolatile dissolved organic carbon (NVDOC). These values are over 10 times higher than benzene and two to three times higher than Diesel Range Organics in the same wells. On the basis of previous work, most of the NVDOC consists of partial transformation products from the crude oil. Monitoring data from 1988 to 2015 at one of the sites located near Bemidji, MN show that the plume of metabolites is expanding toward a lakeshore located 335 m from the source zone. Other mass balance studies of the site have demonstrated that the plume expansion is driven by the combined effect of continued presence of the residual crude oil source and depletion of the electron accepting capacity of solid phase iron oxide and hydroxides on the aquifer sediments. These plumes of metabolites are not covered by regulatory monitoring and reporting requirements in Minnesota and other states. Yet, a review of toxicology studies indicates that polar metabolites of crude oil may pose a risk to aquatic and mammalian species. Together the results suggest that at sites where residual sources are present, monitoring of NVDOC may be warranted to evaluate the fates of plumes of hydrocarbon transformation products.

One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas

PubMed Central

Fung, Rowena K. Y.; Grenga, Lucia; Trampari, Eleftheria; Pepe, Simona

2017-01-01

Effective regulation of primary carbon metabolism is critically important for bacteria to successfully adapt to different environments. We have identified an uncharacterised transcriptional regulator; RccR, that controls this process in response to carbon source availability. Disruption of rccR in the plant-associated microbe Pseudomonas fluorescens inhibits growth in defined media, and compromises its ability to colonise the wheat rhizosphere. Structurally, RccR is almost identical to the Entner-Doudoroff (ED) pathway regulator HexR, and both proteins are controlled by the same ED-intermediate; 2-keto-3-deoxy-6-phosphogluconate (KDPG). Despite these similarities, HexR and RccR control entirely different aspects of primary metabolism, with RccR regulating pyruvate metabolism (aceEF), the glyoxylate shunt (aceA, glcB, pntAA) and gluconeogenesis (pckA, gap). RccR displays complex and unusual regulatory behaviour; switching repression between the pyruvate metabolism and glyoxylate shunt/gluconeogenesis loci depending on the available carbon source. This regulatory complexity is enabled by two distinct pseudo-palindromic binding sites, differing only in the length of their linker regions, with KDPG binding increasing affinity for the 28 bp aceA binding site but decreasing affinity for the 15 bp aceE site. Thus, RccR is able to simultaneously suppress and activate gene expression in response to carbon source availability. Together, the RccR and HexR regulators enable the rapid coordination of multiple aspects of primary carbon metabolism, in response to levels of a single key intermediate. PMID:28658302

Oxides of nitrogen at two sites in New Zealand

NASA Astrophysics Data System (ADS)

Stedman, D. H.; McEwan, M. J.

1983-02-01

Oxides of nitrogen, ozone and solar UV radiation were measured at two New Zealand sites, four months at Mt. John near Lake Tekapo, and one month at the New Zealand Department of scientific and Industrial Research, Physics and Engineering Laboratory Atmospheric Station (PELAS) near Lauder. The former site proved ideal for clean-air measurements. Ozone concentrations of ˜20-25 ppb, with little diurnal variation were accompanied by total nitrogen oxide (NOy) levels frequently less than 150 ppt (parts in 1012 by volume). The noon NO and NO2 data were well correlated with a slope comparable to model values. Gaseous HNO3 was observed to be significantly above the noise level (˜15 ppt) for only twenty-seven four-hour averages. For these a median of 43 ppt was obtained with a median ([NOy]-[HNO3])/[HNO3] ratio of 7.5, not comparable with model values of around 1.1. This low HNO3 may arise from the fact that the Mt. John site is downwind of a mountain range which experiences significant upwind precipitation. At the PELAS site, strong diurnal variation of ozone and much larger NOy concentrations were observed. The difference is apparently caused by local sources of nitrogen oxides and the local meteorology at the fertile valley PELAS site.

Stochastic, goal-oriented rapid impact modeling of uncertainty and environmental impacts in poorly-sampled sites using ex-situ priors

NASA Astrophysics Data System (ADS)

Li, Xiaojun; Li, Yandong; Chang, Ching-Fu; Tan, Benjamin; Chen, Ziyang; Sege, Jon; Wang, Changhong; Rubin, Yoram

2018-01-01

Modeling of uncertainty associated with subsurface dynamics has long been a major research topic. Its significance is widely recognized for real-life applications. Despite the huge effort invested in the area, major obstacles still remain on the way from theory and applications. Particularly problematic here is the confusion between modeling uncertainty and modeling spatial variability, which translates into a (mis)conception, in fact an inconsistency, in that it suggests that modeling of uncertainty and modeling of spatial variability are equivalent, and as such, requiring a lot of data. This paper investigates this challenge against the backdrop of a 7 km, deep underground tunnel in China, where environmental impacts are of major concern. We approach the data challenge by pursuing a new concept for Rapid Impact Modeling (RIM), which bypasses altogether the need to estimate posterior distributions of model parameters, focusing instead on detailed stochastic modeling of impacts, conditional to all information available, including prior, ex-situ information and in-situ measurements as well. A foundational element of RIM is the construction of informative priors for target parameters using ex-situ data, relying on ensembles of well-documented sites, pre-screened for geological and hydrological similarity to the target site. The ensembles are built around two sets of similarity criteria: a physically-based set of criteria and an additional set covering epistemic criteria. In another variation to common Bayesian practice, we update the priors to obtain conditional distributions of the target (environmental impact) dependent variables and not the hydrological variables. This recognizes that goal-oriented site characterization is in many cases more useful in applications compared to parameter-oriented characterization.

Reliability of quadriceps surface electromyography measurements is improved by two vs. single site recordings.

PubMed

Balshaw, T G; Fry, A; Maden-Wilkinson, T M; Kong, P W; Folland, J P

2017-06-01

The reliability of surface electromyography (sEMG) is typically modest even with rigorous methods, and therefore further improvements in sEMG reliability are desirable. This study compared the between-session reliability (both within participant absolute reliability and between-participant relative reliability) of sEMG amplitude from single vs. average of two distinct recording sites, for individual muscle (IM) and whole quadriceps (WQ) measures during voluntary and evoked contractions. Healthy males (n = 20) performed unilateral isometric knee extension contractions: voluntary maximum and submaximum (60%), as well as evoked twitch contractions on two separate days. sEMG was recorded from two distinct sites on each superficial quadriceps muscle. Averaging two recording sites vs. using single site measures improved reliability for IM and WQ measurements during voluntary (16-26% reduction in within-participant coefficient of variation, CV W ) and evoked contractions (40-56% reduction in CV W ). For sEMG measurements from large muscles, averaging the recording of two distinct sites is recommended as it improves within-participant reliability. This improved sensitivity has application to clinical and research measurement of sEMG amplitude.

Detecting a Difference in Clay Minerals at Two Gale Crater Sites

NASA Image and Video Library

2016-12-13

Data graphed here from the Chemistry and Camera (CheMin) instrument on NASA's Mars Curiosity rover show a difference between clay minerals in powder drilled from mudstone outcrops at two locations in Mars' Gale Crater: "Yellowknife Bay" and "Murray Buttes." CheMin's X-ray diffraction analysis reveals information about the crystalline structure of minerals in the rock. The intensity peaks marked with dotted vertical lines in this chart indicate that the crystalline structure of the two sites' clay minerals differs. The difference can be tied to a compositional difference in the clay minerals, as depicted in a diagram at PIA21148. The Yellowknife Bay site is on the floor of Gale Crater. The Murray Buttes site is on lower Mount Sharp, the layered mound in the center of the crater. http://photojournal.jpl.nasa.gov/catalog/PIA21147

Efficient multi-site two-photon functional imaging of neuronal circuits

PubMed Central

Castanares, Michael Lawrence; Gautam, Vini; Drury, Jack; Bachor, Hans; Daria, Vincent R.

2016-01-01

Two-photon imaging using high-speed multi-channel detectors is a promising approach for optical recording of cellular membrane dynamics at multiple sites. A main bottleneck of this technique is the limited number of photons captured within a short exposure time (~1ms). Here, we implement temporal gating to improve the two-photon fluorescence yield from holographically projected multiple foci whilst maintaining a biologically safe incident average power. We observed up to 6x improvement in the signal-to-noise ratio (SNR) in Fluorescein and cultured hippocampal neurons showing evoked calcium transients. With improved SNR, we could pave the way to achieving multi-site optical recording of fluorogenic probes with response times in the order of ~1ms. PMID:28018745

The Asian Monsoon Moisture Transportation Revealed by Two Cave Sites in Myanmar

NASA Astrophysics Data System (ADS)

Liu, G.; Wang, X.; Chiang, H. W.; Maung Maung, P.; Jiang, X.; Aung, L. T.; Tun, S. T.

2014-12-01

Here we present two well-resolved, calcite δ18O records on Myanmar speleothems. The samples were collected from a coastal site in southeastern Myanmar and a plateau site in central Myanmar, respectively. Chronologically determined by high-precision U/Th dating techniques, both records span a large portion of the past 40,000 years. The two records show similar millennial-scale oscillations during the last glacial period, which are also in-phase with the speleothem records from Chinese cave sites located in the downstream of Indian Monsoon trajectories. The δ18O values between the two profiles are virtually the same, ~ -7.5‰, during late Holocene, in concert with the numbers in modern rainfall at the two sites. However, in glacial time, the δ18O value of the central Myanmar record shifts from -6.5‰ to -8‰, approximately 2‰ lower than that in the coastal dataset, which varies from -4.5‰ to -6‰. We interpret the similarly low δ18O values during Holocene in both records as a result of strong monsoonal rainfall and water recycling particularly through forest transpiration. However in glacial time, with a possibly drier and less forested land, water recycling is weaker. Therefore, rainfall δ18O and subsequently speleothem δ18O appear a stronger geographical gradient, possibly dominated by the continental rainout effect. Our interpretation can be supported by the speleothem δ13C records from the two sites. Calcite δ13C from the coastal site varies slightly from ~-7‰ in the last glacial to ~-9‰ in Holocene. Whereas it shares a similar value to the coastal record during Holocene, the δ13C profile from the plateau site shows a much higher value, up to -0.7‰, during the glacial time. This suggests that the mountainous region in central Myanmar was likely dominated by C4 plants (e.g., grass) during the glacial time, while the same region is covered by forests today. Such change on vegetation type and coverage may influence the δ18O of recycling

Two rapid pigmentation tests for identification of Cryptococcus neoformans.

PubMed Central

Kaufmann, C S; Merz, W G

1982-01-01

Two tests were developed for the rapid identification of Cryptococcus neoformans based on pigment produced by the organism's phenoloxidase activity. Caffeic acid was incorporated into cornmeal agar, a medium used routinely for yeast identification. When tested on this medium, only C. neoformans isolates produced brown pigment. All other yeasts maintained their normal morphology and did not produce the reaction product. A non-medium-based test was developed for same-day identification of C. neoformans isolates. Paper strips saturated with a buffered L-beta-3,4-dihydroxyphenylalanine-ferric citrate solution were inoculated with isolates and incubated at 37 degrees C. Pigment production occurred only with C. neoformans isolates, many within 60 to 90 min. All other yeasts remained negative. PMID:7040452

A rapid and effective approach for on-site assessment of total carotenoid content in wolfberry juice during processing.

PubMed

Zheng, Xiaodong; Zhu, Fengtao; Wu, Maoyu; Yan, Xinhuan; Meng, Xiaomeng; Song, Ye

2015-11-01

Carotenoid content analysis in wolfberry processed products has mainly focused on the determination of zeaxanthin or zeaxanthin dipalmitate, which cannot indicate the total carotenoid content (TCC) in wolfberries. We have exploited an effective approach for rapid extraction of carotenoid from wolfberry juice and determined TCC using UV-visible spectrophotometry. Several solvent mixtures, adsorption wavelengths of carotenoid extracts and extraction procedures were investigated. The optimal solvent mixture with broad spectrum polarity was hexane-ethanol-acetone (2:1:1) and optimal wavelength was 456 nm. There was no significant difference of TCC in wolfberry juice between direct extraction and saponification extraction. The developed method for assessment of TCC has been successfully employed in quality evaluation of wolfberry juice under different processing conditions. This measurement approach has inherent advantages (simplicity, rapidity, effectiveness) that make it appropriate for obtaining on-site information of TCC in wolfberry juice during processing. © 2014 Society of Chemical Industry.

Mitochondria-Endoplasmic Reticulum Contact Sites Function as Immunometabolic Hubs that Orchestrate the Rapid Recall Response of Memory CD8+ T Cells.

PubMed

Bantug, Glenn R; Fischer, Marco; Grählert, Jasmin; Balmer, Maria L; Unterstab, Gunhild; Develioglu, Leyla; Steiner, Rebekah; Zhang, Lianjun; Costa, Ana S H; Gubser, Patrick M; Burgener, Anne-Valérie; Sauder, Ursula; Löliger, Jordan; Belle, Réka; Dimeloe, Sarah; Lötscher, Jonas; Jauch, Annaïse; Recher, Mike; Hönger, Gideon; Hall, Michael N; Romero, Pedro; Frezza, Christian; Hess, Christoph

2018-03-20

Glycolysis is linked to the rapid response of memory CD8 + T cells, but the molecular and subcellular structural elements enabling enhanced glucose metabolism in nascent activated memory CD8 + T cells are unknown. We found that rapid activation of protein kinase B (PKB or AKT) by mammalian target of rapamycin complex 2 (mTORC2) led to inhibition of glycogen synthase kinase 3β (GSK3β) at mitochondria-endoplasmic reticulum (ER) junctions. This enabled recruitment of hexokinase I (HK-I) to the voltage-dependent anion channel (VDAC) on mitochondria. Binding of HK-I to VDAC promoted respiration by facilitating metabolite flux into mitochondria. Glucose tracing pinpointed pyruvate oxidation in mitochondria, which was the metabolic requirement for rapid generation of interferon-γ (IFN-γ) in memory T cells. Subcellular organization of mTORC2-AKT-GSK3β at mitochondria-ER contact sites, promoting HK-I recruitment to VDAC, thus underpins the metabolic reprogramming needed for memory CD8 + T cells to rapidly acquire effector function. Copyright © 2018 Elsevier Inc. All rights reserved.

Comparison of the Abbott Architect i2000 assay, the Roche Modular Analytics E170 assay, and an immunoradiometric assay for serum hepatitis B virus markers.

PubMed

Kim, Hyunjung; Oh, Eun-Jee; Kang, Mi-Sook; Kim, Sung Hoon; Park, Yeon-Joon

2007-01-01

Serum hepatitis B virus (HBV) markers are the most important data for epidemiological screening and clinical diagnosis of HBV infection, especially in endemic areas. We compared the results of the Roche Modular Analytics E170 assay, the Abbott Architect i2000 assay, and an immunoradiometric assay (IRMA) for HBV surface antigen (HBsAg), anti-HBV surface antigen (anti-HBs), HBV e antigen (HBeAg), and anti-HBV e antigen (anti-HBe). A number of serum samples (264, 263, 224, and 202 for HBsAg, anti-HBs, HBeAg, and anti-HBe, respectively) were studied. For samples giving discrepant results for HBeAg between methods, real-time PCR assays were performed. The concordance rates among the three methods were high for HBsAg (100%) and HBeAg (94.6), but low for anti-HBs (91.6%) and anti-HBe (82.2%). For anti-HBs, which could be measured quantitatively by the Modular E170 and Architect i2000 procedures, discrepant results were observed at low levels of anti-HBs. For anti-HBe, the positive rate was highest with Modular E170 (60.9%) followed by the IRMA kit (54.1%) and Architect i2000 (51.0%). This study shows substantial differences between the assay results by the three methods, which should be taken into account in determinations of serum HBV markers.

Method for rapid base sequencing in DNA and RNA with two base labeling

DOEpatents

Jett, James H.; Keller, Richard A.; Martin, John C.; Posner, Richard G.; Marrone, Babetta L.; Hammond, Mark L.; Simpson, Daniel J.

1995-01-01

Method for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand.

Explaining the Presence of "Heterosexual" Female Clients of a Rapid HIV Testing Site Located in the Gay Village of Montreal, Quebec.

PubMed

Engler, Kim; Rollet, Kathleen; Lessard, David; Thomas, Réjean; Lebouché, Bertrand

2016-04-01

Increasing access and uptake of HIV testing among at-risk women is needed. Examining women's motives for visiting a community-based rapid HIV testing site (Actuel sur Rue-AsR) oriented to men who have sex with men (MSM) could offer suggestions. To compare the "heterosexual" female and male clients of AsR, located in Montreal's (Canada) gay village, to better understand the women's particular HIV prevention and sexual health service needs. This cross-sectional pilot study analyzed questionnaire data provided by AsR clients and staff (nurse and community agent teams) between July 2012 and November 2013. Women and men reporting only opposite-sex partners were compared with chi-square, Fisher's exact, and Kruskal-Wallis tests, as appropriate, on sociodemographics, HIV-related behaviors, motives for visiting AsR, and health service provision. AsR received 1901 clients. Among these, 55 women and 147 men reported only opposite-sex partners. Women were significantly younger. Significantly greater proportions of women visited AsR because no appointment was necessary (67% vs. 48%), sought testing for condom failure (18% vs. 5%), and had no regular doctor (44% vs. 27%). Both groups mainly chose AsR for the rapid test results (80% and 77%), visited it to receive the rapid HIV test (71% and 76%), and sought testing due to unprotected vaginal sex (44% and 43%). Similar proportions saw the nurse (91% and 89%), received the rapid HIV test (44% and 35%), and were linked to a medical clinic (49% and 52%), especially, to receive complete sexually transmitted infection testing (50% and 44%). The results of this innovative study highlight the draw of rapid HIV testing for "heterosexual" users of a site mainly targeting MSM. They also suggest that further research is warranted into the importance for this group of women clients of drop-in and linkage services, particularly given their possible lesser access to regular care. © The Author(s) 2016.

Division site selection in Escherichia coli involves dynamic redistribution of Min proteins within coiled structures that extend between the two cell poles

NASA Astrophysics Data System (ADS)

Shih, Yu-Ling; Le, Trung; Rothfield, Lawrence

2003-06-01

The MinCDE proteins of Escherichia coli are required for proper placement of the division septum at midcell. The site selection process requires the rapid oscillatory redistribution of the proteins from pole to pole. We report that the three Min proteins are organized into extended membrane-associated coiled structures that wind around the cell between the two poles. The pole-to-pole oscillation of the proteins reflects oscillatory changes in their distribution within the coiled structure. We also report that the E. coli MreB protein, which is required for maintaining the rod shape of the cell, also forms extended coiled structures, which are similar to the MreB structures that have previously been reported in Bacillus subtilis. The MreB and MinCDE coiled arrays do not appear identical. The results suggest that at least two functionally distinct cytoskeletal-like elements are present in E. coli and that structures of this type can undergo dynamic changes that play important roles in division site placement and possibly other aspects of the life of the cell.

Highly Specific Detection of Myostatin Prodomain by an Immunoradiometric Sandwich Assay in Serum of Healthy Individuals and Patients

PubMed Central

Widera, Christian; Gottlieb, Jens; Vogel, Arndt; Schmidt, Sebastian; Brandes, Gudrun; Heuft, Hans-Gert; Lichtinghagen, Ralf; Kempf, Tibor; Wollert, Kai C.; Bauersachs, Johann; Heineke, Joerg

2013-01-01

Background Myostatin is a muscle derived factor that functions as a negative regulator of skeletal muscle growth. Induction of myostatin expression was observed in rodent models of muscle wasting and in cachectic patients with cancer or pulmonary disease. Therefore, there is an increasing interest to use serum myostatin as a biomarker. Methods We established an immunoradiometric sandwich assay (IRMA), which uses a commercially available chicken polyclonal, affinity purified antibody directed against human myostatin prodomain. We determined the serum concentrations of myostatin prodomain in 249 healthy individuals as well as 169 patients with heart failure, 53 patients with cancer and 44 patients with chronic pulmonary disease. Results The IRMA had a detection limit of 0.7ng/ml, an intraassay imprecision of ≤14.1% and an interassay imprecision of ≤ 18.9%. The specificity of our assay was demonstrated by size exclusion chromatography, detection of myostatin by Western-blotting and a SMAD-dependent transcriptional-reporter assay in the signal-rich serum fractions, as well as lack of interference by unspecific substances like albumin, hemoglobin or lipids. Myostatin prodomain was stable at room temperature and resistant to freeze-thaw cycles. Apparently healthy individuals over the age of 55 had a median myostatin prodomain serum concentration of 3.9ng/ml (25th-75th percentiles, 2-7ng/ml) and we could not detect increased levels in patients with stable chronic heart failure or cancer related weight loss. In contrast, we found strongly elevated concentrations of myostatin prodomain (median 26.9ng/ml, 25th-75th percentiles, 7-100ng/ml) in the serum of underweight patients with chronic pulmonary disease. Conclusions We established a highly specific IRMA for the quantification of myostatin prodomain concentration in human serum. Our assay could be useful to study myostatin as a biomarker for example in patients with chronic pulmonary disease, as we detected highly

On-site Rapid Diagnosis of Intracranial Hematoma using Portable Multi-slice Microwave Imaging System.

PubMed

Mobashsher, Ahmed Toaha; Abbosh, A M

2016-11-29

Rapid, on-the-spot diagnostic and monitoring systems are vital for the survival of patients with intracranial hematoma, as their conditions drastically deteriorate with time. To address the limited accessibility, high costs and static structure of currently used MRI and CT scanners, a portable non-invasive multi-slice microwave imaging system is presented for accurate 3D localization of hematoma inside human head. This diagnostic system provides fast data acquisition and imaging compared to the existing systems by means of a compact array of low-profile, unidirectional antennas with wideband operation. The 3D printed low-cost and portable system can be installed in an ambulance for rapid on-site diagnosis by paramedics. In this paper, the multi-slice head imaging system's operating principle is numerically analysed and experimentally validated on realistic head phantoms. Quantitative analyses demonstrate that the multi-slice head imaging system is able to generate better quality reconstructed images providing 70% higher average signal to clutter ratio, 25% enhanced maximum signal to clutter ratio and with around 60% hematoma target localization compared to the previous head imaging systems. Nevertheless, numerical and experimental results demonstrate that previous reported 2D imaging systems are vulnerable to localization error, which is overcome in the presented multi-slice 3D imaging system. The non-ionizing system, which uses safe levels of very low microwave power, is also tested on human subjects. Results of realistic phantom and subjects demonstrate the feasibility of the system in future preclinical trials.

Rapid broad area search and detection of Chinese surface-to-air missile sites using deep convolutional neural networks

NASA Astrophysics Data System (ADS)

Marcum, Richard A.; Davis, Curt H.; Scott, Grant J.; Nivin, Tyler W.

2017-10-01

We evaluated how deep convolutional neural networks (DCNN) could assist in the labor-intensive process of human visual searches for objects of interest in high-resolution imagery over large areas of the Earth's surface. Various DCNN were trained and tested using fewer than 100 positive training examples (China only) from a worldwide surface-to-air-missile (SAM) site dataset. A ResNet-101 DCNN achieved a 98.2% average accuracy for the China SAM site data. The ResNet-101 DCNN was used to process ˜19.6 M image chips over a large study area in southeastern China. DCNN chip detections (˜9300) were postprocessed with a spatial clustering algorithm to produce a ranked list of ˜2100 candidate SAM site locations. The combination of DCNN processing and spatial clustering effectively reduced the search area by ˜660X (0.15% of the DCNN-processed land area). An efficient web interface was used to facilitate a rapid serial human review of the candidate SAM sites in the China study area. Four novice imagery analysts with no prior imagery analysis experience were able to complete a DCNN-assisted SAM site search in an average time of ˜42 min. This search was ˜81X faster than a traditional visual search over an equivalent land area of ˜88,640 km2 while achieving nearly identical statistical accuracy (˜90% F1).

Method for rapid base sequencing in DNA and RNA with two base labeling

DOEpatents

Jett, J.H.; Keller, R.A.; Martin, J.C.; Posner, R.G.; Marrone, B.L.; Hammond, M.L.; Simpson, D.J.

1995-04-11

A method is described for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand. 4 figures.

Development of an on-site rapid real-time polymerase chain reaction system and the characterization of suitable DNA polymerases for TaqMan probe technology.

PubMed

Furutani, Shunsuke; Naruishi, Nahoko; Hagihara, Yoshihisa; Nagai, Hidenori

2016-08-01

On-site quantitative analyses of microorganisms (including viruses) by the polymerase chain reaction (PCR) system are significantly influencing medical and biological research. We have developed a remarkably rapid and portable real-time PCR system that is based on microfluidic approaches. Real-time PCR using TaqMan probes consists of a complex reaction. Therefore, in a rapid real-time PCR, the optimum DNA polymerase must be estimated by using actual real-time PCR conditions. In this study, we compared the performance of three DNA polymerases in actual PCR conditions using our rapid real-time PCR system. Although KAPA2G Fast HS DNA Polymerase has the highest enzymatic activity among them, SpeedSTAR HS DNA Polymerase exhibited better performance to rapidly increase the fluorescence signal in an actual real-time PCR using TaqMan probes. Furthermore, we achieved rapid detection of Escherichia coli in 7 min by using SpeedSTAR HS DNA Polymerase with the same sensitivity as that of a conventional thermal cycler.

Proliferating Cell Nuclear Antigen-dependent Rapid Recruitment of Cdt1 and CRL4Cdt2 at DNA-damaged Sites after UV Irradiation in HeLa Cells*

PubMed Central

Ishii, Takashi; Shiomi, Yasushi; Takami, Toshihiro; Murakami, Yusuke; Ohnishi, Naho; Nishitani, Hideo

2010-01-01

The licensing factor Cdt1 is degraded by CRL4Cdt2 ubiquitin ligase dependent on proliferating cell nuclear antigen (PCNA) during S phase and when DNA damage is induced in G1 phase. Association of both Cdt2 and PCNA with chromatin was observed in S phase and after UV irradiation. Here we used a micropore UV irradiation assay to examine Cdt2 accumulation at cyclobutane pyrimidine dimer-containing DNA-damaged sites in the process of Cdt1 degradation in HeLa cells. Cdt2, present in the nucleus throughout the cell cycle, accumulated rapidly at damaged DNA sites during G1 phase. The recruitment of Cdt2 is dependent on prior PCNA chromatin binding because Cdt2 association was prevented when PCNA was silenced. Cdt1 was also recruited to damaged sites soon after UV irradiation through its PIP-box. As Cdt1 was degraded, the Cdt2 signal at damaged sites was reduced, but PCNA, cyclobutane pyrimidine dimer, and XPA (xeroderma pigmentosum, complementation group A) signals remained at the same levels. These findings suggest that Cdt1 degradation following UV irradiation occurs rapidly at damaged sites due to PCNA chromatin loading and the recruitment of Cdt1 and CRL4Cdt2, before DNA damage repair is completed. PMID:20929861

Crude Oil Metabolites in Groundwater at Two Spill Sites.

PubMed

Bekins, Barbara A; Cozzarelli, Isabelle M; Erickson, Melinda L; Steenson, Ross A; Thorn, Kevin A

2016-09-01

Two groundwater plumes in north central Minnesota with residual crude oil sources have 20 to 50 mg/L of nonvolatile dissolved organic carbon (NVDOC). These values are over 10 times higher than benzene and two to three times higher than Diesel Range Organics in the same wells. On the basis of previous work, most of the NVDOC consists of partial transformation products from the crude oil. Monitoring data from 1988 to 2015 at one of the sites located near Bemidji, MN show that the plume of metabolites is expanding toward a lakeshore located 335 m from the source zone. Other mass balance studies of the site have demonstrated that the plume expansion is driven by the combined effect of continued presence of the residual crude oil source and depletion of the electron accepting capacity of solid phase iron oxide and hydroxides on the aquifer sediments. These plumes of metabolites are not covered by regulatory monitoring and reporting requirements in Minnesota and other states. Yet, a review of toxicology studies indicates that polar metabolites of crude oil may pose a risk to aquatic and mammalian species. Together the results suggest that at sites where residual sources are present, monitoring of NVDOC may be warranted to evaluate the fates of plumes of hydrocarbon transformation products. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Lateral-flow colloidal gold-based immunoassay for the rapid detection of deoxynivalenol with two indicator ranges.

PubMed

Kolosova, Anna Yu; Sibanda, Liberty; Dumoulin, Frédéric; Lewis, Janet; Duveiller, Etienne; Van Peteghem, Carlos; De Saeger, Sarah

2008-06-02

A lateral-flow immunoassay using a colloidal gold-labelled monoclonal antibody was developed for the rapid detection of deoxynivalenol (DON). Different parameters, such as the amount of immunoreagents, type of the materials, composition of the blocking solution and of the detector reagent mixture, were investigated to provide the optimum assay performance. The experimental results demonstrated that such a visual test had an indicator range rather than a cut-off value. Thus, tests for DON determination with two different indicator ranges of 250-500 and 1000-2000 microg kg(-1) were designed. The method allowed detection of DON at low and high concentration levels, which could be useful for research and practical purposes. The assay applied to spiked wheat and pig feed samples demonstrated accurate and reproducible results. The applicability of the developed lateral-flow test was also confirmed under real field conditions. The test strips prepared in Belgium were sent to Mexico, where they were used for the screening of DON contamination in different bread wheat entries from Fusarium Head Blight inoculated plots. The results were compared with those obtained by ELISA and LC-MS/MS. A poor correlation between ELISA and LC-MS/MS was observed. Visual results of the dipstick tests were in a good agreement with the results of the LC-MS/MS method. Coupled with a simple and fast sample preparation, this qualitative one-step test based on the visual evaluation of results did not require any equipment. Results could be obtained within 10 min. The described assay format can be used as a simple, rapid, cost-effective and robust on-site screening tool for mycotoxin contamination in different agricultural commodities.

Between Site Reliability of Startle Prepulse Inhibition Across Two Early Psychosis Consortia

PubMed Central

Addington, Jean; Cannon, Tyrone D.; Cornblatt, Barbara A.; de la Fuente-Sandoval, Camilo; Mathalon, Dan H.; Perkins, Diana O.; Seidman, Larry J.; Tsuang, Ming; Walker, Elaine F.; Woods, Scott W.; Bachman, Peter; Belger, Ayse; Carrión, Ricardo E.; Donkers, Franc C.L.; Duncan, Erica; Johannesen, Jason; León-Ortiz, Pablo; Light, Gregory; Mondragón, Alejandra; Niznikiewicz, Margaret; Nunag, Jason; Roach, Brian J.; Solís-Vivanco, Rodolfo

2014-01-01

Prepulse inhibition (PPI) and reactivity of the acoustic startle response are widely used biobehavioral markers in psychopathology research. Previous studies have demonstrated that PPI and startle reactivity exhibit substantial within-site stability; between-site stability, however, has not been established. In two separate consortia investigating biomarkers of early psychosis, traveling subjects studies were performed as part of quality assurance procedures in order to assess the fidelity of data across sites. In the North American Prodromal Longitudinal Studies (NAPLS) Consortium, 8 normal subjects traveled to each of the 8 NAPLS sites and were tested twice at each site on the startle PPI paradigm. In preparation for a binational study, 10 healthy subjects were assessed twice in both San Diego and Mexico City. Intraclass correlations between and within sites were significant for PPI and startle response parameters, confirming the reliability of startle measures across sites in both consortia. There were between site differences in startle magnitude in the NAPLS study that did not appear to be related to methods or equipment. In planning multi-site studies, it is essential to institute quality assurance procedures early and establish between site reliability to assure comparable data across sites. PMID:23799460

Sensory coding of nest-site value in honeybee swarms.

PubMed

Seeley, Thomas D; Visscher, P Kirk

2008-12-01

This study investigates the first stage of the decision-making process of a honeybee swarm as it chooses a nest site: how a scout bee codes the value of a potential nest site in the waggle dances she produces to represent this site. We presented honeybee swarms with a two-alternative choice between a high-value site and a medium-value site and recorded the behavior of individually identifiable scout bees as they reported on these two alternatives. We found that bees performed equally lengthy inspections at the two sites, but that, on the swarm cluster, they performed more dance circuits per bee for the high-value site. We also found that there was much individual-level noise in the coding of site value, but that there were clear population-level differences in total dance circuits produced for the two sites. The first bee to find a site had a high probability of reporting the site with a waggle dance, regardless of its value. This discoverer-should-dance phenomenon may help ensure that a swarm gives attention to all discovered sites. There was rapid decay in the dance response; the number of dance circuits produced by a bee after visiting a site decreased linearly over sequential visits, and eventually each bee ceased visiting her site. This decay, or ;leakage', in the accumulation of bees at a site improves a swarm's decision-making ability by helping a swarm avoid making fast-decision errors.

A novel bench-scale column assay to investigate site-specific nitrification biokinetics in biological rapid sand filters.

PubMed

Tatari, K; Smets, B F; Albrechtsen, H-J

2013-10-15

A bench-scale assay was developed to obtain site-specific nitrification biokinetic information from biological rapid sand filters employed in groundwater treatment. The experimental set-up uses granular material subsampled from a full-scale filter, packed in a column, and operated with controlled and continuous hydraulic and ammonium loading. Flowrates and flow recirculation around the column are chosen to mimic full-scale hydrodynamic conditions, and minimize axial gradients. A reference ammonium loading rate is calculated based on the average loading experienced in the active zone of the full-scale filter. Effluent concentrations of ammonium are analyzed when the bench-scale column is subject to reference loading, from which removal rates are calculated. Subsequently, removal rates above the reference loading are measured by imposing short-term loading variations. A critical loading rate corresponding to the maximum removal rate can be inferred. The assay was successfully applied to characterize biokinetic behavior from a test rapid sand filter; removal rates at reference loading matched those observed from full-scale observations, while a maximum removal capacity of 6.9 g NH4(+)-N/m(3) packed sand/h could easily be determined at 7.5 g NH4(+)-N/m(3) packed sand/h. This assay, with conditions reflecting full-scale observations, and where the biological activity is subject to minimal physical disturbance, provides a simple and fast, yet powerful tool to gain insight in nitrification kinetics in rapid sand filters. Copyright © 2013 Elsevier Ltd. All rights reserved.

Portable Microplate Analyzer with a Thermostatic Chamber Based on a Smartphone for On-site Rapid Detection.

PubMed

Wan, Zijian; Zhong, Longjie; Pan, Yuxiang; Li, Hongbo; Zou, Quchao; Su, Kaiqi; Wang, Ping

2017-01-01

A microplate method provides an efficient way to use modern detection technology. However, there are some difficulties concerning on-site detection, such as being non-portable and time-consuming. In this work, a novel portable microplate analyzer with a thermostatic chamber based on a smartphone was designed for rapid on-site detection. An analyzer with a wide-angle lens and an optical filter provides a proper environment for the microplate. A smartphone app-iPlate Monitor was used for RGB analyze of image. After a consistency experiment with a microtiter plate reader (MTPR), the normalized calibration curves were y = 0.7276x + 0.0243 (R 2 = 0.9906) and y = 0.3207x + 0.0094 (R 2 = 0.9917) with a BCA protein kit as well as y = 0.182x + 0.0134 (R 2 = 0.994) and y = 0.0674x + 0.0003 (R 2 = 0.9988) with a glucose kit. The times for obtaining the detection requirement were 15 and 10 min for the BCA protein kit and the glucose kit at 37°C; in contrast, it required more than 30 and 20 min at ambient temperature. Meanwhile, it also showed good repeatability for detections.

Sensitivity and specificity of typhoid fever rapid antibody tests for laboratory diagnosis at two sub-Saharan African sites

PubMed Central

Keddy, Karen H; Sooka, Arvinda; Letsoalo, Maupi E; Hoyland, Greta; Chaignat, Claire Lise; Morrissey, Anne B; Crump, John A

2011-01-01

Abstract Objective To evaluate three commercial typhoid rapid antibody tests for Salmonella Typhi antibodies in patients suspected of having typhoid fever in Mpumalanga, South Africa, and Moshi, United Republic of Tanzania. Methods The diagnostic accuracy of Cromotest® (semiquantitative slide agglutination and single tube Widal test), TUBEX® and Typhidot® was assessed against that of blood culture. Performance was modelled for scenarios with pretest probabilities of 5% and 50%. Findings In total 92 patients enrolled: 53 (57.6%) from South Africa and 39 (42.4%) from the United Republic of Tanzania. Salmonella Typhi was isolated from the blood of 28 (30.4%) patients. The semiquantitative slide agglutination and single-tube Widal tests had positive predictive values (PPVs) of 25.0% (95% confidence interval, CI: 0.6–80.6) and 20.0% (95% CI: 2.5–55.6), respectively. The newer typhoid rapid antibody tests had comparable PPVs: TUBEX®, 54.1% (95% CI: 36.9–70.5); Typhidot® IgM, 56.7% (95% CI: 37.4–74.5); and Typhidot® IgG, 54.3% (95% CI: 36.6–71.2). For a pretest probability of 5%, PPVs were: TUBEX®, 11.0% (95% CI: 6.6–17.9); Typhidot® IgM, 9.1% (95% CI: 5.8–14.0); and Typhidot® IgG, 11.0% (6.3–18.4). For a pretest probability of 50%, PPVs were: TUBEX®, 70.2% (95% CI: 57.3–80.5); Typhidot® IgM, 65.6% (95% CI: 54.0–75.6); and Typhidot® IgG, 70.0% (95% CI: 56.0–81.1). Conclusion Semiquantitative slide agglutination and single-tube Widal tests performed poorly. TUBEX® and Typhidot® may be suitable when pretest probability is high and blood cultures are unavailable, but their performance does not justify deployment in routine care settings in sub-Saharan Africa. PMID:21897484

Screening tests for the rapid detection of diarrhetic shellfish toxins in Washington State.

PubMed

Eberhart, Bich-Thuy L; Moore, Leslie K; Harrington, Neil; Adams, Nicolaus G; Borchert, Jerry; Trainer, Vera L

2013-09-30

The illness of three people due to diarrhetic shellfish poisoning (DSP) following their ingestion of recreationally harvested mussels from Sequim Bay State Park in the summer of 2011, resulted in intensified monitoring for diarrhetic shellfish toxins (DSTs) in Washington State. Rapid testing at remote sites was proposed as a means to provide early warning of DST events in order to protect human health and allow growers to test "pre-harvest" shellfish samples, thereby preventing harvest of toxic product that would later be destroyed or recalled. Tissue homogenates from several shellfish species collected from two sites in Sequim Bay, WA in the summer 2012, as well as other sites throughout Puget Sound, were analyzed using three rapid screening methods: a lateral flow antibody-based test strip (Jellett Rapid Test), an enzyme-linked immunosorbent assay (ELISA) and a protein phosphatase 2A inhibition assay (PP2A). The results were compared to the standard regulatory method of liquid chromatography coupled with tandem mass spectroscopy (LC-MS/MS). The Jellett Rapid Test for DSP gave an unacceptable number of false negatives due to incomplete extraction of DSTs using the manufacturer's recommended method while the ELISA antibody had low cross-reactivity with dinophysistoxin-1, the major toxin isomer in shellfish from the region. The PP2A test showed the greatest promise as a screening tool for Washington State shellfish harvesters.

Screening Tests for the Rapid Detection of Diarrhetic Shellfish Toxins in Washington State

PubMed Central

Eberhart, Bich-Thuy L.; Moore, Leslie K.; Harrington, Neil; Adams, Nicolaus G.; Borchert, Jerry; Trainer, Vera L.

2013-01-01

The illness of three people due to diarrhetic shellfish poisoning (DSP) following their ingestion of recreationally harvested mussels from Sequim Bay State Park in the summer of 2011, resulted in intensified monitoring for diarrhetic shellfish toxins (DSTs) in Washington State. Rapid testing at remote sites was proposed as a means to provide early warning of DST events in order to protect human health and allow growers to test “pre-harvest” shellfish samples, thereby preventing harvest of toxic product that would later be destroyed or recalled. Tissue homogenates from several shellfish species collected from two sites in Sequim Bay, WA in the summer 2012, as well as other sites throughout Puget Sound, were analyzed using three rapid screening methods: a lateral flow antibody-based test strip (Jellett Rapid Test), an enzyme-linked immunosorbent assay (ELISA) and a protein phosphatase 2A inhibition assay (PP2A). The results were compared to the standard regulatory method of liquid chromatography coupled with tandem mass spectroscopy (LC-MS/MS). The Jellett Rapid Test for DSP gave an unacceptable number of false negatives due to incomplete extraction of DSTs using the manufacturer’s recommended method while the ELISA antibody had low cross-reactivity with dinophysistoxin-1, the major toxin isomer in shellfish from the region. The PP2A test showed the greatest promise as a screening tool for Washington State shellfish harvesters. PMID:24084788

Two distinctive β subunits are separately involved in two binding sites of imidacloprid with different affinities in Locusta migratoria manilensis.

PubMed

Bao, Haibo; Liu, Yang; Zhang, Yixi; Liu, Zewen

2017-08-01

Due to great diversity of nicotinic acetylcholine receptor (nAChR) subtypes in insects, one β subunit may be contained in numerous nAChR subtypes. In the locust Locusta migratoria, a model insect species with agricultural importance, the third β subunits (Locβ3) was identified in this study, which reveals at least three β subunits in this insect species. Imidacloprid was found to bind nAChRs in L. migratoria central nervous system at two sites with different affinities, with K d values of 0.16 and 10.31nM. The specific antisera (L1-1, L2-1 and L3-1) were raised against fusion proteins at the large cytoplasmic loop of Locβ1, Locβ2 and Locβ3 respectively. Specific immunodepletion of Locβ1 with antiserum L1-1 resulted in the selective loss of the low affinity binding site for imidacloprid, whereas the immunodepletion of Locβ3 with L3-1 caused the selective loss of the high affinity site. Dual immunodepletion with L1-1 and L3-1 could completely abolish imidacloprid binding. In contrast, the immunodepletion of Locβ2 had no significant effect on the specific [ 3 H]imidacloprid binding. Taken together, these data indicated that Locβ1 and Locβ3 were respectively contained in the low- and high-affinity binding sites for imidacloprid in L. migratoria, which is different to the previous finding in Nilaparvata lugens that Nlβ1 was in two binding sites for imidacloprid. The involvement of two β subunits separately in two binding sites may decrease the risk of imidacloprid resistance due to putative point mutations in β subunits in L. migratoria. Copyright © 2017 Elsevier B.V. All rights reserved.

The value of rapid on-site evaluation during EBUS-TBNA.

PubMed

Cardoso, A V; Neves, I; Magalhães, A; Sucena, M; Barroca, H; Fernandes, G

2015-01-01

Rapid on-site evaluation (ROSE) has the potential to increase endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) accuracy in the diagnosis of mediastinal lesions and lung cancer staging. However, studies have reported controversial results. The purpose of our study was to evaluate the influence of ROSE on sample adequacy and diagnostic accuracy of EBUS-TBNA. Prospective observational study that enrolled 81 patients who underwent EBUS-TBNA for investigation of hilo-mediastinal lesions or lung cancer staging. The first 41 patients underwent EBUS-TBNA with ROSE (ROSE group) and the last 40 patients without ROSE (non-ROSE group). Sample adequacy and diagnostic accuracy of EBUS-TBNA in both groups were compared. Adequate samples were obtained in 93% of the patients in the ROSE group and 80% in non-ROSE group (p=0.10). The diagnostic accuracy of EBUS-TBNA was 91% in ROSE group and 83% in non-ROSE group (p=0.08). Analyzing the EBUS-TBNA purpose, in the subgroup of patients who underwent EBUS-TBNA for investigation of hilo-mediastinal lesions, these differences between ROSE and non-ROSE group were higher compared to lung cancer staging, 93% of patients with adequate samples in the ROSE group vs. 75% in the non-ROSE group (p=0.06) and 87% of diagnostic accuracy in ROSE group vs. 77% in non-ROSE group (p=0.10). Despite the lack of statistical significance, ROSE appears to be particularly useful in the diagnostic work-up of hilo-mediastinal lesions, increasing the diagnostic yield of EBUS-TBNA. Copyright © 2014 Sociedade Portuguesa de Pneumologia. Published by Elsevier España, S.L.U. All rights reserved.

An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange

PubMed Central

Baldwin, Andrew J.

2014-01-01

The Carr–Purcell–Meiboom–Gill (CPMG) experiment is widely used to quantitatively analyse the effects of chemical exchange on NMR spectra. In a CPMG experiment, the effective transverse relaxation rate, R2,eff, is typically measured as a function of the pulse frequency, νCPMG. Here, an exact expression for how R2,eff varies with νCPMG is derived for the commonly encountered scenario of two-site chemical exchange of in-phase magnetisation. This result, summarised in Appendix A, generalises a frequently used equation derived by Carver and Richards, published in 1972. The expression enables more rapid analysis of CPMG data by both speeding up calculation of R2,eff over numerical methods by a factor of ca. 130, and yields exact derivatives for use in data analysis. Moreover, the derivation provides insight into the physical principles behind the experiment. PMID:24852115

Roseate Tern breeding dispersal and fidelity: Responses to two newly restored colony sites

USGS Publications Warehouse

Spendelow, Jeffrey A.; Monticelli, David; Nichols, James D.; Hines, James; Nisbet, Ian; Cormons, Grace; Hays, Helen; Hatch, Jeremy; Mostello, Carolyn

2016-01-01

We used 22 yr of capture–mark–reencounter (CMR) data collected from 1988 to 2009 on about 12,500 birds at what went from three to five coastal colony sites in Massachusetts, New York, and Connecticut, United States, to examine spatial and temporal variation in breeding dispersal/fidelity rates of adult Roseate Terns (Sterna dougallii). At the start of our study, Roseate Terns nested at only one site (Bird Island) in Buzzards Bay, Massachusetts, but two more sites in this bay (Ram and Penikese Islands) were subsequently recolonized and became incorporated into our CMR metapopulation study. We examined four major hypotheses about factors we thought might influence colony-site fidelity and movement rates in the restructured system. We found some evidence that colony-site fidelity remained higher at long-established sites compared with newer ones and that breeding dispersal was more likely to occur among nearby sites than distant ones. Sustained predation at Falkner Island, Connecticut, did not result in a sustained drop in fidelity rates of breeders. Patterns of breeding dispersal differed substantially at the two restored sites. The fidelity of Roseate Terns at Bird dropped quickly after nearby Ram was recolonized in 1994, and fidelity rates for Ram soon approached those for Bird. After an oil spill in Buzzards Bay in April 2003, hazing (deliberate disturbance) of the terns at Ram prior to the start of egg-laying resulted in lowering of fidelity at this site, a decrease in immigration from Bird, and recolonization of Penikese by Roseate Terns. Annual fidelity rates at Penikese increased somewhat several years after the initial recolonization, but they remained much lower there than at all the other sites throughout the study period. The sustained high annual rates of emigration from Penikese resulted in the eventual failure of the restoration effort there, and in 2013, no Roseate Terns nested at this site.

Constraints on rapidity-dependent initial conditions from charged-particle pseudorapidity densities and two-particle correlations

NASA Astrophysics Data System (ADS)

Ke, Weiyao; Moreland, J. Scott; Bernhard, Jonah E.; Bass, Steffen A.

2017-10-01

We study the initial three-dimensional spatial configuration of the quark-gluon plasma (QGP) produced in relativistic heavy-ion collisions using centrality and pseudorapidity-dependent measurements of the medium's charged particle density and two-particle correlations. A cumulant-generating function is first used to parametrize the rapidity dependence of local entropy deposition and extend arbitrary boost-invariant initial conditions to nonzero beam rapidities. The model is then compared to p +Pb and Pb + Pb charged-particle pseudorapidity densities and two-particle pseudorapidity correlations and systematically optimized using Bayesian parameter estimation to extract high-probability initial condition parameters. The optimized initial conditions are then compared to a number of experimental observables including the pseudorapidity-dependent anisotropic flows, event-plane decorrelations, and flow correlations. We find that the form of the initial local longitudinal entropy profile is well constrained by these experimental measurements.

Evapotranspiration of rubber (Hevea brasiliensis) cultivated at two plantation sites in Southeast Asia

NASA Astrophysics Data System (ADS)

Giambelluca, Thomas W.; Mudd, Ryan G.; Liu, Wen; Ziegler, Alan D.; Kobayashi, Nakako; Kumagai, Tomo'omi; Miyazawa, Yoshiyuki; Lim, Tiva Khan; Huang, Maoyi; Fox, Jefferson; Yin, Song; Mak, Sophea Veasna; Kasemsap, Poonpipope

2016-02-01

To investigate the effects of expanding rubber (Hevea brasiliensis) cultivation on water cycling in Mainland Southeast Asia (MSEA), evapotranspiration (ET) was measured within rubber plantations at Bueng Kan, Thailand, and Kampong Cham, Cambodia. After energy closure adjustment, mean annual rubber ET was 1211 and 1459 mm yr-1 at the Thailand and Cambodia sites, respectively, higher than that of other tree-dominated land covers in the region, including tropical seasonal forest (812-1140 mm yr-1), and savanna (538-1060 mm yr-1). The mean proportion of net radiation used for ET by rubber (0.725) is similar to that of tropical rainforest (0.729) and much higher than that of tropical seasonal forest (0.595) and savanna (0.548). Plant area index (varies with leaf area changes), explains 88.2% and 73.1% of the variance in the ratio of latent energy flux (energy equivalent of ET) to potential latent energy flux (LE/LEpot) for midday rain-free periods at the Thailand and Cambodia sites, respectively. High annual rubber ET results from high late dry season water use, associated with rapid refoliation by this brevideciduous species, facilitated by tapping of deep soil water, and by very high wet season ET, a characteristic of deciduous trees. Spatially, mean annual rubber ET increases strongly with increasing net radiation (Rn) across the three available rubber plantation observation sites, unlike nonrubber tropical ecosystems, which reduce canopy conductance at high Rn sites. High water use by rubber raises concerns about potential effects of continued expansion of tree plantations on water and food security in MSEA.

Overlaps with arbitrary two-site states in the XXZ spin chain

NASA Astrophysics Data System (ADS)

Pozsgay, B.

2018-05-01

We present a conjectured exact formula for overlaps between the Bethe states of the spin-1/2 XXZ chain and generic two-site states. The result takes the same form as in the previously known cases: it involves the same ratio of two Gaudin-like determinants, and a product of single-particle overlap functions, which can be fixed using a combination of the quench action and quantum transfer matrix methods. Our conjecture is confirmed by numerical data from exact diagonalization. For one-site states, the formula is found to be correct even in chains with odd length. It is also pointed out that the ratio of the Gaudin-like determinants plays a crucial role in the overlap sum rule: it guarantees that in the thermodynamic limit there remains no term in the quench action.

Rapid, Long-term Monitoring of CO2 Concentration and δ13CO2 at CCUS Sites Allows Discrimination of Leakage Patterns from Natural Background Values

NASA Astrophysics Data System (ADS)

Galfond, B.; Riemer, D. D.; Swart, P. K.

2014-12-01

In order for Carbon Capture Utilization and Storage (CCUS) to gain wide acceptance as a method for mitigating atmospheric CO2 concentrations, schemes must be devised to ensure that potential leakage is detected. New regulations from the US Environmental Protection Agency require monitoring and accounting for Class VI injection wells, which will remain a barrier to wide scale CCUS deployment until effective and efficient monitoring techniques have been developed and proven. Monitoring near-surface CO2 at injection sites to ensure safety and operational success requires high temporal resolution CO2 concentration and carbon isotopic (δ13C) measurements. The only technologies currently capable of this rapid measurement of δ13C are optical techniques such as Cavity Ringdown Spectroscopy (CRDS). We have developed a comprehensive remote monitoring approach using CRDS and a custom manifold system to obtain accurate rapid measurements from a large sample area over an extended study period. Our modified Picarro G1101-i CRDS allows for automated rapid and continuous field measurement of δ13CO2 and concentrations of relevant gas species. At our field site, where preparations have been underway for Enhanced Oil Recovery (EOR) operations, we have been able to measure biogenic effects on a diurnal scale, as well as variation due to precipitation and seasonality. Taking these background trends into account, our statistical treatment of real data has been used to improve signal-to-noise ratios by an order of magnitude over published models. Our system has proven field readiness for the monitoring of sites with even modest CO2 fluxes.

Comparative evaluation of two rapid Salmonella-IgM tests and blood culture in the diagnosis of enteric fever.

PubMed

Prasad, K J; Oberoi, J K; Goel, N; Wattal, C

2015-01-01

Enteric fever is a major public health problem in developing countries like India. An early and accurate diagnosis is necessary for a prompt and effective treatment. We have evaluated the diagnostic accuracy of two Rapid Salmonella-IgM tests (Typhidot-IgM and Enteroscreen-IgM) as compared to blood culture in rapid and early diagnosis of enteric fever. A total of 2,699 patients' serum samples were tested by Rapid Salmonella-IgM tests and blood culture. Patients were divided into two groups. Test group - patients with enteric fever and blood culture positives for Salmonella Typhi; and three types of Controls, i.e. patients with non-enteric fever illnesses, normal healthy controls and patients positive for S. Paratyphi- A. In addition to this we have also evaluated the significance of positive Salmonella-IgM tests among blood culture-negative cases. The overall sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the Typhidot-IgM test and Enteroscreen-IgM test considering blood culture as gold standard were 97.29% and 88.13%, 97.40% and 87.83%, 98.18% and 92.03%, 96.15% and 82.27%, respectively. Typhidot-IgM test was found to be significantly more sensitive and specific as compared to Enteroscreen-IgM. Among blood culture-negative patients, Rapid Salmonella-IgM tests detected 72.25% additional cases of enteric fever. Although the Rapid Salmonella-IgM tests are meant to diagnose S. Typhi only, but these tests detect S. Paratyphi- A also. Thirty-eight patients who were blood culture-positive for S. Paratyphi- A were also positive by Rapid Salmonella-IgM tests. Rapid Salmonella-IgM tests offer an advantage of increased sensitivity, rapidity, early diagnosis and simplicity over blood culture.

Rapid mass production of two-dimensional metal oxides and hydroxides via the molten salts method

PubMed Central

Hu, Zhimi; Xiao, Xu; Jin, Huanyu; Li, Tianqi; Chen, Ming; Liang, Zhun; Guo, Zhengfeng; Li, Jia; Wan, Jun; Huang, Liang; Zhang, Yanrong; Feng, Guang; Zhou, Jun

2017-01-01

Because of their exotic electronic properties and abundant active sites, two-dimensional (2D) materials have potential in various fields. Pursuing a general synthesis methodology of 2D materials and advancing it from the laboratory to industry is of great importance. This type of method should be low cost, rapid and highly efficient. Here, we report the high-yield synthesis of 2D metal oxides and hydroxides via a molten salts method. We obtained a high-yield of 2D ion-intercalated metal oxides and hydroxides, such as cation-intercalated manganese oxides (Na0.55Mn2O4·1.5H2O and K0.27MnO2·0.54H2O), cation-intercalated tungsten oxides (Li2WO4 and Na2W4O13), and anion-intercalated metal hydroxides (Zn5(OH)8(NO3)2·2H2O and Cu2(OH)3NO3), with a large lateral size and nanometre thickness in a short time. Using 2D Na2W4O13 as an electrode, a high performance electrochemical supercapacitor is achieved. We anticipate that our method will enable new path to the high-yield synthesis of 2D materials for applications in energy-related fields and beyond. PMID:28555669

Suitability of oyster restoration sites along the Louisiana coast: Examining site and stock × site interaction

USGS Publications Warehouse

Schwarting Miller, Lindsay; La Peyre, Jerome F.; LaPeyre, Megan K.

2017-01-01

Recognition of the global loss of subtidal oyster reefs has led to a rise in reef restoration efforts, including in the Gulf of Mexico. Created reef success depends entirely on selecting a location that supports long-term oyster growth and survival, including the recruitment and survival of on-reef oysters. Significant changes in estuarine salinity through management of freshwater inflows and through changed precipitation patterns may significantly impact the locations of optimal oyster restoration sites. These rapid shifts in conditions necessitate a need to better understand both impacts to on-reef oyster growth and population development, and variation in oyster stock performance. Oyster growth, mortality, condition, and disease prevalence were examined in three different stocks of oysters located in protected cages, as well as oyster recruitment and mortality on experimental reef units in three different locations representing a salinity gradient, along the Louisiana Gulf coast in 2011 and 2012. Over a 2-y period, the high-salinity site had highest oyster growth rate in protected cages but demonstrated the least likelihood for reef development based on on-reef oyster population failure, likely because of predation-related mortality (high recruitment and 100% mortality). In contrast, the midsalinity site with moderate oyster growth and on-reef recruitment and low mortality demonstrated a higher likelihood for reef development. The lowest salinity site exhibited extreme variability in all oyster responses between years because of extreme variation in environmental conditions during the study, indicating a low likelihood of long-term reef development. Whereas limited differences in stock performance between sites were found, the range of site environmental conditions tested was ultimately much lower than expected and may not have provided a wide enough range of conditions. In areas with limited, low recruitment, or rapidly changing environmental conditions

Comparison of treatment outcome using two definitions of rapid cycling in subjects with bipolar II disorder.

PubMed

Amsterdam, Jay D; Lorenzo-Luaces, Lorenzo; DeRubeis, Robert J

2017-02-01

We examined differences in treatment outcome between Diagnostic and Statistical Manual Fourth Edition (DSM-IV)-defined rapid cycling and average lifetime-defined rapid cycling in subjects with bipolar II disorder. We hypothesized that, compared with the DSM-IV definition, the average lifetime definition of rapid cycling may better identify subjects with a history of more mood lability and a greater likelihood of hypomanic symptom induction during long-term treatment. Subjects ≥18 years old with a bipolar II major depressive episode (n=129) were categorized into DSM-IV- and average lifetime-defined rapid cycling and prospectively treated with either venlafaxine or lithium monotherapy for 12 weeks. Responders (n=59) received continuation monotherapy for six additional months. These exploratory analyses found moderate agreement between the two rapid-cycling definitions (κ=0.56). The lifetime definition captured subjects with more chronic courses of bipolar II depression, whereas the DSM-IV definition captured subjects with more acute symptoms of hypomania. There was no difference between rapid-cycling definitions with respect to the response to acute venlafaxine or lithium monotherapy. However, the lifetime definition was slightly superior to the DSM-IV definition in identifying subjects who went on to experience hypomanic symptoms during continuation therapy. Although sample sizes were limited, the findings suggest that the lifetime definition of rapid cycling may identify individuals with a chronic rapid-cycling course and may also be slightly superior to the DSM-IV definition in identifying individuals with hypomania during relapse-prevention therapy. These findings are preliminary in nature and need replication in larger, prospective, bipolar II studies. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Rapid on-site TLC-SERS detection of four antidiabetes drugs used as adulterants in botanical dietary supplements.

PubMed

Zhu, Qingxia; Cao, Yongbing; Cao, Yingying; Chai, Yifeng; Lu, Feng

2014-03-01

A novel facile method has been established for rapid on-site detection of antidiabetes chemicals used to adulterate botanical dietary supplements (BDS) for diabetes. Analytes and components of pharmaceutical matrices were separated by thin-layer chromatography (TLC) then surface-enhanced Raman spectroscopy (SERS) was used for qualitative identification of trace substances on the HPTLC plate. Optimization and standardization of the experimental conditions, for example the method used for preparation of silver colloids, the mobile phase, and the concentration of colloidal silver, resulted in a very robust and highly sensitive method which enabled successful detection when the amount of adulteration was as low as 0.001 % (w/w). The method was also highly selective, enabling successful identification of some chemicals in extremely complex herbal matrices. The established TLC-SERS method was used for analysis of real BDS used to treat diabetes, and the results obtained were verified by liquid chromatography-triple quadrupole mass spectrometry (LC-MS-MS). The study showed that TLC-SERS could be used for effective separation and detection of four chemicals used to adulterate BDS, and would have good prospects for on-site qualitative screening of BDS for adulterants.

Contaminant profiles of two species of shorebirds foraging together at two neighboring sites in south San Francisco Bay, California

USGS Publications Warehouse

Hui, Clifford A.; Takekawa, John Y.; Warnock, Sarah E.

2001-01-01

The San Francisco Bay estuary isused by over one million shorebirds during springmigration and is home to several hundred thousandduring the winter. Most shorebird use occurs in thesouthern reach of the estuary (South Bay). Thereduced water circulation and discharge fromindustrial sources in the South Bay are responsiblefor the highest levels of some trace elements in theestuary. Wintering shorebirds have been found to havestrong site fidelity to areas as small as a fewkilometers in the South Bay, which may increase theirexposure to contaminants near local point sources. Inaddition, different shorebird species foraging at thesame site have been shown to have differentcontaminant burdens. Thus, our objectives were totest whether contaminant burdens differed by species,or whether contaminant burdens differed in shorebirdscollected at adjacent sites. We examined thecontaminant profiles of two species of shorebirds,long-billed dowitchers (Limnodromus scolopaceus)and western sandpipers (Calidris mauri) thatforage together at two sites, Hayward and Newark,separated by 8 km in the South Bay. We usedmultivariate analysis of variance tests to compare thecomposition of 14 elemental analytes in their livertissues and estimated their molar ratios of Hg and Se. Composite samples were used for contaminant analysesbecause of the small body size of the shorebirds. Seven elemental analytes (Ag, Ba, Be, Cr, Ni, Pb, V)were below detection limits in a majority of thesamples so statistical analyses were precluded. Inthe measurable analytes (As, Cd, Cu, Hg, Mn, Se, Zn),we found no significant intra-site differences ofcontaminant profiles for the two species. We pooledthe samples to examine inter-site differences andfound significant differences in contaminant profilesbetween shorebirds at the neighboring sites (P = 0.03). Shorebirds at Newark had higher (P < 0.05) concentrations of As, Cd, and Se than those at Hayward. Dowitchers at Newark had concentrations of Hg and Se which were

A comparison of forest dynamics at two sites in the Southeastern Ozark Mountains of Missouri

Treesearch

Michael A. Jenkins; Stephen G. Pallardy

1993-01-01

Changes in tree species composition and regeneration patterns were studied in 53 permanent vegetation plots located at two sites (Pioneer Forest and University State Forest) in oak-hickory forests of southeastern Missouri where mortality and decline of red oak species have been identified. The two sites also exhibited differing levels of decline and mortality. Between...

A Rapid Diagnostic Technique to Discriminate between Two Pests of Palms, Brontispa longissima and Octodonta nipae (Coleoptera: Chrysomelidae), for Quarantine Applications.

PubMed

Zhang, X; Tang, B; Hou, Y

2015-02-01

Octodonta nipae (Maulik) is morphologically and biologically similar to Brontispa longissima (Gestro), one of the most damaging pests of coconut. The two species share several palm hosts and produce similar symptoms. They are easily confused when they invade a new area, and without professional taxonomic expertise accurate identification is arduous and time-consuming. Thus, a method of rapidly distinguishing these two invasive insects rapidly is critical for quarantine. Based on the first internal transcribed spacer and the mitochondrial cytochrome oxidase I gene, two pairs of special primers and corresponding polymerase chain reaction processes have been developed to enhance a single objective band only from the O. nipae DNA template. This will quickly discriminate between these two species. The present results provide a rapid method of distinguishing O. nipae from B. longissima to help avoid misidentification, and furthermore, to facilitate rapid and appropriate quarantine decisions and effective treatments to the pest. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Mineral Content Comparison at Two Gale Crater Sites

NASA Image and Video Library

2016-12-13

This graphic shows proportions of minerals identified in mudstone exposures at the "Yellowknife Bay" location where NASA's Curiosity Mars rover first analyzed bedrock, in 2013, and at the "Murray Buttes" area investigated in 2016. Minerals were identified by X-ray diffraction analysis of sample powder from the rocks. The samples were acquired by drilling and delivered to the Chemistry and Mineralogy (CheMin) instrument inside the rover. Two key differences in the Murray Buttes mudstone include hematite rather than magnetite, and far less abundance of crystalline mafic minerals, compared to the Yellowknife Bay mudstone composition. Hematite and magnetite are both iron oxide minerals, with hematite as a more oxidized one. That difference could result from the Murray Buttes mudstone layer experiencing more weathering than the Yellowknife Bay mudstone. More weathering could also account for the lower abundance of crystalline mafics, which are volcanic-origin minerals such as pyroxene and olivine. The Yellowknife Bay site is on the floor of Gale Crater. The Murray Buttes site is on lower Mount Sharp, the layered mound in the center of the crater. http://photojournal.jpl.nasa.gov/catalog/PIA21149

Site Preparation and Fertilization Effects on Growth of Slash Pine for Two Rotations

Treesearch

A.E. Tiarks; J.D. Haywood

1996-01-01

Two replicated site preparation studies were used to examine the effect of management on pine height and volume growth in the next rotation on Paleudults. Treatments included notillage,flat disking, bedding, and fertilization. The first rotation of planted slash pine (pinus elliottii Engelm.var. eliottii)was measured for 15 yr on one site and 20 yr at the other,...

Rapid and on-site analysis of illegal drugs on the nano-microscale using a deep ultraviolet-visible reflected optical fiber sensor.

PubMed

Li, Qiang; Qiu, Tian; Hao, Hongxia; Zhou, Hong; Wang, Tongzhou; Zhang, Ye; Li, Xin; Huang, Guoliang; Cheng, Jing

2012-04-07

A deep ultraviolet-visible (DUV-Vis) reflected optical fiber sensor was developed for use in a simple spectrophotometric detection system to detect the absorption of various illegal drugs at wavelengths between 180 and 800 nm. Quantitative analyses performed using the sensor revealed a high specificity and sensitivity for drug detection at a wavelength of approximately 200 nm. Using a double-absorption optical path length, extremely small sample volumes were used (32 to 160 nL), which allowed the use of minimal amounts of samples. A portable spectrophotometric system was established based on our optical fiber sensor for the on-site determination and quantitative analysis of common illegal drugs, such as 3,4-methylenedioxymethamphetamine (MDMA), ketamine hydrochloride, cocaine hydrochloride, diazepam, phenobarbital, and barbital. By analyzing the absorbance spectra, six different drugs were quantified at concentrations that ranged from 0.1 to 1000 μg mL(-1) (16 pg-0.16 μg). A novel Matching Algorithm of Spectra Space (MASS) was used to accurately distinguish between each drug in a mixture. As an important supplement to traditional methods, such as mass spectrometry or chromatography, our optical fiber sensor offers rapid and low-cost on-site detection using trace amounts of sample. This rapid and accurate analytical method has wide-ranging applications in forensic science, law enforcement, and medicine.

Quality of stormwater runoff from paved surfaces of two production sites.

PubMed

Gnecco, I; Berretta, C; Lanza, L G; La Barbera, P

2006-01-01

In order to investigate stormwater pollutant loads associated with different anthropic activities and the related pollutant build-up and wash-off processes, two pilot sites have been equipped in the Liguria Region (Italy) for monitoring first flush water quality in a gas station and an auto dismantler facility. TSS, COD, HCtot and heavy metals in dissolved form (Zn, Pb, Cu, Ni, Cd, Cr) have been analyzed during the monitoring campaign (started in February 2004). Stormwater flow and quality data collected in both production sites confirm that EMC values are significantly higher than those observed in an urban site. In the auto dismantler site, the EMC values for TSS, COD and HC largely exceed the standard values (EC 91/271). Contrary to urban surface runoff, scarce correlation between TSS and COD concentrations is observed in runoff from both production sites. The occurrence and nature of the pollutant load connected to first flush flows is discussed by inspection of the M(V)-curves that are provided for all monitored water quality parameters. Significant first flush phenomenon is evidenced for TSS and HC, while such clear behavior doesn't emerge for heavy metals. Hydrologic and climatic characteristics (ADWP, rainfall intensity/depth) appear to scarcely affect the build-up and wash-off processes.

Applicability of rapid and on-site measured enzyme activity for surface water quality monitoring in an agricultural catchment

NASA Astrophysics Data System (ADS)

Stadler, Philipp; Farnleitner, Andreas H.; Sommer, Regina; Kumpan, Monika; Zessner, Matthias

2014-05-01

For the near real time and on-site detection of microbiological fecal pollution of water, the measurement of beta-D- Glucuronidase (GLUC) enzymatic activity has been suggested as a surrogate parameter and has been already successfully operated for water quality monitoring of ground water resources (Ryzinska-Paier et al. 2014). Due to possible short measure intervals of three hours, this method has high potential as a water quality monitoring tool. While cultivation based standard determination takes more than one working day (Cabral 2010) the potential advantage of detecting the GLUC activity is the high temporal measuring resolution. Yet, there is still a big gap of knowledge on the fecal indication capacity of GLUC (specificity, sensitivity, persistence, etc.) in relation to potential pollution sources and catchment conditions (Cabral 2010, Ryzinska-Paier et al. 2014). Furthermore surface waters are a big challenge for automated detection devices in a technical point of view due to the high sediment load during event conditions. This presentation shows results gained form two years of monitoring in an experimental catchment (HOAL) dominated by agricultural land use. Two enzymatic measurement devices are operated parallel at the catchment outlet to test the reproducibility and precision of the method. Data from continuous GLUC monitoring under both base flow and event conditions is compared with reference samples analyzed by standardized laboratory methods for fecal pollution detection (e.g. ISO 16649-1, Colilert18). It is shown that rapid enzymatic on-site GLUC determination can successfully be operated from a technical point of view for surface water quality monitoring under the observed catchment conditions. The comparison of enzyme activity with microbiological standard analytics reveals distinct differences in the dynamic of the signals during event conditions. Cabral J. P. S. (2010) "Water Microbiology. Bacterial Pathogens and Water" International Journal of

Rapid calculation method for Frenkel-type two-exciton states in one to three dimensions

NASA Astrophysics Data System (ADS)

Ajiki, Hiroshi

2014-07-01

Biexciton and two-exciton dissociated states of Frenkel-type excitons are well described by a tight-binding model with a nearest-neighbor approximation. Such two-exciton states in a finite-size lattice are usually calculated by numerical diagonalization of the Hamiltonian, which requires an increasing amount of computational time and memory as the lattice size increases. I develop here a rapid, memory-saving method to calculate the energies and wave functions of two-exciton states by employing a bisection method. In addition, an attractive interaction between two excitons in the tight-binding model can be obtained directly so that the biexciton energy agrees with the observed energy, without the need for the trial-and-error procedure implemented in the numerical diagonalization method.

Reliable Refuge: Two Sky Island Scorpion Species Select Larger, Thermally Stable Retreat Sites.

PubMed

Becker, Jamie E; Brown, Christopher A

2016-01-01

Sky island scorpions shelter under rocks and other surface debris, but, as with other scorpions, it is unclear whether these species select retreat sites randomly. Furthermore, little is known about the thermal preferences of scorpions, and no research has been done to identify whether reproductive condition might influence retreat site selection. The objectives were to (1) identify physical or thermal characteristics for retreat sites occupied by two sky island scorpions (Vaejovis cashi Graham 2007 and V. electrum Hughes 2011) and those not occupied; (2) determine whether retreat site selection differs between the two study species; and (3) identify whether thermal selection differs between species and between gravid and non-gravid females of the same species. Within each scorpion's habitat, maximum dimensions of rocks along a transect line were measured and compared to occupied rocks to determine whether retreat site selection occurred randomly. Temperature loggers were placed under a subset of occupied and unoccupied rocks for 48 hours to compare the thermal characteristics of these rocks. Thermal gradient trials were conducted before parturition and after dispersal of young in order to identify whether gravidity influences thermal preference. Vaejovis cashi and V. electrum both selected larger retreat sites that had more stable thermal profiles. Neither species appeared to have thermal preferences influenced by reproductive condition. However, while thermal selection did not differ among non-gravid individuals, gravid V. electrum selected warmer temperatures than its gravid congener. Sky island scorpions appear to select large retreat sites to maintain thermal stability, although biotic factors (e.g., competition) could also be involved in this choice. Future studies should focus on identifying the various biotic or abiotic factors that could influence retreat site selection in scorpions, as well as determining whether reproductive condition affects thermal

Reliability of rapid reporting of cancers in New Hampshire.

PubMed

Celaya, Maria O; Riddle, Bruce L; Cherala, Sai S; Armenti, Karla R; Rees, Judy R

2010-01-01

The New Hampshire State Cancer Registry (NHSCR) has a 2-phase reporting system. An abbreviated, "rapid" report of cancer diagnosis or treatment is due to the central registry within 45 days of diagnosis and a more detailed, definitive report is due within 180 days. Rapid reports are used for various research studies, but researchers who contact patients are warned that the rapid reports may contain inaccuracies. This study aimed to assess the reliability of rapid cancer reports. For diagnosis years 2000-2004, we compared the rapid and definitive reports submitted to NHSCR. We calculated the sensitivity and positive predictive value of rapid reports; the reliability of key data items overall and for major sites; and the time between diagnosis and submission of the report. Rapid reports identified incident cancer cases with a sensitivity of 88.5%. The overall accuracy of key data items was high. The accuracy of primary sites identified by rapid reports was high generally but lower for ovarian and unknown primaries. A subset analysis showed that 47% of cancers were reported within 90 days of diagnosis. Rapid reports submitted to NHSCR are generally of high quality and present a useful opportunity for research investigations in New Hampshire.

Two schemes for rapid generation of digital video holograms using PC cluster

NASA Astrophysics Data System (ADS)

Park, Hanhoon; Song, Joongseok; Kim, Changseob; Park, Jong-Il

2017-12-01

Computer-generated holography (CGH), which is a process of generating digital holograms, is computationally expensive. Recently, several methods/systems of parallelizing the process using graphic processing units (GPUs) have been proposed. Indeed, use of multiple GPUs or a personal computer (PC) cluster (each PC with GPUs) enabled great improvements in the process speed. However, extant literature has less often explored systems involving rapid generation of multiple digital holograms and specialized systems for rapid generation of a digital video hologram. This study proposes a system that uses a PC cluster and is able to more efficiently generate a video hologram. The proposed system is designed to simultaneously generate multiple frames and accelerate the generation by parallelizing the CGH computations across a number of frames, as opposed to separately generating each individual frame while parallelizing the CGH computations within each frame. The proposed system also enables the subprocesses for generating each frame to execute in parallel through multithreading. With these two schemes, the proposed system significantly reduced the data communication time for generating a digital hologram when compared with that of the state-of-the-art system.

Ambient airborne solids concentrations including volcanic ash at Hanford, Washington sampling sites subsequent to the Mount St. Helens eruption

NASA Technical Reports Server (NTRS)

Sehmel, G. A.

1982-01-01

Airborne solids concentrations were measured on a near daily basis at two Hanford, Washington sites after the eruption of Mount St. Helens on May 18, 1980. These sites are about 211 km east of Mount St. Helens. Collected airborne solids included resuspended volcanic ash plus normal ambient solids. Average airborne solids concentrations were greater at the Hanford meteorological station sampling site which is 24 km northwest of the Horn Rapids dam sampling site. These increased concentrations reflect the sampling site proximity to greater ash fallout depths. Both sites are in low ash fallout areas although the Hanford meteorological station site is closer to the greater ash fallout areas. Airborne solids concentrations were decreased by rain, but airborne solids concentrations rapidly increased as surfaces dried. Airborne concentrations tended to become nearly the same at both sampling sites only for July 12 and 13.

Nitrogen conversion under rapid pyrolysis of two types of aquatic biomass and corresponding blends with coal.

PubMed

Yuan, Shuai; Chen, Xue-li; Li, Wei-feng; Liu, Hai-feng; Wang, Fu-chen

2011-11-01

Rapid pyrolysis of two types of aquatic biomass (blue-green algae and water hyacinth), and their blends with two coals (bituminous and anthracite) was carried out in a high-frequency furnace. Nitrogen conversions during rapid pyrolysis of the two biomass and the interactions between the biomass and coals on nitrogen conversions were investigated. Results show that little nitrogen retained in char after the biomass pyrolysis, and NH(3) yields were higher than HCN. During co-pyrolysis of biomass and coal, interactions between biomass and coal decreased char-N yields and increased volatile-N yields, but the total yields of NH(3)+HCN in volatile-N were decreased in which HCN formations were decreased consistently, while NH(3) formations were only decreased in the high-temperature range but promoted in the low-temperature range. Interactions between blue-green algae and coals are stronger than those between water hyacinth and coal, and interactions between biomass and bituminous are stronger than those between biomass and anthracite. Copyright © 2011 Elsevier Ltd. All rights reserved.

A Two-Tiered Model for Analyzing Library Web Site Usage Statistics, Part 1: Web Server Logs.

ERIC Educational Resources Information Center

Cohen, Laura B.

2003-01-01

Proposes a two-tiered model for analyzing web site usage statistics for academic libraries: one tier for library administrators that analyzes measures indicating library use, and a second tier for web site managers that analyzes measures aiding in server maintenance and site design. Discusses the technology of web site usage statistics, and…

Field comparison of OraQuick® ADVANCE Rapid HIV-1/2 antibody test and two blood-based rapid HIV antibody tests in Zambia

PubMed Central

2012-01-01

Background Zambia’s national HIV testing algorithm specifies use of two rapid blood based antibody assays, Determine®HIV-1/2 (Inverness Medical) and if positive then Uni-GoldTM Recombigen HIV-1/2 (Trinity Biotech). Little is known about the performance of oral fluid based HIV testing in Zambia. The aims of this study are two-fold: 1) to compare the diagnostic accuracy (sensitivity and specificity) under field conditions of the OraQuick® ADVANCE® Rapid HIV-1/2 (OraSure Technologies, Inc.) to two blood-based rapid antibody tests currently in use in the Zambia National Algorithm, and 2) to perform a cost analysis of large-scale field testing employing the OraQuick®. Methods This was a operational retrospective research of HIV testing and questionnaire data collected in 2010 as part of the ZAMSTAR (Zambia South Africa TB and AIDS reduction) study. Randomly sampled individuals in twelve communities were tested consecutively with OraQuick® test using oral fluid versus two blood-based rapid HIV tests, Determine® and Uni-GoldTM. A cost analysis of four algorithms from health systems perspective were performed: 1) Determine® and if positive, then Uni-GoldTM (Determine®/Uni-GoldTM); based on current algorithm, 2) Determine® and if positive, then OraQuick® (Determine®/OraQuick®), 3) OraQuick® and if positive, then Determine® (OraQuick®/Determine®), 4) OraQuick® and if positive, then Uni-GoldTM (OraQuick®/Uni-GoldTM). This information was then used to construct a model using a hypothetical population of 5,000 persons with varying prevalence of HIV infection from 1–30%. Results 4,458 participants received both a Determine® and OraQuick® test. The sensitivity and specificity of the OraQuick® test were 98.7 (95%CI, 97.5–99.4) and 99.8 (95%CI, 99.6–99.9), respectively when compared to HIV positive serostatus. The average unit costs per algorithm were US$3.76, US$4.03, US$7.35, and US$7.67 for Determine®/Uni-GoldTM, Determine®/OraQuick®, Ora

Acceleration of Binding Site Comparisons by Graph Partitioning.

PubMed

Krotzky, Timo; Klebe, Gerhard

2015-08-01

The comparison of protein binding sites is a prominent task in computational chemistry and has been studied in many different ways. For the automatic detection and comparison of putative binding cavities the Cavbase system has been developed which uses a coarse-grained set of pseudocenters to represent the physicochemical properties of a binding site and employs a graph-based procedure to calculate similarities between two binding sites. However, the comparison of two graphs is computationally quite demanding which makes large-scale studies such as the rapid screening of entire databases hardly feasible. In a recent work, we proposed the method Local Cliques (LC) for the efficient comparison of Cavbase binding sites. It employs a clique heuristic to detect the maximum common subgraph of two binding sites and an extended graph model to additionally compare the shape of individual surface patches. In this study, we present an alternative to further accelerate the LC method by partitioning the binding-site graphs into disjoint components prior to their comparisons. The pseudocenter sets are split with regard to their assigned phyiscochemical type, which leads to seven much smaller graphs than the original one. Applying this approach on the same test scenarios as in the former comprehensive way results in a significant speed-up without sacrificing accuracy. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Contrasting microbial functional genes in two distinct saline-alkali and slightly acidic oil-contaminated sites.

PubMed

Liang, Yuting; Zhao, Huihui; Zhang, Xu; Zhou, Jizhong; Li, Guanghe

2014-07-15

To compare the functional gene structure and diversity of microbial communities in saline-alkali and slightly acidic oil-contaminated sites, 40 soil samples were collected from two typical oil exploration sites in North and South China and analyzed with a comprehensive functional gene array (GeoChip 3.0). The overall microbial pattern was significantly different between the two sites, and a more divergent pattern was observed in slightly acidic soils. Response ratio was calculated to compare the microbial functional genes involved in organic contaminant degradation and carbon, nitrogen, phosphorus, and sulfur cycling. The results indicated a significantly low abundance of most genes involved in organic contaminant degradation and in the cycling of nitrogen and phosphorus in saline-alkali soils. By contrast, most carbon degradation genes and all carbon fixation genes had similar abundance at both sites. Based on the relationship between the environmental variables and microbial functional structure, pH was the major factor influencing the microbial distribution pattern in the two sites. This study demonstrated that microbial functional diversity and heterogeneity in oil-contaminated environments can vary significantly in relation to local environmental conditions. The limitation of nitrogen and phosphorus and the low degradation capacity of organic contaminant should be carefully considered, particularly in most oil-exploration sites with saline-alkali soils. Copyright © 2014 Elsevier B.V. All rights reserved.

Differential arsenic binding in the sediments of two sites in Chile's lower Loa River basin.

PubMed

Bugueño, Manuel P; Acevedo, Sara E; Bonilla, Carlos A; Pizarro, Gonzalo E; Pasten, Pablo A

2014-01-01

Fluvial sediments from two lower Loa River basin sites in northern Chile were compared in order to probe the effects of vegetation and organic matter (OM) on As accumulation in fluvial environments. The two sites were the Sloman dam, which lacks macrophytes and has a low OM content (2.4%) in sediments, and the Quillagua Oasis, which is 23 km downstream from the Sloman site and has a higher OM (6.2%) in sediments and abundant aquatic plant life. The Quillagua site had preferential As enrichment with a co-occurrence pattern that differed from that of the Sloman site, which had a lower As concentration (1528 vs. 262 mg/kg d.w., respectively). At the Quillagua site, As concentration was strongly correlated with Mn and OM (r = 0.91 and 0.85, respectively); while at the Sloman site, As concentration in sediments was significantly correlated with Ca and Sr (r = 0.63 and 0.54, respectively). Sequential extraction analyses showed that the Sloman site had higher percentage of easily exchangeable As within the surface sediment (12%, 45 mg/kg d.w.) compared with the Quillagua site (3%, 40 mg/kg d.w.). These contrasting results suggest that both vegetation and OM control the immobilization and accumulation of As in the arid Loa River basin. © 2013 Elsevier B.V. All rights reserved.

Seasonal and latitudinal variations of surface fluxes at two Arctic terrestrial sites

NASA Astrophysics Data System (ADS)

Grachev, Andrey A.; Persson, P. Ola G.; Uttal, Taneil; Akish, Elena A.; Cox, Christopher J.; Morris, Sara M.; Fairall, Christopher W.; Stone, Robert S.; Lesins, Glen; Makshtas, Alexander P.; Repina, Irina A.

2017-11-01

This observational study compares seasonal variations of surface fluxes (turbulent, radiative, and soil heat) and other ancillary atmospheric/surface/permafrost data based on in-situ measurements made at terrestrial research observatories located near the coast of the Arctic Ocean. Hourly-averaged multiyear data sets collected at Eureka (Nunavut, Canada) and Tiksi (East Siberia, Russia) are analyzed in more detail to elucidate similarities and differences in the seasonal cycles at these two Arctic stations, which are situated at significantly different latitudes (80.0°N and 71.6°N, respectively). While significant gross similarities exist in the annual cycles of various meteorological parameters and fluxes, the differences in latitude, local topography, cloud cover, snowfall, and soil characteristics produce noticeable differences in fluxes and in the structures of the atmospheric boundary layer and upper soil temperature profiles. An important factor is that even though higher latitude sites (in this case Eureka) generally receive less annual incoming solar radiation but more total daily incoming solar radiation throughout the summer months than lower latitude sites (in this case Tiksi). This leads to a counter-intuitive state where the average active layer (or thaw line) is deeper and the topsoil temperature in midsummer are higher in Eureka which is located almost 10° north of Tiksi. The study further highlights the differences in the seasonal and latitudinal variations of the incoming shortwave and net radiation as well as the moderating cloudiness effects that lead to temporal and spatial differences in the structure of the atmospheric boundary layer and the uppermost ground layer. Specifically the warm season (Arctic summer) is shorter and mid-summer amplitude of the surface fluxes near solar noon is generally less in Eureka than in Tiksi. During the dark Polar night and cold seasons (Arctic winter) when the ground is covered with snow and air temperatures

Rac1 GTPase activates the WAVE regulatory complex through two distinct binding sites.

PubMed

Chen, Baoyu; Chou, Hui-Ting; Brautigam, Chad A; Xing, Wenmin; Yang, Sheng; Henry, Lisa; Doolittle, Lynda K; Walz, Thomas; Rosen, Michael K

2017-09-26

The Rho GTPase Rac1 activates the WAVE regulatory complex (WRC) to drive Arp2/3 complex-mediated actin polymerization, which underpins diverse cellular processes. Here we report the structure of a WRC-Rac1 complex determined by cryo-electron microscopy. Surprisingly, Rac1 is not located at the binding site on the Sra1 subunit of the WRC previously identified by mutagenesis and biochemical data. Rather, it binds to a distinct, conserved site on the opposite end of Sra1. Biophysical and biochemical data on WRC mutants confirm that Rac1 binds to both sites, with the newly identified site having higher affinity and both sites required for WRC activation. Our data reveal that the WRC is activated by simultaneous engagement of two Rac1 molecules, suggesting a mechanism by which cells may sense the density of active Rac1 at membranes to precisely control actin assembly.

Greenhouse gas emission and mitigation potential of changes in water management for two rice sites in Bangladesh

NASA Astrophysics Data System (ADS)

Begum, Khadiza; Kuhnert, Matthias; Yeluripati, Jagadeesh; Smith, Pete; Ogle, Stephen; Parton, William; Kader, Abdul; Sleutel, Steven

2017-04-01

Agriculture is one of the main contributors to greenhouse gas (GHG) emissions in Bangladesh and rice production is one of the largest sources of GHG emissions. This study considers measurements from two test sites, situated in Mymensingh (Bangladesh), to calibrate and validate the biogeochemical model DailyDayCent and estimate the mitigation potential of alternative management practices at the sites. There are two different N application treatments on the two test sites, which are on the first site a control with no N application and a mineral fertilizer application (120 kg N ha-1) and on the second site only a mineral fertilizer application (110 kg N ha-1). For mitigation, the water management is modified in a modelling approach to estimate the mitigation potential for reducing GHG emissions. The model shows partial agreement with the observations. The modifications to the water management, by changing from permanent wetting to alternate wetting, shows a decrease in GHG emissions of up to 46 % and 37 % for the two test sites, respectively. These tests enable an optimization of the management options to reduce the GHG emissions while maintaining yields.

Glyphosate resistance in Ambrosia trifida: Part 1. Novel rapid cell death response to glyphosate.

PubMed

Van Horn, Christopher R; Moretti, Marcelo L; Robertson, Renae R; Segobye, Kabelo; Weller, Stephen C; Young, Bryan G; Johnson, William G; Schulz, Burkhard; Green, Amanda C; Jeffery, Taylor; Lespérance, Mackenzie A; Tardif, François J; Sikkema, Peter H; Hall, J Christopher; McLean, Michael D; Lawton, Mark B; Sammons, R Douglas; Wang, Dafu; Westra, Philip; Gaines, Todd A

2018-05-01

Glyphosate-resistant (GR) Ambrosia trifida is now present in the midwestern United States and in southwestern Ontario, Canada. Two distinct GR phenotypes are known, including a rapid response (GR RR) phenotype, which exhibits cell death within hours after treatment, and a non-rapid response (GR NRR) phenotype. The mechanisms of resistance in both GR RR and GR NRR remain unknown. Here, we present a description of the RR phenotype and an investigation of target-site mechanisms on multiple A. trifida accessions. Glyphosate resistance was confirmed in several accessions, and whole-plant levels of resistance ranged from 2.3- to 7.5-fold compared with glyphosate-susceptible (GS) accessions. The two GR phenotypes displayed similar levels of resistance, despite having dramatically different phenotypic responses to glyphosate. Glyphosate resistance was not associated with mutations in EPSPS sequence, increased EPSPS copy number, EPSPS quantity, or EPSPS activity. These encompassing results suggest that resistance to glyphosate in these GR RR A. trifida accessions is not conferred by a target-site resistance mechanism. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

An investigation of solar erythemal ultraviolet radiation at two sites in tourist attraction areas of Thailand

NASA Astrophysics Data System (ADS)

Buntoung, Sumaman; Pattarapanitchai, Somjet; Wattan, Rungrat; Masiri, Itsara; Promsen, Worrapass; Tohsing, Korntip; Janjai, Serm

2013-05-01

Islands on the southern coasts of Thailand are famous attractions for local and foreign tourists. Tourists usually expose their skins to solar radiation for tanning. Thus information on solar ultraviolet radiation (UV) is of importance for tourists to protect themselves from adverse effects of UV. In this work, solar erythemal ultraviolet radiation (EUV) at two touristic sites namely Samui island (9.451°N, 100.033°E) and Phuket island (8.104°N, 98.304°E) was investigated. In investigating EUV, broadband UV radiometers (Kipp & Zonen, model UVS-B-C) were installed at existing meteorological stations in Samui and Phuket islands. A one-year period of EUV data from these two sites was analyzed. The level of UV index at these sites was studied. The values of UV index higher than 12 at noon time of clear days are usually found in the summer at both sites. Seasonal variation of EUV at both sites was investigated. It was found that the tropical monsoons have strong influence on this variation. Finally, global broadband radiation measured at the sites was also used to establish a correlation between EUV and global broadband radiation. Higher correlation was found for the case of clear sky, as compared to the case of cloudy sky. The correlation obtained from this analysis can be used to estimate EUV from global broadband radiation at these two sites.

Analysis of ground-water flow in the Madison aquifer using fluorescent dyes injected in Spring Creek and Rapid Creek near Rapid City, South Dakota, 2003-04

USGS Publications Warehouse

Putnam, Larry D.; Long, Andrew J.

2007-01-01

The Madison aquifer, which contains fractures and solution openings in the Madison Limestone, is used extensively for water supplies for the city of Rapid City and other suburban communities in the Rapid City, S. Dak., area. The 48 square-mile study area includes the west-central and southwest parts of Rapid City and the outcrops of the Madison Limestone extending from south of Spring Creek to north of Rapid Creek. Recharge to the Madison Limestone occurs when streams lose flow as they cross the outcrop. The maximum net loss rate for Spring and Rapid Creek loss zones are 21 and 10 cubic feet per second (ft3/s), respectively. During 2003 and 2004, fluorescent dyes were injected in the Spring and Rapid Creek loss zones to estimate approximate locations of preferential flow paths in the Madison aquifer and to measure the response and transit times at wells and springs. Four injections of about 2 kilograms of fluorescein dye were made in the Spring Creek loss zone during 2003 (sites S1, S2, and S3) and 2004 (site S4). Injection at site S1 was made in streamflow just upstream from the loss zone over a 12-hour period when streamflow was about equal to the maximum loss rate. Injections at sites S2, S3, and S4 were made in specific swallow holes located in the Spring Creek loss zone. Injection at site R1 in 2004 of 3.5 kilograms of Rhodamine WT dye was made in streamflow just upstream from the Rapid Creek loss zone over about a 28-hour period. Selected combinations of 27 wells, 6 springs, and 3 stream sites were monitored with discrete samples following the injections. For injections at sites S1-S3, when Spring Creek streamflow was greater than or equal to 20 ft3/s, fluorescein was detected in samples from five wells that were located as much as about 2 miles from the loss zone. Time to first arrival (injection at site S1) ranged from less than 1 to less than 10 days. The maximum fluorescein concentration (injection at site S1) of 120 micrograms per liter (ug/L) at well CO

Nicked-site substrates for a serine recombinase reveal enzyme-DNA communications and an essential tethering role of covalent enzyme-DNA linkages.

PubMed

Olorunniji, Femi J; McPherson, Arlene L; Pavlou, Hania J; McIlwraith, Michael J; Brazier, John A; Cosstick, Richard; Stark, W Marshall

2015-07-13

To analyse the mechanism and kinetics of DNA strand cleavages catalysed by the serine recombinase Tn3 resolvase, we made modified recombination sites with a single-strand nick in one of the two DNA strands. Resolvase acting on these sites cleaves the intact strand very rapidly, giving an abnormal half-site product which accumulates. We propose that these reactions mimic second-strand cleavage of an unmodified site. Cleavage occurs in a synapse of two sites, held together by a resolvase tetramer; cleavage at one site stimulates cleavage at the partner site. After cleavage of a nicked-site substrate, the half-site that is not covalently linked to a resolvase subunit dissociates rapidly from the synapse, destabilizing the entire complex. The covalent resolvase-DNA linkages in the natural reaction intermediate thus perform an essential DNA-tethering function. Chemical modifications of a nicked-site substrate at the positions of the scissile phosphodiesters result in abolition or inhibition of resolvase-mediated cleavage and effects on resolvase binding and synapsis, providing insight into the serine recombinase catalytic mechanism and how resolvase interacts with the substrate DNA. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.

PubMed

Li, Fuyi; Li, Chen; Marquez-Lago, Tatiana T; Leier, André; Akutsu, Tatsuya; Purcell, Anthony W; Smith, A Ian; Lithgow, Trevor; Daly, Roger J; Song, Jiangning; Chou, Kuo-Chen

2018-06-27

Kinase-regulated phosphorylation is a ubiquitous type of post-translational modification (PTM) in both eukaryotic and prokaryotic cells. Phosphorylation plays fundamental roles in many signalling pathways and biological processes, such as protein degradation and protein-protein interactions. Experimental studies have revealed that signalling defects caused by aberrant phosphorylation are highly associated with a variety of human diseases, especially cancers. In light of this, a number of computational methods aiming to accurately predict protein kinase family-specific or kinase-specific phosphorylation sites have been established, thereby facilitating phosphoproteomic data analysis. In this work, we present Quokka, a novel bioinformatics tool that allows users to rapidly and accurately identify human kinase family-regulated phosphorylation sites. Quokka was developed by using a variety of sequence scoring functions combined with an optimized logistic regression algorithm. We evaluated Quokka based on well-prepared up-to-date benchmark and independent test datasets, curated from the Phospho.ELM and UniProt databases, respectively. The independent test demonstrates that Quokka improves the prediction performance compared with state-of-the-art computational tools for phosphorylation prediction. In summary, our tool provides users with high-quality predicted human phosphorylation sites for hypothesis generation and biological validation. The Quokka webserver and datasets are freely available at http://quokka.erc.monash.edu/. Supplementary data are available at Bioinformatics online.

Effigy mound sites as cultural landscapes: A geophysical spatial analysis of two Late Woodland sites in southeastern Wisconsin

NASA Astrophysics Data System (ADS)

Kaufmann, Kira E.

This dissertation is a spatial analysis of a class of sacred sites known as Effigy Mounds during the Late Woodland period in southeast Wisconsin, circa A.D. 700--1100. Effigy Mounds are earthworks in the shape of animals, conical, linear, or geometric shapes. The research is focused on the upper Rock River Drainage in southern Wisconsin, a region where Effigy Mounds are very common. Although there are many theories concerning the meanings of Effigy Mounds, there is no cohesive description of Effigy Mounds as landscape elements and their function in the use of space by Late Woodland people. This research connects cultural and cognitive aspects of Native American cosmology with physical manifestations on the landscape. Effigy Mounds are examined from ideological and physical perspectives that are not mutually exclusive. Effigy Mounds are viewed as signifiers with multiple levels of function and meaning including sacred space, territorial markers, and mechanisms of social control and cohesion. Investigation at two Late Woodland Effigy Mound sites, Indian Mounds County Park in Jefferson County and Nitschke Mounds County Park in Dodge County, shows that landscape utilization varied significantly within and among Effigy Mound sites. An alternative model to understand Late Woodland Effigy Mound sites as ritual landscapes explores these features, their distribution across space, and the connection to internal site structures by synthesizing multidisciplinary data from historical ethnographic accounts, previous archaeological surveys, and new geophysical data. This multidisciplinary approach provides an example applicable to other landscape studies.

Bacterial Abundance and Activity across Sites within Two Northern Wisconsin Sphagnum Bogs.

PubMed

Fisher; Graham; Graham

1998-11-01

Abstract Bacterial abundance, temperature, pH, and dissolved organic carbon (DOC) concentration were compared across surface sites within and between two northern Wisconsin Sphagnum peatlands over the summer seasons in 1995 and 1996. Sites of interest were the Sphagnum mat surface, the water-filled moat (lagg) at the bog margin, and the bog lake littoral zone. Significant differences in both bacterial populations and water chemistry were observed between sites. pH was highest in the lake and lowest in the mat at both bogs; the opposite was true for DOC. Large populations of bacteria were present in surface interstitial water from the mat; abundance in this site was consistently higher than in the moat or lake. Bacterial abundance also increased across sites of increasing DOC concentration and declining pH. Bacterial activities (rates of [3H]leucine incorporation) and growth in dilution cultures (with grazers removed) were also assessed in lake, moat, and mat sites. Results using these measures generally supported the trends observed in abundance, although high rates of [3H]leucine incorporation were recorded in the moat at one of the bogs. Our results indicate that bacterial populations in Sphagnum peatlands are not adversely affected by acidity, and that DOC may be more important than pH in determining bacterial abundance in these environments.

Two Drosophila chorion genes terminate transcription in discrete regions near their poly(A) sites.

PubMed Central

Osheim, Y N; Miller, O L; Beyer, A L

1986-01-01

We have examined transcription termination of two closely linked Drosophila melanogaster chorion genes, s36-1 and s38-1, using the electron microscope. Our method is unusual and is independent of in vitro nuclear run-on transcription. By measuring transcription unit lengths in chromatin spreads, we can localize efficient termination sites to a region of approximately 210 bp for s36-1 and approximately 365 bp for s38-1. The center of this region is approximately 105 nucleotides downstream of the poly(A) site for the s36-1 gene, and approximately 400 nucleotides downstream for the s38-1 gene. Thus, these two Drosophila chorion genes terminate more closely to their poly(A) addition sites and in a shorter region than many other polyadenylated genes examined to date. Images Fig. 1. Fig. 2. PMID:3104029

PM2.5 Indoor Air Quality at Two Sites in London Ontario - A Case Study

NASA Astrophysics Data System (ADS)

Mates, A. V.; Xu, X.; Gilliland, J.; Maltby, M. J.

2010-12-01

Studies have shown an association between ambient fine particulate matter (PM2.5) and health impacts, particularly for the elderly and children. As part of a larger study, PM2.5 concentrations were measured using the DustTrak (Model 8520, TSI, St. Paul, MN, USA) at two schools within the city of London, Ontario (Canada). Site A was in a suburban environment while site B was in an urban setting. Monitoring took place for 3 weeks during winter (Feb. 16 - Mar. 8) and 3 weeks during spring (May 05 - 25) of 2010. The winter campaign monitored indoor PM2.5 only, while the spring campaign added outdoor monitors (PM2.5 and CO2) after the first week. Ten min. concentrations were used for analysis. Indoor measurements were split into weekday and weekend. For the same time interval, the outdoor concentrations showed mean values of 18 and 21 μg/m3 for sites A & B, respectively, both under the Canada Wide Standard of 30 μg/m3. Measurements at the two sites showed good associations (R^2 = 0.44), during the spring campaign. This indicates that the outdoor PM2.5 had similar sources. For indoor concentrations, Site B showed a significantly different mean concentration 5 times higher compared to site A during the winter ( 8.1 vs. 1.5 μg/m3 ) and 3 times higher (11.9 vs. 3.7 μg/m3) during the spring campaign. Since the outdoor concentrations were similar the large difference in indoor concentrations could be attributed to the following factors: site B being an older building, and the different physical characteristics between the two sites. The spring measurements showed an increase of 50% from weekday to weekend for site A and 22% for site B. The higher level of PM2.5 during weekends is possibly due to the infiltration of outdoor air while the ventilation/filtration system is shut off. During the winter campaign, Site A showed a 14% higher concentration during weekdays compared to weekends while site B weekend concentrations were 17% higher compared to weekday, which will be

History of Tree Growth Declines Recorded in Old Trees at Two Sacred Sites in Northern China

PubMed Central

Li, Yan; Zhang, Qi-Bin

2017-01-01

Old forests are an important component in sacred sites, yet they are at risk of growth decline from ongoing global warming and increased human activities. Growth decline, characterized by chronic loss of tree vigor, is not a recent phenomenon. Knowledge of past occurrence of declines is useful for preparing conservation plans because it helps understand if present day forests are outside the natural range of variation in tree health. We report a dendroecological study of growth decline events in the past two centuries at two sacred sites, Hengshan and Wutaishan, in Shanxi province of northern China. Tree rings collected at both sites show distinct periods of declining growth evident as narrow rings. These occurred in the 1830s in both sites, in the 1920s in Wutaishan and in the 2000s in Hengshan. By comparing the pattern of grow declines at the two sites, we hypothesize that resistance of tree growth to external disturbances is forest size dependent, and increased human activity might be a factor additional to climatic droughts in causing the recent strong growth decline at Hengshan Park. Despite these past declines, the forests at both sites have high resilience to disturbances as evidenced by the ability of trees to recover their growth rates to levels comparable to the pre-decline period. Managers should consider reducing fragmentation and restoring natural habitat of old forests, especially in areas on dry sites. PMID:29163557

History of Tree Growth Declines Recorded in Old Trees at Two Sacred Sites in Northern China.

PubMed

Li, Yan; Zhang, Qi-Bin

2017-01-01

Old forests are an important component in sacred sites, yet they are at risk of growth decline from ongoing global warming and increased human activities. Growth decline, characterized by chronic loss of tree vigor, is not a recent phenomenon. Knowledge of past occurrence of declines is useful for preparing conservation plans because it helps understand if present day forests are outside the natural range of variation in tree health. We report a dendroecological study of growth decline events in the past two centuries at two sacred sites, Hengshan and Wutaishan, in Shanxi province of northern China. Tree rings collected at both sites show distinct periods of declining growth evident as narrow rings. These occurred in the 1830s in both sites, in the 1920s in Wutaishan and in the 2000s in Hengshan. By comparing the pattern of grow declines at the two sites, we hypothesize that resistance of tree growth to external disturbances is forest size dependent, and increased human activity might be a factor additional to climatic droughts in causing the recent strong growth decline at Hengshan Park. Despite these past declines, the forests at both sites have high resilience to disturbances as evidenced by the ability of trees to recover their growth rates to levels comparable to the pre-decline period. Managers should consider reducing fragmentation and restoring natural habitat of old forests, especially in areas on dry sites.

Specific phospholipid binding to Na,K-ATPase at two distinct sites.

PubMed

Habeck, Michael; Kapri-Pardes, Einat; Sharon, Michal; Karlish, Steven J D

2017-03-14

Membrane protein function can be affected by the physical state of the lipid bilayer and specific lipid-protein interactions. For Na,K-ATPase, bilayer properties can modulate pump activity, and, as observed in crystal structures, several lipids are bound within the transmembrane domain. Furthermore, Na,K-ATPase activity depends on phosphatidylserine (PS) and cholesterol, which stabilize the protein, and polyunsaturated phosphatidylcholine (PC) or phosphatidylethanolamine (PE), known to stimulate Na,K-ATPase activity. Based on lipid structural specificity and kinetic mechanisms, specific interactions of both PS and PC/PE have been inferred. Nevertheless, specific binding sites have not been identified definitively. We address this question with native mass spectrometry (MS) and site-directed mutagenesis. Native MS shows directly that one molecule each of 18:0/18:1 PS and 18:0/20:4 PC can bind specifically to purified human Na,K-ATPase (α 1 β 1 ). By replacing lysine residues at proposed phospholipid-binding sites with glutamines, the two sites have been identified. Mutations in the cytoplasmic αL8-9 loop destabilize the protein but do not affect Na,K-ATPase activity, whereas mutations in transmembrane helices (TM), αTM2 and αTM4, abolish the stimulation of activity by 18:0/20:4 PC but do not affect stability. When these data are linked to crystal structures, the underlying mechanism of PS and PC/PE effects emerges. PS (and cholesterol) bind between αTM 8, 9, 10, near the FXYD subunit, and maintain topological integrity of the labile C terminus of the α subunit (site A). PC/PE binds between αTM2, 4, 6, and 9 and accelerates the rate-limiting E 1 P-E 2 P conformational transition (site B). We discuss the potential physiological implications.

Metal and metalloid accumulation in shrews (Soricomorpha, Mammalia) from two protected Mediterranean coastal sites.

PubMed

Sánchez-Chardi, Alejandro; López-Fuster, María José

2009-04-01

Although ecotoxicological data on heavy metals are abundant, information on other potentially toxic elements with attributed deficiency and/or toxic disturbances is scarce. Here we quantify zinc, copper, iron, manganese, chromium, molybdenum, strontium, barium, and boron in bones of greater white-toothed shrews, Crocidura russula, inhabiting two protected Mediterranean coastal sites: the Ebro Delta, a wetland impacted by human activities, and the Medas Islands, a reference site. Natural and anthropogenic inputs significantly increase Fe, Mn, Mo, Sr, Ba, and B in specimens from the Ebro Delta, whereas Cu and Cr were higher in Medas' shrews. Principal component analysis allowed complete separation between sites along the first two axes in particular due to B, Sr, and Cu. This study provides metal reference values in bones of insectivores, explores their variability and bioaccumulation patterns in depth, and assesses the potential environmental risk and toxicity for biota exposed to the above elements.

Rapid, all-optical crystal orientation imaging of two-dimensional transition metal dichalcogenide monolayers

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

David, Sabrina N.; Zhai, Yao; van der Zande, Arend M.

Two-dimensional (2D) atomic materials such as graphene and transition metal dichalcogenides (TMDCs) have attracted significant research and industrial interest for their electronic, optical, mechanical, and thermal properties. While large-area crystal growth techniques such as chemical vapor deposition have been demonstrated, the presence of grain boundaries and orientation of grains arising in such growths substantially affect the physical properties of the materials. There is currently no scalable characterization method for determining these boundaries and orientations over a large sample area. We here present a second-harmonic generation based microscopy technique for rapidly mapping grain orientations and boundaries of 2D TMDCs. We experimentallymore » demonstrate the capability to map large samples to an angular resolution of ±1° with minimal sample preparation and without involved analysis. A direct comparison of the all-optical grain orientation maps against results obtained by diffraction-filtered dark-field transmission electron microscopy plus selected-area electron diffraction on identical TMDC samples is provided. This rapid and accurate tool should enable large-area characterization of TMDC samples for expedited studies of grain boundary effects and the efficient characterization of industrial-scale production techniques.« less

DC-Analyzer-facilitated combinatorial strategy for rapid directed evolution of functional enzymes with multiple mutagenesis sites.

PubMed

Wang, Xiong; Zheng, Kai; Zheng, Huayu; Nie, Hongli; Yang, Zujun; Tang, Lixia

2014-12-20

Iterative saturation mutagenesis (ISM) has been shown to be a powerful method for directed evolution. In this study, the approach was modified (termed M-ISM) by combining the single-site saturation mutagenesis method with a DC-Analyzer-facilitated combinatorial strategy, aiming to evolve novel biocatalysts efficiently in the case where multiple sites are targeted simultaneously. Initially, all target sites were explored individually by constructing single-site saturation mutagenesis libraries. Next, the top two to four variants in each library were selected and combined using the DC-Analyzer-facilitated combinatorial strategy. In addition to site-saturation mutagenesis, iterative saturation mutagenesis also needed to be performed. The advantages of M-ISM over ISM were that the screening effort is greatly reduced, and the entire M-ISM procedure was less time-consuming. The M-ISM strategy was successfully applied to the randomization of halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) when five interesting sites were targeted simultaneously. After screening 900 clones in total, six positive mutants were obtained. These mutants exhibited 4.0- to 9.3-fold higher k(cat) values than did the wild-type HheC toward 1,3-dichloro-2-propanol. However, with the ISM strategy, the best hit showed a 5.9-fold higher k(cat) value toward 1,3-DCP than the wild-type HheC, which was obtained after screening 4000 clones from four rounds of mutagenesis. Therefore, M-ISM could serve as a simple and efficient version of ISM for the randomization of target genes with multiple positions of interest.

Endobronchial ultrasound-guided transbronchial needle aspiration: performance of biomedical scientists on rapid on-site evaluation and preliminary diagnosis.

PubMed

Schacht, M J; Toustrup, C B; Madsen, L B; Martiny, M S; Larsen, B B; Simonsen, J T

2016-10-01

Rapid on-site evaluation (ROSE) of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) followed by a subsequent preliminary adequacy assessment and a preliminary diagnosis, was performed at Aarhus University Hospital by biomedical scientists (BMS). The aim of this study was to evaluate the BMS accuracy of ROSE adequacy assessment, the preliminary adequacy assessment and the preliminary diagnosis as compared with the cytopathologist-rendered final adequacy assessment and final diagnosis. The BMS-rendered assessments for 717 sites from 319 consecutive patients over a 4-month period were compared with the cytopathologist-rendered assessments. Comparisons of adequacy and preliminary diagnoses were based on inter-observer Cohen's Kappa coefficient with a 95% confidence interval (CI). Strong correlations between ROSE and final adequacy assessments [Kappa coefficient of 0.90 (CI: 0.85-0.96)] and between the preliminary and final adequacy assessments [Kappa coefficient of 0.93 (CI: 0.87-0.99)] were found. As for the correlation between the preliminary and final diagnoses, the Kappa coefficient was 0.99 (CI: 0.98-1). Both ROSE and preliminary adequacy assessments as well as preliminary diagnoses, all performed by BMS, were highly accurate when compared with the final assessment by the cytopathologist. © 2016 John Wiley & Sons Ltd.

The dynamics of genetic draft in rapidly adapting populations.

PubMed

Kosheleva, Katya; Desai, Michael M

2013-11-01

The accumulation of beneficial mutations on competing genetic backgrounds in rapidly adapting populations has a striking impact on evolutionary dynamics. This effect, known as clonal interference, causes erratic fluctuations in the frequencies of observed mutations, randomizes the fixation times of successful mutations, and leaves distinct signatures on patterns of genetic variation. Here, we show how this form of "genetic draft" affects the forward-time dynamics of site frequencies in rapidly adapting asexual populations. We calculate the probability that mutations at individual sites shift in frequency over a characteristic timescale, extending Gillespie's original model of draft to the case where many strongly selected beneficial mutations segregate simultaneously. We then derive the sojourn time of mutant alleles, the expected fixation time of successful mutants, and the site frequency spectrum of beneficial and neutral mutations. Finally, we show how this form of draft affects inferences in the McDonald-Kreitman test and how it relates to recent observations that some aspects of genetic diversity are described by the Bolthausen-Sznitman coalescent in the limit of very rapid adaptation.

User compliance with documenting on a track and trigger-based observation and response chart: a two-phase multi-site audit study.

PubMed

Elliott, Doug; Allen, Emily; McKinley, Sharon; Perry, Lin; Duffield, Christine; Fry, Margaret; Gallagher, Robyn; Iedema, Rick; Roche, Michael

2017-12-01

To examine user compliance and completeness of documentation with a newly designed observation and response chart and whether a rapid response system call was triggered when clinically indicated. Timely recognition and responses to patient deterioration in hospital general wards remain a challenge for healthcare systems globally. Evaluating practice initiatives to improve recognition and response are required. Two-phase audit. Following introduction of the charts in ten health service sites in Australia, an audit of chart completion was conducted during a short trial for initial usability (Phase 1; 2011). After chart adoption as routine use in practice, retrospective and prospective chart audits were conducted (Phase 2; 2012). Overall, 818 and 1,058 charts were audited during the two phases respectively. Compliance was mixed but improved with the new chart (4%-14%). Contrary to chart guidelines, numbers rather than dots were written in the graphing section in 60% of cases. Rates of recognition of abnormal vital signs improved slightly with new charts in use, particularly for higher levels of surveillance and clinical review. Based on local calling criteria, an emergency call was initiated in 33% of cases during the retrospective audit and in 41% of cases with the new chart. User compliance was less than optimal, limiting full function of the chart sections and compliance with local calling criteria. Overcoming apparent behavioural and work culture barriers may improve chart completion, aiding identification of abnormal vital signs and triggering a rapid response system activation when clinical deterioration is detected. © 2017 The Authors. Journal of Advanced Nursing Published by John Wiley & Sons Ltd.

Modified two-sources quantum statistical model and multiplicity fluctuation in the finite rapidity region

NASA Astrophysics Data System (ADS)

Ghosh, Dipak; Sarkar, Sharmila; Sen, Sanjib; Roy, Jaya

1995-06-01

In this paper the behavior of factorial moments with rapidity window size, which is usually explained in terms of ``intermittency,'' has been interpreted by simple quantum statistical properties of the emitting system using the concept of ``modified two-source model'' as recently proposed by Ghosh and Sarkar [Phys. Lett. B 278, 465 (1992)]. The analysis has been performed using our own data of 16Ag/Br and 24Ag/Br interactions at a few tens of GeV energy regime.

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

PubMed

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

2014-10-01

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

Clinical utility of RapidArc™ radiotherapy technology

PubMed Central

Infusino, Erminia

2015-01-01

RapidArc™ is a radiation technique that delivers highly conformal dose distributions through the complete rotation (360°) and speed variation of the linear accelerator gantry. This technique, called volumetric modulated arc therapy (VMAT), compared with conventional radiotherapy techniques, can achieve high-target volume coverage and sparing damage to normal tissues. RapidArc delivers precise dose distribution and conformity similar to or greater than intensity-modulated radiation therapy in a short time, generally a few minutes, to which image-guided radiation therapy is added. RapidArc has become a currently used technology in many centers, which use RapidArc technology to treat a large number of patients. Large and small hospitals use it to treat the most challenging cases, but more and more frequently for the most common cancers. The clinical use of RapidArc and VMAT technology is constantly growing. At present, a limited number of clinical data are published, mostly concerning planning and feasibility studies. Clinical outcome data are increasing for a few tumor sites, even if only a little. The purpose of this work is to discuss the current status of VMAT techniques in clinical use through a review of the published data of planning systems and clinical outcomes in several tumor sites. The study consisted of a systematic review based on analysis of manuscripts retrieved from the PubMed, BioMed Central, and Scopus databases by searching for the keywords “RapidArc”, “Volumetric modulated arc radiotherapy”, and “Intensity-modulated radiotherapy”. PMID:26648755

Evaluation of Two Statistical Methods Provides Insights into the Complex Patterns of Alternative Polyadenylation Site Switching

PubMed Central

Li, Jie; Li, Rui; You, Leiming; Xu, Anlong; Fu, Yonggui; Huang, Shengfeng

2015-01-01

Switching between different alternative polyadenylation (APA) sites plays an important role in the fine tuning of gene expression. New technologies for the execution of 3’-end enriched RNA-seq allow genome-wide detection of the genes that exhibit significant APA site switching between different samples. Here, we show that the independence test gives better results than the linear trend test in detecting APA site-switching events. Further examination suggests that the discrepancy between these two statistical methods arises from complex APA site-switching events that cannot be represented by a simple change of average 3’-UTR length. In theory, the linear trend test is only effective in detecting these simple changes. We classify the switching events into four switching patterns: two simple patterns (3’-UTR shortening and lengthening) and two complex patterns. By comparing the results of the two statistical methods, we show that complex patterns account for 1/4 of all observed switching events that happen between normal and cancerous human breast cell lines. Because simple and complex switching patterns may convey different biological meanings, they merit separate study. We therefore propose to combine both the independence test and the linear trend test in practice. First, the independence test should be used to detect APA site switching; second, the linear trend test should be invoked to identify simple switching events; and third, those complex switching events that pass independence testing but fail linear trend testing can be identified. PMID:25875641

Rapid Construction of a Benzo-Fused Indoxamycin Core Enabled by Site-Selective C-H Functionalizations.

PubMed

Bedell, T Aaron; Hone, Graham A B; Valette, Damien; Yu, Jin-Quan; Davies, Huw M L; Sorensen, Erik J

2016-07-11

Methods for functionalizing carbon-hydrogen bonds are featured in a new synthesis of the tricyclic core architecture that characterizes the indoxamycin family of secondary metabolites. A unique collaboration between three laboratories has engendered a design for synthesis featuring two sequential C-H functionalization reactions, namely a diastereoselective dirhodium carbene insertion followed by an ester-directed oxidative Heck cyclization, to rapidly assemble the congested tricyclic core of the indoxamycins. This project exemplifies how multi-laboratory collaborations can foster conceptually novel approaches to challenging problems in chemical synthesis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Geophysical survey of two rural sites in Mallorca (Balearic Islands, Spain): Unveiling Roman villae

NASA Astrophysics Data System (ADS)

Mas Florit, Catalina; Cau Ontiveros, Miguel Ángel; Goossens, Lise; Meyer, Cornelius; Sala, Roger; Ortiz, Helena

2018-03-01

Two rural sites on the island of Mallorca (Balearic Islands, Spain) have been investigated with geophysical methods. A previous archaeological field survey provided surface ceramics that allowed for a first classification of the sites as possible Roman rural settlements, possibly villae. The objective of the investigation was to work towards the identification of architectural remains to better understand the true nature of the sites. Using the 7-probe fluxgate gradiometer array LEA MAX, magnetic measurements were executed on a large area on each site. GPR measurements were subsequently carried out to examine selected areas of interest in detail by means of the IDS GPR system based on the Fast-Wave module. The investigated areas demonstrated excellent surface conditions with a negligible number of sources of disturbance, permitting a detailed interpretation of the geophysical data. The results helped to reveal the presence of architectural remains beneath the soil at both sites.

Site-specific early performance and nutrition of two Salix species in SRIC in southern Quebec (Canada)

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

Labrecque, M.; Teodorescu, T.I.; Daigle, S.

1996-12-31

Salix discolor WU and Salix viminalis L. were planted under short-rotation intensive culture (SRIC) in three unirrigated and unfertilized abandoned farmland sites (S1, S2, S3) showing different soil textures: sandy loam, clay silt and clay loam. The aims of the experiment were to: (i) investigate first year response to site nutrient condition and (ii) diagnose factors limiting performance. Over the first season, stem biomass productivity was superior on the sandy site (S1) for S. discolor and did not vary between species on clay sites (S2, S3). The inferior performance of plants on clay sites was related to difficulty implanting unrootedmore » cuttings in compacted soil during an exceptionally dry period (May and June). The change in nutrient status was unapparent solely from comparison of critical levels or optimum ratios because leaf nutrient concentration was less affected by site. Diagnostic techniques based on vector analysis of leaf nutrient concentration, content, and dry mass allowed simultaneous comparison of the nutrient status of two species planted on three sites. The relative deficiency of all nutrients, based on vector magnitude and direction, on the two other clay sites (S2, S3) supports the hypothesis that specific edaphic conditions and dryness induced nutrient disorders in willows. Successful establishment of willows in SRIC depends strongly on the characteristics of the plantation site and on precipitation during the establishment phase in the first year of growth.« less

A High-Resolution Chronology of Rapid Forest Transitions following Polynesian Arrival in New Zealand

PubMed Central

McWethy, David B.; Wilmshurst, Janet M.; Whitlock, Cathy; Wood, Jamie R.; McGlone, Matt S.

2014-01-01

Human-caused forest transitions are documented worldwide, especially during periods when land use by dense agriculturally-based populations intensified. However, the rate at which prehistoric human activities led to permanent deforestation is poorly resolved. In the South Island, New Zealand, the arrival of Polynesians c. 750 years ago resulted in dramatic forest loss and conversion of nearly half of native forests to open vegetation. This transformation, termed the Initial Burning Period, is documented in pollen and charcoal records, but its speed has been poorly constrained. High-resolution chronologies developed with a series of AMS radiocarbon dates from two lake sediment cores suggest the shift from forest to shrubland occurred within decades rather than centuries at drier sites. We examine two sites representing extreme examples of the magnitude of human impacts: a drier site that was inherently more vulnerable to human-set fires and a wetter, less burnable site. The astonishing rate of deforestation at the hands of small transient populations resulted from the intrinsic vulnerability of the native flora to fire and from positive feedbacks in post-fire vegetation recovery that increased landscape flammability. Spatially targeting burning in highly-flammable seral vegetation in forests rarely experiencing fire was sufficient to create an alternate fire-prone stable state. The New Zealand example illustrates how seemingly stable forest ecosystems can experience rapid and permanent conversions. Forest loss in New Zealand is among the fastest ecological transitions documented in the Holocene; yet equally rapid transitions can be expected in present-day regions wherever positive feedbacks support alternate fire-inhibiting, fire-prone stable states. PMID:25372150

A two-step method for rapid characterization of electroosmotic flows in capillary electrophoresis.

PubMed

Zhang, Wenjing; He, Muyi; Yuan, Tao; Xu, Wei

2017-12-01

The measurement of electroosmotic flow (EOF) is important in a capillary electrophoresis (CE) experiment in terms of performance optimization and stability improvement. Although several methods exist, there are demanding needs to accurately characterize ultra-low electroosmotic flow rates (EOF rates), such as in coated capillaries used in protein separations. In this work, a new method, called the two-step method, was developed to accurately and rapidly measure EOF rates in a capillary, especially for measuring the ultra-low EOF rates in coated capillaries. In this two-step method, the EOF rates were calculated by measuring the migration time difference of a neutral marker in two consecutive experiments, in which a pressure driven was introduced to accelerate the migration and the DC voltage was reversed to switch the EOF direction. Uncoated capillaries were first characterized by both this two-step method and a conventional method to confirm the validity of this new method. Then this new method was applied in the study of coated capillaries. Results show that this new method is not only fast in speed, but also better in accuracy. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Long-range electrostatics-induced two-proton transfer captured by neutron crystallography in an enzyme catalytic site

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

Gerlits, Oksana; Wymore, Troy; Das, Amit

Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other asparticmore » proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.« less

Long-range electrostatics-induced two-proton transfer captured by neutron crystallography in an enzyme catalytic site

DOE PAGES

Gerlits, Oksana; Wymore, Troy; Das, Amit; ...

2016-03-09

Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other asparticmore » proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.« less

Modified two-sources quantum statistical model and multiplicity fluctuation in the finite rapidity region

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

Ghosh, D.; Sarkar, S.; Sen, S.

1995-06-01

In this paper the behavior of factorial moments with rapidity window size, which is usually explained in terms of ``intermittency,`` has been interpreted by simple quantum statistical properties of the emitting system using the concept of ``modified two-source model`` as recently proposed by Ghosh and Sarkar [Phys. Lett. B 278, 465 (1992)]. The analysis has been performed using our own data of {sup 16}O-Ag/Br and {sup 24}Mg-Ag/Br interactions at a few tens of GeV energy regime.

Maize Cropping Systems Mapping Using RapidEye Observations in Agro-Ecological Landscapes in Kenya.

PubMed

Richard, Kyalo; Abdel-Rahman, Elfatih M; Subramanian, Sevgan; Nyasani, Johnson O; Thiel, Michael; Jozani, Hosein; Borgemeister, Christian; Landmann, Tobias

2017-11-03

Cropping systems information on explicit scales is an important but rarely available variable in many crops modeling routines and of utmost importance for understanding pests and disease propagation mechanisms in agro-ecological landscapes. In this study, high spatial and temporal resolution RapidEye bio-temporal data were utilized within a novel 2-step hierarchical random forest (RF) classification approach to map areas of mono- and mixed maize cropping systems. A small-scale maize farming site in Machakos County, Kenya was used as a study site. Within the study site, field data was collected during the satellite acquisition period on general land use/land cover (LULC) and the two cropping systems. Firstly, non-cropland areas were masked out from other land use/land cover using the LULC mapping result. Subsequently an optimized RF model was applied to the cropland layer to map the two cropping systems (2nd classification step). An overall accuracy of 93% was attained for the LULC classification, while the class accuracies (PA: producer's accuracy and UA: user's accuracy) for the two cropping systems were consistently above 85%. We concluded that explicit mapping of different cropping systems is feasible in complex and highly fragmented agro-ecological landscapes if high resolution and multi-temporal satellite data such as 5 m RapidEye data is employed. Further research is needed on the feasibility of using freely available 10-20 m Sentinel-2 data for wide-area assessment of cropping systems as an important variable in numerous crop productivity models.

Self-reported drug use among secondary school students in two rapidly developing Nigerian towns.

PubMed

Nevadomsky, J

1982-01-01

A 32-item standardized multiple-choice and open-ended questionnaire was completed by nearly 500 male and female secondary school students in two rapidly developing Nigerian towns. About two thirds of the students reported some exposure to alcohol, and about one quarter reported some experience with tobacco. There was much less use of caffeine, methaqualone in combination with diphenhydramine, 2-ethylamino-3-phenylorcamphane in combination with vitamins, chlordiazepoxide, diazepam, cannabis and dexamphetamine. Many students fell into the "past use" category. Parents were extremely disapproving of the use of almost any drug. Many students supported stronger penalties for the use of cannabis. Non-users claimed that drugs were dangerous to health. In addition, religious beliefs were associated with abstinence from drugs.

Two years experience with quality assurance protocol for patient related Rapid Arc treatment plan verification using a two dimensional ionization chamber array

PubMed Central

2011-01-01

Purpose To verify the dose distribution and number of monitor units (MU) for dynamic treatment techniques like volumetric modulated single arc radiation therapy - Rapid Arc - each patient treatment plan has to be verified prior to the first treatment. The purpose of this study was to develop a patient related treatment plan verification protocol using a two dimensional ionization chamber array (MatriXX, IBA, Schwarzenbruck, Germany). Method Measurements were done to determine the dependence between response of 2D ionization chamber array, beam direction, and field size. Also the reproducibility of the measurements was checked. For the patient related verifications the original patient Rapid Arc treatment plan was projected on CT dataset of the MatriXX and the dose distribution was calculated. After irradiation of the Rapid Arc verification plans measured and calculated 2D dose distributions were compared using the gamma evaluation method implemented in the measuring software OmniPro (version 1.5, IBA, Schwarzenbruck, Germany). Results The dependence between response of 2D ionization chamber array, field size and beam direction has shown a passing rate of 99% for field sizes between 7 cm × 7 cm and 24 cm × 24 cm for measurements of single arc. For smaller and larger field sizes than 7 cm × 7 cm and 24 cm × 24 cm the passing rate was less than 99%. The reproducibility was within a passing rate of 99% and 100%. The accuracy of the whole process including the uncertainty of the measuring system, treatment planning system, linear accelerator and isocentric laser system in the treatment room was acceptable for treatment plan verification using gamma criteria of 3% and 3 mm, 2D global gamma index. Conclusion It was possible to verify the 2D dose distribution and MU of Rapid Arc treatment plans using the MatriXX. The use of the MatriXX for Rapid Arc treatment plan verification in clinical routine is reasonable. The passing rate should be 99% than the verification

HIV-1 protease cleavage site prediction based on two-stage feature selection method.

PubMed

Niu, Bing; Yuan, Xiao-Cheng; Roeper, Preston; Su, Qiang; Peng, Chun-Rong; Yin, Jing-Yuan; Ding, Juan; Li, HaiPeng; Lu, Wen-Cong

2013-03-01

Knowledge of the mechanism of HIV protease cleavage specificity is critical to the design of specific and effective HIV inhibitors. Searching for an accurate, robust, and rapid method to correctly predict the cleavage sites in proteins is crucial when searching for possible HIV inhibitors. In this article, HIV-1 protease specificity was studied using the correlation-based feature subset (CfsSubset) selection method combined with Genetic Algorithms method. Thirty important biochemical features were found based on a jackknife test from the original data set containing 4,248 features. By using the AdaBoost method with the thirty selected features the prediction model yields an accuracy of 96.7% for the jackknife test and 92.1% for an independent set test, with increased accuracy over the original dataset by 6.7% and 77.4%, respectively. Our feature selection scheme could be a useful technique for finding effective competitive inhibitors of HIV protease.

Strategy for selecting Mars Pathfinder landing sites

NASA Technical Reports Server (NTRS)

Greeley, Ronald; Kuzmin, Ruslin O.

1994-01-01

A strategy for Pathfinder site selection must be developed that is fundamentally different from most previous considerations. At least two approaches can be identified. In one approach, the objective is to select a site representing a key geologic unit on Mars, i.e., a unit that is widespread, easily recognized, and used frequently as a datum in various investigations. The second approach is to select a site that potentially affords access to a wide variety of rock types. Because rover range is limited, rocks from a variety of sources must be assembled in a small area for sampling. Regardless of the approach taken in site selection, the Pathfinder site should include eolian deposits and provisions should be made to obtain measurements on soils. A recommended approach for selecting the Mars Pathfinder landing site is to identify a deltaic deposit, composed of sediments derived from sources of various ages and geologic units that shows evidence of eolian activity. The site should be located as close as possible to the part of the outwash where rapid deposition occurred because the likelihood of 'sorting' by size and composition increases with distance, decreasing the probability of heterogeneity. In addition, it is recommended that field operation tests be conducted to gain experience and insight into conducting science with Pathfinder.

Two classes of ouabain binding sites in ferret heart and two forms of Na+-K+-ATPase

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

Ng, Y.C.; Akera, T.

1987-05-01

In partially purified Na+-K+-adenosinetriphosphatase (ATPase) obtained from ferret heart, ouabain produced a monophasic inhibition curve; however, the curve spanned over 5 logarithmic units, indicating the presence of more than one classes of enzyme. (/sup 3/H)ouabain binding studies revealed high-and low-affinity binding sites in approximately equal abundance, with apparent dissociation constants of 10 and 230 nM, respectively. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of phosphoenzyme formed from (gamma-/sup 32/P)ATP showed two distinct K+-sensitive bands of approximately 100,000 molecular weight. Phosphoenzyme formation from the high-molecular-weight alpha(+) form was selectively inhibited by N-ethylmaleimide. Ouabain caused a 50% inhibition of phosphorylation of the alpha(+) formmore » at 40 nM and the lower-molecular-weight alpha form at 300 nM. In papillary muscle preparations, 1-30 nM ouabain produced a modest positive inotropic effect that reached an apparent plateau at 30 nM. Further increases in ouabain concentrations, however, produced additional and prominent inotropic effects at 0.1-10 microM. These results indicate for the first time in cardiac muscle that the high- and low-affinity ouabain binding sites are associated with the alpha(+) and alpha forms of the Na+-K+-ATPase, respectively, and that binding of ouabain to either of these sites causes enzyme inhibition and the positive inotropic effect.« less

Runoff and soil erosion from two rangeland sites

USDA-ARS?s Scientific Manuscript database

Historically over 50 years of rainfall/runoff research using rainfall simulators has been conducted at various rangeland sites in the West, however these sites rarely have consecutive yearly measurements. This limits the understanding of dynamic annual conditions and the interactions of grazing, pla...

Interannual consistency in fractal snow depth patterns at two Colorado mountain sites

Treesearch

Jeffrey S. Deems; Steven R. Fassnacht; Kelly J. Elder

2008-01-01

Fractal dimensions derived from log-log variograms are useful for characterizing spatial structure and scaling behavior in snow depth distributions. This study examines the temporal consistency of snow depth scaling features at two sites using snow depth distributions derived from lidar datasets collected in 2003 and 2005. The temporal snow accumulation patterns in...

Monitoring of two rapidly changing glacier tongues in the Swiss Alps by new drone data and historical documents

NASA Astrophysics Data System (ADS)

Nussbaumer, Samuel U.; Jörg, Philip C.; Gärtner-Roer, Isabelle; Rastner, Philipp; Ruff, Alexander; Steiner, Daniel; Vieli, Andreas; Zumbühl, Heinz J.

2015-04-01

Glaciers are considered among the most sensitive indicators of climate change. One of the most visually compelling examples of recent climate change is the retreat of glaciers in mountain regions, and knowledge about the past evolution of glacier fluctuations has been proven to be crucial for studying past decadal to century-scale climate variability. In this presentation, we evaluate the potential of a light fixed-wing UAV (unmanned aerial vehicle; drone) designed for surveying and remote sensing purposes, for monitoring glacier changes. We focus on the frontal zones of two well-known glaciers in the Swiss Alps: Unterer Grindelwaldgletscher in the Bernese Oberland, and Findelengletscher near Zermatt, Valais. We used a professional mapping drone (eBee by senseFly) to cover both frontal areas of the glaciers in the summer/autumn of 2014. We used a Canon IXUS 125HS RGB camera on-board the drone to collect overlapping nadir images for both study sites. For Unterer Grindelwaldgletscher (Findelengletscher), 187 (421) images were taken for a surveyed area of 3.2 km2 (2.9 km2) resulting in digital surface models and orthophotos with a very high spatial resolution of 0.16 m (0.11 m). The high number of images collected per area resulted in accurate elevation models and no detectable systematic horizontal shifts. Analysis of these images reveal in great detail the typical processes and features known for down-wasting and rapidly disintegrating Alpine glacier tongues: formation of (pro-)glacial lakes, dead ice, thermokarst phenomena, collapse of lateral moraines, and a complex interplay between many of those processes. Typically glacio-fluvial, gravitational, and periglacial processes occur in close vicinity and on different temporal scales (continuous, sporadic). We compare both glacier landscapes and address the important processes identified to be responsible for the glacier change at both sites. Finally, to set the observed geomorphological processes and the rapid

Safe and rapid resolution of severe hypertriglyceridaemia in two patients with intravenous insulin.

PubMed

Triay, J M; Day, A; Singhal, P

2010-09-01

To rapidly reduce serum triglyceride to a safe serum level. Severe hypertriglyceridaemia is associated with uncontrolled diabetes, obesity and poor physical activity. Even moderate increases in triglyceride levels (> 5mmol/L) confer an increased risk of pancreatitis and coronary artery disease. We present two patients with diabetes and serum triglyceride levels of greater than 85mmol/L despite polypharmacy intervention. 72-hour intravenous insulin infusion was administered. Serum triglyceride levels fell to 9.4 and 4.6 mmol/L respectively, without adverse events and sustained effect over several months. We suggest the use of intravenous insulin infusion where lifestyle and oral drug therapies have failed can impact on severe hypertriglyceridaemia.

Comparative analysis of complete orthologous centromeres from two subspecies of rice reveals rapid variation of centromere organization and structure.

PubMed

Wu, Jianzhong; Fujisawa, Masaki; Tian, Zhixi; Yamagata, Harumi; Kamiya, Kozue; Shibata, Michie; Hosokawa, Satomi; Ito, Yukiyo; Hamada, Masao; Katagiri, Satoshi; Kurita, Kanako; Yamamoto, Mayu; Kikuta, Ari; Machita, Kayo; Karasawa, Wataru; Kanamori, Hiroyuki; Namiki, Nobukazu; Mizuno, Hiroshi; Ma, Jianxin; Sasaki, Takuji; Matsumoto, Takashi

2009-12-01

Centromeres are sites for assembly of the chromosomal structures that mediate faithful segregation at mitosis and meiosis. This function is conserved across species, but the DNA components that are involved in kinetochore formation differ greatly, even between closely related species. To shed light on the nature, evolutionary timing and evolutionary dynamics of rice centromeres, we decoded a 2.25-Mb DNA sequence covering the centromeric region of chromosome 8 of an indica rice variety, 'Kasalath' (Kas-Cen8). Analysis of repetitive sequences in Kas-Cen8 led to the identification of 222 long terminal repeat (LTR)-retrotransposon elements and 584 CentO satellite monomers, which account for 59.2% of the region. A comparison of the Kas-Cen8 sequence with that of japonica rice 'Nipponbare' (Nip-Cen8) revealed that about 66.8% of the Kas-Cen8 sequence was collinear with that of Nip-Cen8. Although the 27 putative genes are conserved between the two subspecies, only 55.4% of the total LTR-retrotransposon elements in 'Kasalath' had orthologs in 'Nipponbare', thus reflecting recent proliferation of a considerable number of LTR-retrotransposons since the divergence of two rice subspecies of indica and japonica within Oryza sativa. Comparative analysis of the subfamilies, time of insertion, and organization patterns of inserted LTR-retrotransposons between the two Cen8 regions revealed variations between 'Kasalath' and 'Nipponbare' in the preferential accumulation of CRR elements, and the expansion of CentO satellite repeats within the core domain of Cen8. Together, the results provide insights into the recent proliferation of LTR-retrotransposons, and the rapid expansion of CentO satellite repeats, underlying the dynamic variation and plasticity of plant centromeres.

Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site.

PubMed

Gerlits, Oksana; Wymore, Troy; Das, Amit; Shen, Chen-Hsiang; Parks, Jerry M; Smith, Jeremy C; Weiss, Kevin L; Keen, David A; Blakeley, Matthew P; Louis, John M; Langan, Paul; Weber, Irene T; Kovalevsky, Andrey

2016-04-11

Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid prototyping modelling in oral and maxillofacial surgery: A two year retrospective study.

PubMed

Suomalainen, Anni; Stoor, Patricia; Mesimäki, Karri; Kontio, Risto K

2015-12-01

The use of rapid prototyping (RP) models in medicine to construct bony models is increasing. The aim of the study was to evaluate retrospectively the indication for the use of RP models in oral and maxillofacial surgery at Helsinki University Central Hospital during 2009-2010. Also, the used computed tomography (CT) examination - multislice CT (MSCT) or cone beam CT (CBCT) - method was evaluated. In total 114 RP models were fabricated for 102 patients. The mean age of the patients at the time of the production of the model was 50.4 years. The indications for the modelling included malignant lesions (29%), secondary reconstruction (25%), prosthodontic treatment (22%), orthognathic surgery or asymmetry (13%), benign lesions (8%), and TMJ disorders (4%). MSCT examination was used in 92 and CBCT examination in 22 cases. Most of the models (75%) were conventional hard tissue models. Models with colored tumour or other structure(s) of interest were ordered in 24%. Two out of the 114 models were soft tissue models. The main benefit of the models was in treatment planning and in connection with the production of pre-bent plates or custom made implants. The RP models both facilitate and improve treatment planning and intraoperative efficiency. Rapid prototyping, radiology, computed tomography, cone beam computed tomography.

NEKTON HABITAT QUALITY AT SHALLOW-WATER SITES IN TWO RHODE ISLAND COASTAL SYSTEMS

EPA Science Inventory

We evaluated nekton habitat quality at five shallow-water sites in two Rhode Island systems by comparing nekton densities and biomass, number of species, prey availability and feeding, and abundance of winter flounder Pseudopleuronectes americanus. Nekton density and biomass wer...

Screening guide for rapid assessment of liquefaction hazard at highway bridge sites

DOT National Transportation Integrated Search

1998-06-16

As an aid to seismic hazard assessment, this report provides a "screening guide" for systematic evaluation of liquefactin hazard at bridge sites and a guide for prioritizing sites for further investigation or mitigation. The guide presents a systemat...

RAPID ASSESSMENT OF POTENTIAL GROUND-WATER CONTAMINATION UNDER EMERGENCY RESPONSE CONDITIONS

EPA Science Inventory

Emergency response actions at chemical spills and abandoned hazardous waste sites often require rapid assessment of the potential for groundwater contamination by the chemical or waste compound. This manual provides a rapid assessment methodology for performing such an evaluation...

Hydrogeology and leachate movement near two chemical-waste sites in Oswego County, New York

USGS Publications Warehouse

Anderson, H.R.; Miller, Todd S.

1986-01-01

Forty-five observation wells and test holes were installed at two chemical waste disposal sites in Oswego County, New York, to evaluate the hydrogeologic conditions and the rate and direction of leachate migration. At the site near Oswego groundwater moves northward at an average velocity of 0.4 ft/day through unconsolidated glacial deposits and discharges into White Creek and Wine Creek, which border the site and discharge to Lake Ontario. Leaking barrels by chemical wastes have contaminated the groundwater within the site, as evidenced by detection of 10 ' priority pollutant ' organic compounds, and elevated values of specific conductance, chloride, arsenic, lead, and mercury. At the site near Fulton, where 8,000 barrels of chemical wastes are buried, groundwater in the sandy surficial aquifer bordering the landfill on the south and east moves southward and eastward at an average velocity of 2.8 ft/day and discharges to Bell Creek, which discharges to the Oswego River, or moves beneath the landfill. Leachate is migrating eastward, southeastward, and southwestward, as evidenced by elevated values of specific conductance, temperature, and concentrations of several trace metals at wells east, southeast, and southwest of the site. (USGS)

[Comparison of two methods for rapid determination of C-reactive protein with the Tina-quant].

PubMed

Oremek, G M; Luksaite, R; Bretschneider, I

2008-03-01

C-reactive protein (CRP) as an acute phase protein is an important diagnostic marker for the presence and course of human processes. Out of the acute phase proteins it is one of those the concentrations increase most rapidly with its sensitivity being superior to other markers of inflammation, such as leukocytosis, erythrocytic sedimentation rate, and fever. This study compared two-point-of-care assays with the standard laboratory method Tina-quant CRP processed on a Hitachi 917: the immunofiltration assay NycoCard CRP Whole Blood and the turbidimetric immunoassay Micros CRP. Both methods are carried in the presence of a patient, by using capillary or venous blood. Seventy-eight blood samples were analyzed first in the standard laboratory routine and then by both rapid test assays. The precision of both assays was determined from the confidence interval. The results were statistically analyzed by arithmetic standard deviation mean method, variation coefficient, Spearman correlation index, Wilcoxon and Bland-Altman tests, and Passing-Bablock regression. NycoCard CRP Whole Blood showed a correlation coefficient of R = 0.9838; the precision had a coefficient of variation of CV = 1.8759% while As compared with Tina-quant CRP had R = 0.9934 and CV = 0.9160%. Both assays indicated the same results as Tina-quant CRP. Both Tina-quant CRP and NycoCard CRP Whole Blood give the best fit for the rapid determination of CRP.

Preliminary Geotechnical Investigation of Two Basaltic Landslide Sites in Mauritius, Offshore Africa

NASA Astrophysics Data System (ADS)

Bhoopendra, D.; Fukuoka, H.; Kuwano, T.; Ichikawa, K.

2016-12-01

Landslide hazards in developing areas in Mauritius became a great challenge as well as a fundamental concern for the government and the citizen of the country. In recent years, landslide disasters have caused losses of both public and private properties. In 2005, a large-scale landslide at Chitrakoot affected 54 houses and infrastructures, and it was reactivated in 2006, damaging another 14 houses. Vallee Pitot landslide is frequently reactivated in these years and threatening several houses in the densely-populated zone. Being of volcanic origin, Mauritius has observed dramatic and quick weathering of the soil which may partly contribute to creating landslide-prone geo-environment. This study focuses on the preliminary geotechnical investigation of the two basaltic landslide areas in Mauritius. A recent investigation was conducted jointly by JICA (Japan International Cooperation Agency) and Ministry of Public Infrastructure and Land Transport of Government of Mauritius on both sites from 2012 to 2015 to survey the landslide surface and to implement countermeasures works.Both sites are located in the highly populated area in the capital city of Mauritius.The geological features of the sites were studied with the borehole core logging data obtained from 6 boreholes and it was found that possible sliding surface was observed in the colluvium layer consisting of gravels and stiff silty-clays, at depths from 6 to 10 m below the ground surface. The rate of landslide movement during heavy rainfall amount exceeding 100 mm/hr was elaborated with past records of extensometers installed on these sites. Colluvium samples from both sites of the same characteristics with the sliding surface were tested in the ring shear apparatus in Japan under different normal stresses reducing from 300 kPa to 50 kPa step-wise at a shear velocity of 0.02 mm/min under drained condition to obtain the residual friction angle (φ) and the cohesion (c). Obtained residual friction angle and cohesion

Rapid bacteriophage MS2 transport in an oxic sandy aquifer in cold climate: Field experiments and modeling

NASA Astrophysics Data System (ADS)

Kvitsand, Hanne M. L.; Ilyas, Aamir; Østerhus, Stein W.

2015-12-01

Virus removal during rapid transport in an unconfined, low-temperature (6°C) sand and gravel aquifer was investigated at a riverbank field site, 25 km south of Trondheim in central Norway. The data from bacteriophage MS2 inactivation and transport experiments were applied in a two-site kinetic transport model using HYDRUS-1D, to evaluate the mechanisms of virus removal and whether these mechanisms were sufficient to protect the groundwater supplies. The results demonstrated that inactivation was negligible to the overall removal and that irreversible MS2 attachment to aquifer grains, coated with iron precipitates, played a dominant role in the removal of MS2; 4.1 log units of MS2 were removed by attachment during 38 m travel distance and less than 2 days residence time. Although the total removal was high, pathways capable of allowing virus migration at rapid velocities were present in the aquifer. The risk of rapid transport of viable viruses should be recognized, particularly for water supplies without permanent disinfection.

Development of a Rapid Assessment Method for Quantifying Carbon Sequestration on Reclaimed Coal Mine Sites

NASA Astrophysics Data System (ADS)

Maharaj, S.; Barton, C. D.; Karathanasis, A. D.

2005-12-01

Projected climate change resulting from elevated atmospheric carbon dioxide has given rise to various strategies designed to sequester carbon in various terrestrial ecosystems. Reclaimed coal mine soils present one such potential carbon sink where traditional reclamation objectives can complement carbon sequestration. However, quantifying new carbon (carbon that has been added to soil through recent biological processes) on reclaimed mine soils have proven to be difficult due to carbonates and coal particles present in the reclaimed coal mine spoils. Visible coal particles can be removed, but the microscopic coal dust particles remain. Additionally, with the advent of carbon trading on the stock market, rapid quantification of newly sequestered carbon has proven to be elusive. The focus of this project is to assess the potential of thermogravimetric analysis as a rapid, simple and direct method for differentiating and quantifying new carbon from old carbon (carbon of geologic origin) on reclaimed coal mine sites and provide a standard procedure for determining carbon sequestered in soil sinks. Thermogravimetry is a physico-chemical technique where the weight change is measured and recorded during the incremental heating of the soil sample over a temperature range of 25 to 1000 ° C. Grass litter and limestone were used as representative organic and inorganic carbon fractions, while coal was used to differentiate the old and new carbon within the organic fraction. Recoveries of mixtures at the 95 % confidence interval were found to be 94.49 ± 4.23 % (coal) , 93.67 ± 2.11 % (litter) , and 108.88 ± 2.88 % (limestone) respectively. Each of the above components appeared as distinct separate peaks on the thermograph, with litter appearing between 260 to 390 ° C, coal 425 to 480 ° C, and limestone 640 to 740 ° C. Overlapping peaks for the organic carbon represented by the grass litter may be indicative of cellulose and lignin fractions. Ongoing work in this area is

Two rapidly evolving genes contribute to male fitness in Drosophila

PubMed Central

Reinhardt, Josephine A; Jones, Corbin D

2013-01-01

Purifying selection often results in conservation of gene sequence and function. The most functionally conserved genes are also thought to be among the most biologically essential. These observations have led to the use of sequence conservation as a proxy for functional conservation. Here we describe two genes that are exceptions to this pattern. We show that lack of sequence conservation among orthologs of CG15460 and CG15323 – herein named jean-baptiste (jb) and karr respectively – does not necessarily predict lack of functional conservation. These two Drosophila melanogaster genes are among the most rapidly evolving protein-coding genes in this species, being nearly as diverged from their D. yakuba orthologs as random sequences are. jb and karr are both expressed at an elevated level in larval males and adult testes, but they are not accessory gland proteins and their loss does not affect male fertility. Instead, knockdown of these genes in D. melanogaster via RNA interference caused male-biased viability defects. These viability effects occur prior to the third instar for jb and during late pupation for karr. We show that putative orthologs to jb and karr are also expressed strongly in the testes of other Drosophila species and have similar gene structure across species despite low levels of sequence conservation. While standard molecular evolution tests could not reject neutrality, other data hint at a role for natural selection. Together these data provide a clear case where a lack of sequence conservation does not imply a lack of conservation of expression or function. PMID:24221639

Rapid Estimation of TPH Reduction in Oil-Contaminated Soils Using the MED Method

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

Edenborn, H.M.; Zenone, V.A.

2007-09-01

Oil-contaminated soil and sludge generated during federal well plugging activities in northwestern Pennsylvania are currently remediated on small landfarm sites in lieu of more expensive landfill disposal. Bioremediation success at these sites in the past has been gauged by the decrease in total petroleum hydrocarbon (TPH) concentrations to less than 10,000 mg/kg measured using EPA Method 418.1. We tested the “molarity of ethanol droplet” (MED) water repellency test as a rapid indicator of TPH concentration in soil at one landfarm near Bradford, PA. MED was estimated by determining the minimum ethanol concentration (0 – 6 M) required to penetrate air-driedmore » and sieved soil samples within 10 sec. TPH in soil was analyzed by rapid fluorometric analysis of methanol soil extracts, which correlated well with EPA Method 1664. Uncontaminated landfarm site soil amended with increasing concentrations of waste oil sludge showed a high correlation between MED and TPH. MED values exceeded the upper limit of 6 M as TPH estimates exceed ca. 25,000 mg/kg. MED and TPH at the land farm were sampled monthly during summer months over two years in a grid pattern that allowed spatial comparisons of site remediation effectiveness. MED and TPH decreased at a constant rate over time and remained highly correlated. Inexpensive alternatives to reagent-grade ethanol gave comparable results. The simple MED approach served as an inexpensive alternative to the routine laboratory analysis of TPH during the monitoring of oily waste bioremediation at this landfarm site.« less

Rapid development of stable transgene CHO cell lines by CRISPR/Cas9-mediated site-specific integration into C12orf35.

PubMed

Zhao, Menglin; Wang, Jiaxian; Luo, Manyu; Luo, Han; Zhao, Meiqi; Han, Lei; Zhang, Mengxiao; Yang, Hui; Xie, Yueqing; Jiang, Hua; Feng, Lei; Lu, Huili; Zhu, Jianwei

2018-07-01

Chinese hamster ovary (CHO) cells are the most widely used mammalian hosts for recombinant protein production. However, by conventional random integration strategy, development of a high-expressing and stable recombinant CHO cell line has always been a difficult task due to the heterogenic insertion and its caused requirement of multiple rounds of selection. Site-specific integration of transgenes into CHO hot spots is an ideal strategy to overcome these challenges since it can generate isogenic cell lines with consistent productivity and stability. In this study, we investigated three sites with potential high transcriptional activities: C12orf35, HPRT, and GRIK1, to determine the possible transcriptional hot spots in CHO cells, and further construct a reliable site-specific integration strategy to develop recombinant cell lines efficiently. Genes encoding representative proteins mCherry and anti-PD1 monoclonal antibody were targeted into these three loci respectively through CRISPR/Cas9 technology. Stable cell lines were generated successfully after a single round of selection. In comparison with a random integration control, all the targeted integration cell lines showed higher productivity, among which C12orf35 locus was the most advantageous in both productivity and cell line stability. Binding affinity and N-glycan analysis of the antibody revealed that all batches of product were of similar quality independent on integrated sites. Deep sequencing demonstrated that there was low level of off-target mutations caused by CRISPR/Cas9, but none of them contributed to the development process of transgene cell lines. Our results demonstrated the feasibility of C12orf35 as the target site for exogenous gene integration, and strongly suggested that C12orf35 targeted integration mediated by CRISPR/Cas9 is a reliable strategy for the rapid development of recombinant CHO cell lines.

Remote sensing-based estimation of annual soil respiration at two contrasting forest sites

NASA Astrophysics Data System (ADS)

Huang, Ni; Gu, Lianhong; Black, T. Andrew; Wang, Li; Niu, Zheng

2015-11-01

Soil respiration (Rs), an important component of the global carbon cycle, can be estimated using remotely sensed data, but the accuracy of this technique has not been thoroughly investigated. In this study, we proposed a methodology for the remote estimation of annual Rs at two contrasting FLUXNET forest sites (a deciduous broadleaf forest and an evergreen needleleaf forest). A version of the Akaike's information criterion was used to select the best model from a range of models for annual Rs estimation based on the remotely sensed data products from the Moderate Resolution Imaging Spectroradiometer and root-zone soil moisture product derived from assimilation of the NASA Advanced Microwave Scanning Radiometer soil moisture products and a two-layer Palmer water balance model. We found that the Arrhenius-type function based on nighttime land surface temperature (LST-night) was the best model by comprehensively considering the model explanatory power and model complexity at the Missouri Ozark and BC-Campbell River 1949 Douglas-fir sites. In addition, a multicollinearity problem among LST-night, root-zone soil moisture, and plant photosynthesis factor was effectively avoided by selecting the LST-night-driven model. Cross validation showed that temporal variation in Rs was captured by the LST-night-driven model with a mean absolute error below 1 µmol CO2 m-2 s-1 at both forest sites. An obvious overestimation that occurred in 2005 and 2007 at the Missouri Ozark site reduced the evaluation accuracy of cross validation because of summer drought. However, no significant difference was found between the Arrhenius-type function driven by LST-night and the function considering LST-night and root-zone soil moisture. This finding indicated that the contribution of soil moisture to Rs was relatively small at our multiyear data set. To predict intersite Rs, maximum leaf area index (LAImax) was used as an upscaling factor to calibrate the site-specific reference respiration

The enzymatic processing of α-dystroglycan by MMP-2 is controlled by two anchoring sites distinct from the active site

PubMed Central

Fasciglione, Giovanni Francesco; Sbardella, Diego; Sciandra, Francesca; Casella, MariaLuisa; Camerini, Serena; Crescenzi, Marco; Gori, Alessandro; Tarantino, Umberto; Cozza, Paola; Brancaccio, Andrea; Coletta, Massimo; Bozzi, Manuela

2018-01-01

Dystroglycan (DG) is a membrane receptor, belonging to the dystrophin-glycoprotein complex (DGC) and formed by two subunits, α-dystroglycan (α-DG) and β-dystroglycan (β -DG). The C-terminal domain of α-DG and the N-terminal extracellular domain of β -DG are connected, providing a link between the extracellular matrix and the cytosol. Under pathological conditions, such as cancer and muscular dystrophies, DG may be the target of metalloproteinases MMP-2 and MMP-9, contributing to disease progression. Previously, we reported that the C-terminal domain α-DG (483–628) domain is particularly susceptible to the catalytic activity of MMP-2; here we show that the α-DG 621–628 region is required to carry out its complete digestion, suggesting that this portion may represent a MMP-2 anchoring site. Following this observation, we synthesized an α-DG based-peptide, spanning the (613–651) C-terminal region. The analysis of the kinetic and thermodynamic parameters of the whole and the isolated catalytic domain of MMP-2 (cdMMP-2) has shown its inhibitory properties, indicating the presence of (at least) two binding sites for the peptide, both located within the catalytic domain, only one of the two being topologically distinct from the catalytic active groove. However, the different behavior between whole MMP-2 and cdMMP-2 envisages the occurrence of an additional binding site for the peptide on the hemopexin-like domain of MMP-2. Interestingly, mass spectrometry analysis has shown that α-DG (613–651) peptide is cleavable even though it is a very poor substrate of MMP-2, a feature that renders this molecule a promising template for developing a selective MMP-2 inhibitor. PMID:29447293

Predicting stem borer density in maize using RapidEye data and generalized linear models

NASA Astrophysics Data System (ADS)

Abdel-Rahman, Elfatih M.; Landmann, Tobias; Kyalo, Richard; Ong'amo, George; Mwalusepo, Sizah; Sulieman, Saad; Ru, Bruno Le

2017-05-01

Average maize yield in eastern Africa is 2.03 t ha-1 as compared to global average of 6.06 t ha-1 due to biotic and abiotic constraints. Amongst the biotic production constraints in Africa, stem borers are the most injurious. In eastern Africa, maize yield losses due to stem borers are currently estimated between 12% and 21% of the total production. The objective of the present study was to explore the possibility of RapidEye spectral data to assess stem borer larva densities in maize fields in two study sites in Kenya. RapidEye images were acquired for the Bomet (western Kenya) test site on the 9th of December 2014 and on 27th of January 2015, and for Machakos (eastern Kenya) a RapidEye image was acquired on the 3rd of January 2015. Five RapidEye spectral bands as well as 30 spectral vegetation indices (SVIs) were utilized to predict per field maize stem borer larva densities using generalized linear models (GLMs), assuming Poisson ('Po') and negative binomial ('NB') distributions. Root mean square error (RMSE) and ratio prediction to deviation (RPD) statistics were used to assess the models performance using a leave-one-out cross-validation approach. The Zero-inflated NB ('ZINB') models outperformed the 'NB' models and stem borer larva densities could only be predicted during the mid growing season in December and early January in both study sites, respectively (RMSE = 0.69-1.06 and RPD = 8.25-19.57). Overall, all models performed similar when all the 30 SVIs (non-nested) and only the significant (nested) SVIs were used. The models developed could improve decision making regarding controlling maize stem borers within integrated pest management (IPM) interventions.

Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB.

PubMed

Kirshner, Daniel A; Nilmeier, Jerome P; Lightstone, Felice C

2013-07-01

The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov.

Rapid prototyping modelling in oral and maxillofacial surgery: A two year retrospective study

PubMed Central

Stoor, Patricia; Mesimäki, Karri; Kontio, Risto K.

2015-01-01

Background The use of rapid prototyping (RP) models in medicine to construct bony models is increasing. Material and Methods The aim of the study was to evaluate retrospectively the indication for the use of RP models in oral and maxillofacial surgery at Helsinki University Central Hospital during 2009-2010. Also, the used computed tomography (CT) examination – multislice CT (MSCT) or cone beam CT (CBCT) - method was evaluated. Results In total 114 RP models were fabricated for 102 patients. The mean age of the patients at the time of the production of the model was 50.4 years. The indications for the modelling included malignant lesions (29%), secondary reconstruction (25%), prosthodontic treatment (22%), orthognathic surgery or asymmetry (13%), benign lesions (8%), and TMJ disorders (4%). MSCT examination was used in 92 and CBCT examination in 22 cases. Most of the models (75%) were conventional hard tissue models. Models with colored tumour or other structure(s) of interest were ordered in 24%. Two out of the 114 models were soft tissue models. Conclusions The main benefit of the models was in treatment planning and in connection with the production of pre-bent plates or custom made implants. The RP models both facilitate and improve treatment planning and intraoperative efficiency. Key words:Rapid prototyping, radiology, computed tomography, cone beam computed tomography. PMID:26644837

Identification of two integration sites in favor of transgene expression in Trichoderma reesei.

PubMed

Qin, Lina; Jiang, Xianzhang; Dong, Zhiyang; Huang, Jianzhong; Chen, Xiuzhen

2018-01-01

The ascomycete fungus Trichoderma reesei was widely used as a biotechnological workhorse for production of cellulases and recombinant proteins due to its large capacity of protein secretion. Transgenesis by random integration of a gene of interest (GOI) into the genome of T. reesei can generate series of strains that express different levels of the indicated transgene. The insertion site of the GOI plays an important role in the ultimate production of the targeted proteins. However, so far no systematic studies have been made to identify transgene integration loci for optimal expression of the GOI in T. reesei . Currently, only the locus of exocellobiohydrolases I encoding gene ( cbh1) is widely used as a promising integration site to lead to high expression level of the GOI. No additional sites associated with efficient gene expression have been characterized. To search for gene integration sites that benefit for the secreted expression of GOI, the food-and-mouth disease virus 2A protein was applied for co-expression of an Aspergillus niger lipA gene and Discosoma sp. DsRed1 gene in T. reesei, by random integration of the expression cassette into the genome. We demonstrated that the fluorescent intensity of RFP (red fluorescent protein) inside of the cell was well correlated with the secreted lipase yields, based on which, we successfully developed a high-throughput screening method to screen strains with relatively higher secreted expression of the GOI (in this study, lipase). The copy number and the insertion sites of the transgene were investigated among the selected highly expressed strains. Eventually, in addition to cbh1 gene locus, two other genome insertion loci that efficiently facilitate gene expression in T. reesei were identified. We have successfully developed a high-throughput screening method to screen strains with optimal expression of the indicated secreted proteins in T. reesei . Moreover, we identified two optimal genome loci for transgene

Isolated colostomy site recurrence in rectal cancer-two cases with review of literature

PubMed Central

Chintamani; Singhal, Vinay; Bansal, Anju; Bhatnagar, Dinesh; Saxena, Sunita

2007-01-01

Background Colostomy site carcinomas are rare with only eight cases reported in the world literature. Various etiological factors like adenoma-cancer sequence, bile acids, recurrent and persistent physical damage at the colostomy site by faecal matter due to associated stomal stenosis have been considered responsible. Two such cases are being reported and in both cases there was no evidence of any local recurrence in the pelvis or liver and distant metastasis. Both patients had received adjuvant chemotherapy following surgery. Case presentation First case was a 30-year-old male that had reported with large bowel obstruction due to an obstructing ulcero-proliferative growth (poorly differentiated adenocarcinoma) at the colostomy site after abdomino-perineal resection, performed for low rectal cancer six years previously. Wide local excision with microscopically free margins was performed with a satisfactory outcome. Four years later he presented with massive malignant ascites, cachexia and multiple liver metastasis and succumbed to his disease. Second case was a 47-year-old male that presented with acute large bowel obstruction due to an annular growth (well differentiated adenocarcinoma) in the upper rectum. He was managed by Hartmann's operation and the sigmoid colostomy was closed six months later. Five years following closure of colostomy, he presented with two parietal masses at the previous colostomy site scar, which, on fine needle aspiration cytology were found to be well-differentiated adenocarcinomas of colorectal type. Surgery in the form of wide local resection with free margins was performed. He presented again after five years with recurrence along the previous surgery scar and an incisional hernia and was managed by wide local excision along with hernioplasty. Follow-up of nine years following first surgery is satisfactory. Conclusion Colostomy site/scar recurrence of rectal carcinoma is rare and could be due to various etiological factors, although

Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation

PubMed Central

Pleiner, Tino; Bates, Mark; Trakhanov, Sergei; Lee, Chung-Tien; Schliep, Jan Erik; Chug, Hema; Böhning, Marc; Stark, Holger; Urlaub, Henning; Görlich, Dirk

2015-01-01

Nanobodies are single-domain antibodies of camelid origin. We generated nanobodies against the vertebrate nuclear pore complex (NPC) and used them in STORM imaging to locate individual NPC proteins with <2 nm epitope-label displacement. For this, we introduced cysteines at specific positions in the nanobody sequence and labeled the resulting proteins with fluorophore-maleimides. As nanobodies are normally stabilized by disulfide-bonded cysteines, this appears counterintuitive. Yet, our analysis showed that this caused no folding problems. Compared to traditional NHS ester-labeling of lysines, the cysteine-maleimide strategy resulted in far less background in fluorescence imaging, it better preserved epitope recognition and it is site-specific. We also devised a rapid epitope-mapping strategy, which relies on crosslinking mass spectrometry and the introduced ectopic cysteines. Finally, we used different anti-nucleoporin nanobodies to purify the major NPC building blocks – each in a single step, with native elution and, as demonstrated, in excellent quality for structural analysis by electron microscopy. The presented strategies are applicable to any nanobody and nanobody-target. DOI: http://dx.doi.org/10.7554/eLife.11349.001 PMID:26633879

Rapid-estimation method for assessing scour at highway bridges

USGS Publications Warehouse

Holnbeck, Stephen R.

1998-01-01

A method was developed by the U.S. Geological Survey for rapid estimation of scour at highway bridges using limited site data and analytical procedures to estimate pier, abutment, and contraction scour depths. The basis for the method was a procedure recommended by the Federal Highway Administration for conducting detailed scour investigations, commonly referred to as the Level 2 method. Using pier, abutment, and contraction scour results obtained from Level 2 investigations at 122 sites in 10 States, envelope curves and graphical relations were developed that enable determination of scour-depth estimates at most bridge sites in a matter of a few hours. Rather than using complex hydraulic variables, surrogate variables more easily obtained in the field were related to calculated scour-depth data from Level 2 studies. The method was tested by having several experienced individuals apply the method in the field, and results were compared among the individuals and with previous detailed analyses performed for the sites. Results indicated that the variability in predicted scour depth among individuals applying the method generally was within an acceptable range, and that conservatively greater scour depths generally were obtained by the rapid-estimation method compared to the Level 2 method. The rapid-estimation method is considered most applicable for conducting limited-detail scour assessments and as a screening tool to determine those bridge sites that may require more detailed analysis. The method is designed to be applied only by a qualified professional possessing knowledge and experience in the fields of bridge scour, hydraulics, and flood hydrology, and having specific expertise with the Level 2 method.

A Case Study of District Decentralization and Site-Based Budgeting: Cordell Place School District.

ERIC Educational Resources Information Center

Fermanich, Mark; Odden, Allan; Archibald, Sarah

A previously high-ranking suburban school district with declining student achievement changed to site-based budgeting. The account of the change may also be a cautionary tale about change taken too rapidly. Although a poor economy, the annexation of two Department of Defense schools, and organizational stagnation helped to create lower student…

High Resolution Rapid Revisits Insar Monitoring of Surface Deformation

NASA Astrophysics Data System (ADS)

Singhroy, V.; Li, J.; Charbonneau, F.

2014-12-01

Monitoring surface deformation on strategic energy and transportation corridors requires high resolution spatial and temporal InSAR images for mitigation and safety purposes. High resolution air photos, lidar and other satellite images are very useful in areas where the landslides can be fatal. Recently, radar interferometry (InSAR) techniques using more rapid revisit images from several radar satellites are increasingly being used in active deformation monitoring. The Canadian RADARSAT Constellation (RCM) is a three-satellite mission that will provide rapid revisits of four days interferometric (InSAR) capabilities that will be very useful for complex deformation monitoring. For instance, the monitoring of surface deformation due to permafrost activity, complex rock slide motion and steam assisted oil extraction will benefit from this new rapid revisit capability. This paper provide examples of how the high resolution (1-3 m) rapid revisit InSAR capabilities will improve our monitoring of surface deformation and provide insights in understanding triggering mechanisms. We analysed over a hundred high resolution InSAR images over a two year period on three geologically different sites with various configurations of topography, geomorphology, and geology conditions. We show from our analysis that the more frequent InSAR acquisitions are providing more information in understanding the rates of movement and failure process of permafrost triggered retrogressive thaw flows; the complex motion of an asymmetrical wedge failure of an active rock slide and the identification of over pressure zones related to oil extraction using steam injection. Keywords: High resolution, InSAR, rapid revisits, triggering mechanisms, oil extraction.

A rapid lateral-flow immunoassay for phytosanitary detection of Erwinia amylovora and on-site fire blight diagnosis.

PubMed

Braun-Kiewnick, A; Altenbach, D; Oberhänsli, T; Bitterlin, W; Duffy, B

2011-10-01

Fire blight is an invasive disease caused by Erwinia amylovora that threatens pome fruit production globally. Effective implementation of phytosanitary control measures depends upon rapid, reliable pathogen detection and disease diagnosis. We developed a lateral-flow immunoassay specific for E. amylovora with a detection limit of log 5.7 CFU/ml, typical of pathogen concentrations in symptomatic plant material. The simple assay had comparable sensitivity to standard culture plating, serum agglutination and nested PCR when validated for application in a phytosanitary laboratory as a confirmatory test of cultured isolates and for first-line diagnosis of phytosanitary samples that represent the full range of commercial, ornamental and forestry host species. On-site validation in ring-trials with local plant inspectors demonstrated robust and reliable detection (compared to subsequent plating and PCR analysis). The simplicity, inspector acceptance and facilitation of expedited diagnosis (from 2 days for laboratory submitted samples to 15 min with the immunoassay), offers a valuable tool for improved phytosanitary control of fire blight. Copyright © 2011 Elsevier B.V. All rights reserved.

A highly selective and sensitive fluorescent chemosensor and its application for rapid on-site detection of Al3 +

NASA Astrophysics Data System (ADS)

Yue, Xiao-li; Wang, Zhao-qing; Li, Chao-rui; Yang, Zheng-yin

2018-03-01

In this paper, a simple naphthalene-based derivative (HL) has been designed and synthesized as a Al3 +-selective fluorescent chemosensor based on the PET mechanism. HL exhibited high selectivity and sensitivity towards Al3 + over other commonly coexisting metal ions in ethanol with a detection limit of 2.72 nM. The 1:1 binding stoichiometry of the complex (HL-Al3 +) was determined from the Job's plot based on fluorescence titrations and the ESI-MS spectrum data. Moreover, the binding site of HL with Al3 + was assured by the 1H NMR titration experiment. The binding constant (Ka) of the complex (HL-Al3 +) was calculated to be 5.06 × 104 M- 1 according to the Benesi-Hildebrand equation. In addition, the recognizing process of HL towards Al3 + was chemically reversible by adding Na2EDTA. Importantly, HL could directly and rapidly detect aluminum ion through the filter paper without resorting to additional instrumental analysis.

When Is Rapid On-Site Evaluation Cost-Effective for Fine-Needle Aspiration Biopsy?

PubMed Central

Schmidt, Robert L.; Walker, Brandon S.; Cohen, Michael B.

2015-01-01

Background Rapid on-site evaluation (ROSE) can improve adequacy rates of fine-needle aspiration biopsy (FNAB) but increases operational costs. The performance of ROSE relative to fixed sampling depends on many factors. It is not clear when ROSE is less costly than sampling with a fixed number of needle passes. The objective of this study was to determine the conditions under which ROSE is less costly than fixed sampling. Methods Cost comparison of sampling with and without ROSE using mathematical modeling. Models were based on a societal perspective and used a mechanistic, micro-costing approach. Sampling policies (ROSE, fixed) were compared using the difference in total expected costs per case. Scenarios were based on procedure complexity (palpation-guided or image-guided), adequacy rates (low, high) and sampling protocols (stopping criteria for ROSE and fixed sampling). One-way, probabilistic, and scenario-based sensitivity analysis was performed to determine which variables had the greatest influence on the cost difference. Results ROSE is favored relative to fixed sampling under the following conditions: (1) the cytologist is accurate, (2) the total variable cost ($/hr) is low, (3) fixed costs ($/procedure) are high, (4) the setup time is long, (5) the time between needle passes for ROSE is low, (6) when the per-pass adequacy rate is low, and (7) ROSE stops after observing one adequate sample. The model is most sensitive to variation in the fixed cost, the per-pass adequacy rate, and the time per needle pass with ROSE. Conclusions Mathematical modeling can be used to predict the difference in cost between sampling with and without ROSE. PMID:26317785

Characterization of Fe(II) oxidizing bacterial activities and communities at two acidic Appalachian coalmine drainage-impacted sites

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

Senko, John M.; Wanjugi, Pauline; Lucas, Melanie

2008-06-12

We characterized the microbiologically mediated oxidative precipitation of Fe(II) from coalminederived acidic mine drainage (AMD) along flow-paths at two sites in northern Pennsylvania. At the Gum Boot site, dissolved Fe(II) was efficiently removed from AMD whereas minimal Fe(II) removal occurred at the Fridays-2 site. Neither site received human intervention to treat the AMD. Culturable Fe(II) oxidizing bacteria were most abundant at sampling locations along the AMD flow path corresponding to greatest Fe(II) removal and where overlying water contained abundant dissolved O2. Rates of Fe(II) oxidation determined in laboratory-based sediment incubations were also greatest at these sampling locations. Ribosomal RNA intergenicmore » spacer analysis and sequencing of partial 16S rRNA genes recovered from sediment bacterial communities revealed similarities among populations at points receiving regular inputs of Fe(II)-rich AMD and provided evidence for the presence of bacterial lineages capable of Fe(II) oxidation. A notable difference between bacterial communities at the two sites was the abundance of Chloroflexi-affiliated 16S rRNA gene sequences in clone libraries derived from the Gum Boot sediments. Our results suggest that inexpensive and reliable AMD treatment strategies can be implemented by mimicking the conditions present at the Gum Boot field site.« less

Catalytic site identification—a web server to identify catalytic site structural matches throughout PDB

PubMed Central

Kirshner, Daniel A.; Nilmeier, Jerome P.; Lightstone, Felice C.

2013-01-01

The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov. PMID:23680785

Implementing a Measurement Feedback System: A Tale of Two Sites

PubMed Central

Douglas, Susan R.; Vides De Andrade, Ana Regina; Tomlinson, Michele; Gleacher, Alissa; Olin, Serene; Hoagwood, Kimberly

2015-01-01

A randomized experiment was conducted in two outpatient clinics evaluating a measurement feedback system called contextualized feedback systems. The clinicians of 257 Youth 11–18 received feedback on progress in mental health symptoms and functioning either every 6 months or as soon as the youth’s, clinician’s or caregiver’s data were entered into the system. The ITT analysis showed that only one of the two participating clinics (Clinic R) had an enhanced outcome because of feedback, and only for the clinicians’ ratings of youth symptom severity on the SFSS. A dose–response effect was found only for Clinic R for both the client and clinician ratings. Implementation analyses showed that Clinic R had better implementation of the feedback intervention. Clinicians’ questionnaire completion rate and feedback viewing at Clinic R were 50 % higher than clinicians at Clinic U. The discussion focused on the differences in implementation at each site and how these differences may have contributed to the different outcomes of the experiment. PMID:25876736

Rapid on-site detection of ephedrine and its analogues used as adulterants in slimming dietary supplements by TLC-SERS.

PubMed

Lv, Diya; Cao, Yan; Lou, Ziyang; Li, Shujin; Chen, Xiaofei; Chai, Yifeng; Lu, Feng

2015-02-01

Ephedrine and its analogues are in the list of prohibited substance in adulteration to botanical dietary supplements (BDS) for their uncontrollable stimulating side effects. However, they were always adulterated illegally in BDS to promote losing weight. In order to avoid detection, various kinds of ephedrine analogues were added rather than ephedrine itself. This has brought about great difficulties in authentication of BDS. In this study, we put forward for the first time a method which combined thin-layer chromatography (TLC) and surface-enhanced Raman scattering (SERS) to directly identify trace adulterant. Ephedrine, pseudoephedrine, methylephedrine, and norephedrine were mixed and used in this method to develop an analytical model. As a result, the four analogues were separated efficiently in TLC analysis, and trace-components and low-background SERS detection was realized. The limit of detection (LOD) of the four analogues was 0.01 mg/mL. Eight common Raman peaks (△υ = 620, 1003, 1030, 1159, 1181, 1205, 1454, 1603 cm(-1)) were extracted experimentally and statistically to characterize the common feature of ephedrine analogues. A TLC-SERS method coupled with common-peak model was adopted to examine nine practical samples, two of which were found to be adulterated with ephedrine analogues. Identification results were then confirmed by UPLC-QTOF/MS analysis. The proposed method was simple, rapid, and accurate and can also be employed to trace adulterant identification even when there are no available reference derivatives on-site or unknown types of ephedrine analogues are adulterated.

Evaluation of HART MetroRapid BRT.

DOT National Transportation Integrated Search

2015-08-01

This report is a limited scope evaluation of the MetroRapids first two years of operation. The : MetroRapid represents Hillsborough Area Regional Transits first foray into bus rapid transit. Built at a : total cost of $34.75 million, or $1.98 m...

Preliminary Geotechnical Investigation of Two Basaltic Landslide Sites in Mauritius, Offshore Africa

NASA Astrophysics Data System (ADS)

Dabycharun, Bhoopendra; Kuwano, Takeshi; Ichikawa, Kensuke; Fukuoka, Hiroshi

2016-04-01

Landslide hazards in developing areas in Mauritius became a great challenge as well as a fundamental concern for the government and the citizen of the country. In recent years, landslide disasters have caused losses of both public and private properties. In 2005, a large-scale landslide at Chitrakoot affected 54 houses and infrastructures, and it was reactivated in 2006, damaging another 14 houses. Vallee Pitot landslide is frequently reactivated in these years and threatening several houses in densely-populated zone. Although the long-term annual precipitation show slightly decreasing trend, number of tropical cyclone over Mauritius is clearly increasing at least in the past 3 decades. Being of volcanic origin, Mauritius has observed dramatic and quick weathering of the soil which may partly contributes to creating landslide-prone geo-environment. This study focuses on the preliminary geotechnical investigation of the above-mentioned two basaltic landslide areas in Mauritius. Recent investigation was conducted jointly by JICA (Japan International Cooperation Agency) and Ministry of Public Infrastructure and Land Transport of Government of Mauritius on both sites from 2012 to 2015 to survey the landslide surface and to implement countermeasures works. In the field investigation, aerial photo interpretation was used to investigate the zone of cracks and scarps for both sites. The landslide areas for Chitrakoot and Vallee Pitot were estimated to 1.8 km2 and 5,000 m2 respectively. Both sites are located in the highly populated area in the capital city of Mauritius. The geological features of the sites were studied with the borehole core logging data obtained from 6 boreholes and it was found that possible sliding surface was observed in the colluvium layer consisting of gravels and stiff silty-clays, at depths from 6 to 10 m below the ground surface. The rate of landslide movement during heavy rainfall amount exceeding 100 mm/hr was elaborated with past records of

Equivalence of two approaches for modeling ion permeation through a transmembrane channel with an internal binding site

NASA Astrophysics Data System (ADS)

Zhou, Huan-Xiang

2011-04-01

Ion permeation through transmembrane channels has traditionally been modeled using two different approaches. In one approach, the translocation of the permeant ion through the channel pore is modeled as continuous diffusion and the rate of ion transport is obtained from solving the steady-state diffusion equation. In the other approach, the translocation of the permeant ion through the pore is modeled as hopping along a discrete set of internal binding sites and the rate of ion transport is obtained from solving a set of steady-state rate equations. In a recent work [Zhou, J. Phys. Chem. Lett. 1, 1973 (2010)], the rate constants for binding to an internal site were further calculated by modeling binding as diffusion-influenced reactions. That work provided the foundation for bridging the two approaches. Here we show that, by representing a binding site as an energy well, the two approaches indeed give the same result for the rate of ion transport.

Two distinct modes of metal ion binding in the nuclease active site of a viral DNA-packaging terminase: insight into the two-metal-ion catalytic mechanism

PubMed Central

Zhao, Haiyan; Lin, Zihan; Lynn, Anna Y.; Varnado, Brittany; Beutler, John A.; Murelli, Ryan P.; Le Grice, Stuart F. J.; Tang, Liang

2015-01-01

Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg2+. A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 Å. Such proximity of the two metal ions may play an essential role in catalysis by generating a highly positive electrostatic niche to enable formation of the negatively charged pentacovalent phosphate transition state, and provides the structural basis for distinguishing Mg2+ from Ca2+. Using a metal ion chelator β-thujaplicinol as a molecular probe, we observed a second mode of metal ion binding at the active site, mimicking the DNA binding state. Arrangement of the active site residues differs drastically from those in RNase H-like nucleases, suggesting a drifting of the active site configuration during evolution. The two distinct metal ion binding modes unveiled mechanistic details of the two-metal-ion catalysis at atomic resolution. PMID:26450964

Remote sensing-based estimation of annual soil respiration at two contrasting forest sites

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

Huang, Ni; Gu, Lianhong; Black, T. Andrew

Here, soil respiration (R s), an important component of the global carbon cycle, can be estimated using remotely sensed data, but the accuracy of this technique has not been thoroughly investigated. In this study, we proposed a methodology for the remote estimation of annual R s at two contrasting FLUXNET forest sites (a deciduous broadleaf forest and an evergreen needleleaf forest). A version of the Akaike's information criterion was used to select the best model from a range of models for annual R s estimation based on the remotely sensed data products from the Moderate Resolution Imaging Spectroradiometer and root-zonemore » soil moisture product derived from assimilation of the NASA Advanced Microwave Scanning Radiometer soil moisture products and a two-layer Palmer water balance model. We found that the Arrhenius-type function based on nighttime land surface temperature (LST-night) was the best model by comprehensively considering the model explanatory power and model complexity at the Missouri Ozark and BC-Campbell River 1949 Douglas-fir sites.« less

Desert tortoise (Gopherus agassizii) survival at two eastern Mojave Desert sites: Death by short-term drought?

USGS Publications Warehouse

Longshore, Kathleen M.; Jaeger, Jef R.; Sappington, J. Mark

2003-01-01

Survival of adult Desert Tortoises (Gopherus agassizii) appears related to site-specific variation in precipitation and productivity of annual plants. We studied adult tortoise survival rates at two closely situated, but physiographically different, sites in the eastern Mojave Desert over a nine-year period (spring 1992 to spring 2001). Survival rates were initially derived from population surveys conducted over a three-year period and by radio-telemetry monitoring over a seven-year period beginning in 1994. After a period of initial stability, survival rates on the two sites diverged over the study period, and seven-year survival rates estimated from radio-telemetry monitoring were 0.900 and 0.269, respectively. A die-off in 1996 on the latter site appears to have been triggered by a period of drought, which began in the summer of 1995, coupled with a failure of annual vegetation production in 1996. Depressed survival rates on this site were associated with drought conditions during three of four years. Although the decline had the appearance of an epizootic, there were no clinical signs of disease. Relatively short-term drought, combined with little or no annual biomass, appears to have caused severe reductions in tortoise survival. If periods of drought-induced low survival are common over relatively small areas, then source-sink population dynamics may be an important factor determining tortoise population densities.

Detection of hepatitis A viral antigen by radioimmunoassay

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

Hollinger, F.B.; Bradley, D.W.; Maynard, J.E.

1975-11-01

With coded samples, the effectiveness and specificity of a micro-SPIRA procedure for rapidly and quantitatively detecting type A hepatitis-associated antigen in large numbers of specimens from infected liver, stool, or serum has been demonstrated. Samples which were judged to be negative by IEM were found to contain significant levels of HAV antigen by this immunoradiometric technique. The detection of significant levels of HAV antigen in infected chimpanzees supports epidemiologic evidence of viremia during the acute stage of the disease. The results of this study suggest that the diagnosis of type A hepatitis by a convention serologic procedure may now bemore » at hand. (auth)« less

Establishment of an Arbitrary PCR for Rapid Identification of Tn917 Insertion Sites in Staphylococcus epidermidis: Characterization of Biofilm-Negative and Nonmucoid Mutants

PubMed Central

Knobloch, Johannes K.-M.; Nedelmann, Max; Kiel, Kathrin; Bartscht, Katrin; Horstkotte, Matthias A.; Dobinsky, Sabine; Rohde, Holger; Mack, Dietrich

2003-01-01

Transposon mutagenesis with the Enterococcus faecalis transposon Tn917 is a genetic approach frequently used to identify genes related with specific phenotypes in gram-positive bacteria. We established an arbitrary PCR for the rapid and easy identification of Tn917 insertion sites in Staphylococcus epidermidis with six independent, well-characterized biofilm-negative Tn917 transposon mutants, which were clustered in the icaADBC gene locus or harbor Tn917 in the regulatory gene rsbU. For all six of these mutants, short chromosomal DNA fragments flanking both transposon ends could be amplified. All fragments were sufficient to correctly identify the Tn917 insertion sites in the published S. epidermidis genomes. By using this technique, the Tn917 insertion sites of three not-yet-characterized biofilm-negative or nonmucoid mutants were identified. In the biofilm-negative and nonmucoid mutant M12, Tn917 is inserted into a gene homologous to the regulatory gene purR of Bacillus subtilis and Staphylococcus aureus. The Tn917 insertions of the nonmucoid but biofilm-positive mutants M16 and M20 are located in genes homologous to components of the phosphoenolpyruvate-sugar phosphotransferase system (PTS) of B. subtilis, S. aureus, and Staphylococcus carnosus, indicating an influence of the PTS on the mucoid phenotype in S. epidermidis. PMID:14532029

Rapid orthodontic treatment after the ridge-splitting technique--a combined surgical-orthodontic approach for implant site development: case report.

PubMed

Amato, Francesco; Mirabella, A Davide; Borlizzi, Diego

2012-08-01

This article presents a clinical case of bilateral partial edentulism in the posterior mandible with severe horizontal and moderate vertical bone atrophy. A new technique using rapid orthodontics after ridge splitting is presented. The split-crest technique was carried out using piezosurgical instruments in the first molar and second premolar areas to widen the bone crest and open a channel for tooth movement. Immediately after, orthodontic appliances were used to move the first premolars distally and the second molars mesially into the surgical site. The rationale was to facilitate and accelerate orthodontic movement of the teeth, which is otherwise difficult in a cortical knife-edged ridge. The bone defect was filled with the alveolar bone of the adjacent teeth that were moved into the surgically opened path. Adequate bone volume for implant placement was generated in the first premolar area. Implants were then inserted, and the patient was rehabilitated.

FAST TRACK COMMUNICATION: A Temperley-Lieb quantum chain with two- and three-site interactions

NASA Astrophysics Data System (ADS)

Ikhlef, Y.; Jacobsen, J. L.; Saleur, H.

2009-07-01

We study the phase diagram of a quantum chain of spin-1/2 particles whose world lines form a dense loop gas with loop weight n. In addition to the usual two-site interaction corresponding to the XXZ spin chain, we introduce a three-site interaction. The resulting model contains a Majumdar-Ghosh-like gapped phase and a new integrable point, which we solve exactly. We also locate a critical line realizing dilute O(n) criticality, without introducing explicit dilution in the loops. Our results have implications for anisotropic spin chains, as well as anyonic quantum chains.

Site-specific cleavage of the transactivation response site of human immunodeficiency virus RNA with a tat-based chemical nuclease.

PubMed Central

Jayasena, S D; Johnston, B H

1992-01-01

tat, an essential transactivator of gene transcription in the human immunodeficiency virus (HIV), is believed to activate viral gene expression by binding to the transactivation response (TAR) site located at the 5' end of all viral mRNAs. The TAR element forms a stem-loop structure containing a 3-nucleotide bulge that is the site for tat binding and is required for transactivation. Here we report the synthesis of a site-specific chemical ribonuclease based on the TAR binding domain of the HIV type 1 (HIV-1) tat. A peptide consisting of this 24-amino acid domain plus an additional C-terminal cysteine residue was chemically synthesized and covalently linked to 1,10-phenanthroline at the cysteine residue. The modified peptide binds to TAR sequences of both HIV-1 and HIV-2 and, in the presence of cupric ions and a reducing agent, cleaves these RNAs at specific sites. Cleavage sites on TAR sequences are consistent with peptide binding to the 3-nucleotide bulge, and the relative displacement of cleavage sites on the two strands suggests peptide binding to the major groove of the RNA. These results and existing evidence of the rapid cellular uptake of tat-derived peptides suggest that chemical nucleases based on tat may be useful for inactivating HIV mRNA in vivo. Images PMID:1565648

Autoradiographic evidence for two classes of mu opioid binding sites in rat brain using (/sup 125/I)FK33824

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

Rothman, R.B.; Jacobson, A.E.; Rice, K.C.

1987-11-01

Previous studies demonstrated that pretreatment of brain membranes with the irreversible mu antagonist, beta-funaltrexamine (beta-FNA), partially eliminated mu binding sites (25,35), consistent with the existence of two mu binding sites distinguished by beta-FNA. This paper tests the hypothesis that the FNA-sensitive and FNA-insensitive mu binding sites have different anatomical distributions in rat brain. Prior to autoradiographic visualization of mu binding sites, (/sup 3/H)oxymorphone, (/sup 3/H)D-ala2-MePhe4, Gly-ol5-enkephalin (DAGO), and (/sup 125/I)D-ala2-Me-Phe4-met(o)-ol)enkephalin (FK33824) were shown to selectively label mu binding sites using slide mounted sections of molded minced rat brain. As found using membranes, beta-FNA eliminated only a portion of mu bindingmore » sites. Autoradiographic visualization of mu binding sites using the mu-selective ligand (/sup 125/I)FK33824 in control and FNA-treated sections of rat brain demonstrated that the proportion of mu binding sites sensitive to beta-FNA varied across regions of the brain, particularly the dorsal thalamus, ventrobasal complex and the hypothalamus, providing anatomical data supporting the existence of two classes of mu binding sites in rat brain.« less

A Rapid Method to Test for Chloroplast DNA Involvement in Atrazine Resistance

PubMed Central

McNally, Sheila; Bettini, Priscilla; Sevignac, Mireille; Darmency, Henry; Gasquez, Jacques; Dron, Michel

1987-01-01

A point mutation in the chloroplast psbA gene at codon 264 resulting in an animo acid substitution (ser-gly) manifests itself as atrazine resistance in all recognized weed species studied to date. The single base substitution overlaps a highly conserved Mae1 restriction site which is present in susceptible but not in resistant plants. This restriction enzyme, recently commercialized, has been used to show that it is now possible to discriminate rapidly between the two biotypes without the need for DNA sequencing. Images Fig. 1 PMID:16665229

Comparison of the Sensitivity of Surface Downward Longwave Radiation to Changes in Water Vapor at Two High Elevation Sites

NASA Technical Reports Server (NTRS)

Chen, Yonghua; Naud, Catherine M.; Rangwala, Imtiaz; Landry, Christopher C.; Miller, James R.

2014-01-01

Among the potential reasons for enhanced warming rates in many high elevation regions is the nonlinear relationship between surface downward longwave radiation (DLR) and specific humidity (q). In this study we use ground-based observations at two neighboring high elevation sites in Southwestern Colorado that have different local topography and are 1.3 kilometers apart horizontally and 348 meters vertically. We examine the spatial consistency of the sensitivities (partial derivatives) of DLR with respect to changes in q, and the sensitivities are obtained from the Jacobian matrix of a neural network analysis. Although the relationship between DLR and q is the same at both sites, the sensitivities are higher when q is smaller, which occurs more frequently at the higher elevation site. There is a distinct hourly distribution in the sensitivities at both sites especially for high sensitivity cases, although the range is greater at the lower elevation site. The hourly distribution of the sensitivities relates to that of q. Under clear skies during daytime, q is similar between the two sites, however under cloudy skies or at night, it is not. This means that the DLR-q sensitivities are similar at the two sites during daytime but not at night, and care must be exercised when using data from one site to infer the impact of water vapor feedbacks at another site, particularly at night. Our analysis suggests that care should be exercised when using the lapse rate adjustment to infill high frequency data in a complex topographical region, particularly when one of the stations is subject to cold air pooling as found here.

Development of the SAFE Checklist Tool for Assessing Site-Level Threats to Child Protection: Use of Delphi Methods and Application to Two Sites in India.

PubMed

Betancourt, Theresa S; Zuilkowski, Stephanie S; Ravichandran, Arathi; Einhorn, Honora; Arora, Nikita; Bhattacharya Chakravarty, Aruna; Brennan, Robert T

2015-01-01

The child protection community is increasingly focused on developing tools to assess threats to child protection and the basic security needs and rights of children and families living in adverse circumstances. Although tremendous advances have been made to improve measurement of individual child health status or household functioning for use in low-resource settings, little attention has been paid to a more diverse array of settings in which many children in adversity spend time and how context contributes to threats to child protection. The SAFE model posits that insecurity in any of the following fundamental domains threatens security in the others: Safety/freedom from harm; Access to basic physiological needs and healthcare; Family and connection to others; Education and economic security. Site-level tools are needed in order to monitor the conditions that can dramatically undermine or support healthy child growth, development and emotional and behavioral health. From refugee camps and orphanages to schools and housing complexes, site-level threats exist that are not well captured by commonly used measures of child health and well-being or assessments of single households (e.g., SDQ, HOME). The present study presents a methodology and the development of a scale for assessing site-level child protection threats in various settings of adversity. A modified Delphi panel process was enhanced with two stages of expert review in core content areas as well as review by experts in instrument development, and field pilot testing. Field testing in two diverse sites in India-a construction site and a railway station-revealed that the resulting SAFE instrument was sensitive to the differences between the sites from the standpoint of core child protection issues.

Harpacticoid copepod diversity at two physically reworked sites in the deep sea

NASA Astrophysics Data System (ADS)

Thistle, David

1998-01-01

Grassle's and Jumars' theories of diversity maintenance in the quiescent deep sea view millimeter-to-meter-scale patchiness (mostly of biological origin) as crucial. In other deep-sea regions, episodes of strong near-bottom flow put the surficial sediment layers into motion, obliterating the biologically produced, millimeter-to-meter-scale patchiness. Under these theories, sites eroded so frequently that such patchiness is eliminated almost as soon as it is created should have lower diversities than sites where the time between erosive events is sufficient for this type of patchiness to be produced and exploited. I tested this prediction by comparing the diversities of harpacticoid copepods at two sites on Fieberling Guyot to determine whether Grassle's and Jumars' theories can be extended to the portion of the deep sea that experiences episodic erosive flows. At White Sand Swale (=WSS) (32°27.581'N, 127°47.839'W), strong near-bottom flows erode the surficial sediment daily. At Sea Pen Rim (=SPR) (32°27.631'N, 127°49.489'W), strong near-bottom flows erode the surficial sediment a few times annually. Contrary to expectation, the diversity of harpacticoid copepods was significantly greater at WSS than at SPR. However, the erosion regime at WSS may create small-scale patchiness that promotes harpacticoid diversity.

Sensitivity and specificity of HIV rapid tests used for research and voluntary counselling and testing.

PubMed

Anzala, O; Sanders, E J; Kamali, A; Katende, M; Mutua, G N; Ruzagira, E; Stevens, G; Simek, M; Price, M

2008-10-01

HIV rapid tests (RT) are a quick and non-technically demanding means to perform HIV voluntary counselling and testing (VCT) but understanding their limitations is vital to delivering quality VCT. To determine the sensitivity and specificity of HIV rapid tests used for research and voluntary counselling and testing at four sites in East Africa. Cross-sectional study. Masaka District, Uganda; a sugar plantation in Kakira, Uganda; Coastal Villages in the Kilifi District of Kenya; and the Urban slum of Kangemi located West of Nairobi, Kenya. Six thousands two hundred and fifty five consenting volunteers were enrolled into the study, and 675 prevalent HIV infections were identified. The RT sensitivity tended to be high for all assays at all sites (97.63-100%) with the exception of the Uni-Gold assay (90.24% in Kangemi, 96.58% in Kilifi). Twenty four RT results were recorded as 'weak positives', 22 (92%) of which were negative by ELISA. There was a high rate of RT false positives in Uganda (positive predictive values ranging from 45.70% to 86.62%). The sensitivity and specificity of the RT varied significantly across sites. The rate of RT misclassification in Uganda suggests that a multiple test algorithm may be preferable to a single test as screener for HIV VCT.

Fire Impact on Surface Fuels and Carbon Emissions in Scots pine Logged Sites of Siberia

NASA Astrophysics Data System (ADS)

Ivanova, G. A.; Kukavskaya, E. A.; Bogorodskaya, A. V.; Ivanov, V. A.; Zhila, S. V.; Conard, S. G.

2012-04-01

Forest fire and large-scale forest harvesting are the two major disturbances in the Russian boreal forests. Non-recovered logged sites total about a million hectares. Logged sites are characterized by higher fire hazard than forest sites due great amounts of logging slash, which dries out much more rapidly compared to understory fuels. Moreover, most logging sites can be easily accessed by local population. Both legal and illegal logging are also increasing rapidly in many forest areas of Siberia. Fire effects on forest overstory, subcanopy woody layer, and ground vegetation biomass were estimated on logged vs. unlogged sites in the Central Siberia region in 2009-2012 as a part of the project "The Influence of Changing Forestry Practices on the Effects of Wildfire and on Interactions Between Fire and Changing Climate in Central Siberia" supported by NASA (NEESPI). Dead down woody fuels are significantly less at unburned/logged area of dry southern regions compared to more humid northern regions. Fuel consumption was typically less in spring fires than during summer fires. Fire-caused carbon emissions on logged sites appeared to be twice that on unlogged sites. Soil respiration is less at logged areas compared to undisturbed forest. After fire soil respiration decreases both at logged and unlogged areas. arbon emissions from fire and post-fire ecosystem damage on logged sites are expected to increase under changing climate conditions and as a result of anticipated increases in future forest harvesting in Siberia.

A Rapid and Quantitative Recombinase Activity Assay

USDA-ARS?s Scientific Manuscript database

We present here a comparison between the recombinase systems FLP-FRT and Cre-loxP. A transient excision based dual luciferase expression assay is used for its rapid and repeatable nature. The detection system was designed within an intron to remove the remaining recombinase recognition site and no...

Distribution of diffuse flow megafauna in two sites on the Eastern Lau Spreading Center, Tonga

NASA Astrophysics Data System (ADS)

Podowski, Elizabeth L.; Moore, Tom S.; Zelnio, Kevin A.; Luther, George W., III; Fisher, Charles R.

2009-11-01

Hydrothermal vent environments are characterized by large gradients of toxic chemicals and high temperatures, which play a significant role in defining species' distributions. We used high-resolution imagery and spatially explicit in-situ physico-chemical measurements analyzed within a Geographic Information System (GIS) in order to characterize the spatial relations among different groups of megafauna, temperature, and chemistry within two discrete vent communities (40 and 50 m 2) on the Eastern Lau Spreading Center (ELSC). Chemical (sulfide and O 2 concentrations) and temperature data were obtained from approximately 75 different locations within each community using in-situ instruments. All data were integrated into a GIS, which served as a visualization tool and enabled the data to be analyzed in a spatial context. Our results confirm the importance of abiotic variables in defining the distributions of some fauna and elucidate several biological associations that are consistent between the two communities. The provannid snail, Alviniconcha spp., appears to actively avoid temperatures above 32-46 °C and/or sulfide concentrations exceeding approximately 260 μM. Slightly higher average sulfide concentrations and temperatures were measured among aggregations of Ifremeria nautilei compared to aggregations of the mussel Bathymodiolus brevior; however, the presence of mixed aggregations of the two species indicates an overlap in requirements. The brachyuran crab, Austinograea spp., was consistently observed directly on symbiont-containing species, particularly Alviniconcha spp. The solitary snail, Eosipho desbruyeresi, was rarely observed on biological substrata, but was often (60% of its population at the most active site) within 5 cm of symbiont-containing fauna, indicating a tolerance and preference for proximity to areas of high productivity. Densities and coverage of species differed substantially between the two communities despite high species overlap

Vertical Seafloor Geodesy at Two Mid-ocean Ridge Sites: Recent Results and Lessons Learned (Invited)

NASA Astrophysics Data System (ADS)

Nooner, S. L.; Chadwick, B.; Webb, S. C.

2013-12-01

Precise measurements of ambient seawater pressure can be used as a proxy for seafloor depth and can be used to track vertical movements of the seafloor with time. We have employed two measurement techniques simultaneously to track both episodic and long-term deformation signals at active volcanic sites on mid-ocean ridges. The first technique is through the use of Bottom Pressure Recorders (BPRs), which are instruments that sit on the seafloor recording pressure continuously for 1-3 years until they are recovered for data download and battery replacement. BPRs are essential for measuring episodic events but suffer from slow instrument drift that is indistinguishable from long-term deformation. To track the long-term deformation signals and quantify drift in the BPRs, we developed a technique using ROV deployed Mobile Pressure Recorders (MPRs). In 2000 we began making MPR measurements on top of seafloor benchmarks at Axial Seamount on the Juan de Fuca Ridge after it's 1998 eruption. The combined BPR and MPR measurements have allowed us to observe and quantify an entire eruption cycle at the intermediate spreading Axial Seamount. From 2008-2011 we established another geodetic network at the fast spreading East Pacific Rise (EPR) at the site of a 2005/2006 eruption near 9°50' N. Here we show the results to date from both Axial Seamount and the EPR, and discuss lessons learned during the last 14 years. Measurements at Axial Seamount were all made using ROVs, while measurements at the EPR were made using the manned submersible Alvin in 2008 and 2009 and the Jason ROV in 2011. Our observations at Axial Seamount have enabled us to characterize its eruption cycle into 4 distinct phases: 1.) pre-eruption short-term rapid inflation, 2.) co-eruption deflation, 3.) rapid post-eruption reinflation, and 4.) subsequent long-term steady inflation. The transition between the phases 3 and 4 was not captured after the 1998 eruption and is an important impetus for continued

Physical, chemical, and biological data for two sites on the upper Kenai River, Alaska, 1998

USGS Publications Warehouse

Dorava, Joseph M.; Ness, Lee

1999-01-01

Water-quality data were collected and stream characteristics were documented from two sites along the upper Kenai River in the Kenai National Wildlife Refuge, Alaska. These data were collected to describe the current status of the sites and to provide baseline information from which changes in the future could be evaluated. Physical characteristics included channel geometry surveys, and measurements of channel widths and water discharge at each site. Chemical data included stream water temperature, dissolved-oxygen concentration, pH, specific conductance, E. coli and fecal coliform counts, and nutrient concentration. Data on concentrations of trace elements and various organic compounds in bed sediments and the tissue of slimy sculpin were also collected. Biological characteristics were evaluated using measurements of the bacteria, benthic macroinvertebrate, and fish communities.

Analysis of variable sites between two complete South China tiger (Panthera tigris amoyensis) mitochondrial genomes.

PubMed

Zhang, Wenping; Yue, Bisong; Wang, Xiaofang; Zhang, Xiuyue; Xie, Zhong; Liu, Nonglin; Fu, Wenyuan; Yuan, Yaohua; Chen, Daqing; Fu, Danghua; Zhao, Bo; Yin, Yuzhong; Yan, Xiahui; Wang, Xinjing; Zhang, Rongying; Liu, Jie; Li, Maoping; Tang, Yao; Hou, Rong; Zhang, Zhihe

2011-10-01

In order to investigate the mitochondrial genome of Panthera tigris amoyensis, two South China tigers (P25 and P27) were analyzed following 15 cymt-specific primer sets. The entire mtDNA sequence was found to be 16,957 bp and 17,001 bp long for P25 and P27 respectively, and this difference in length between P25 and P27 occurred in the number of tandem repeats in the RS-3 segment of the control region. The structural characteristics of complete P. t. amoyensis mitochondrial genomes were also highly similar to those of P. uncia. Additionally, the rate of point mutation was only 0.3% and a total of 59 variable sites between P25 and P27 were found. Out of the 59 variable sites, 6 were located in 6 different tRNA genes, 6 in the 2 rRNA genes, 7 in non-coding regions (one located between tRNA-Asn and tRNA-Tyr and six in the D-loop), and 40 in 10 protein-coding genes. COI held the largest amount of variable sites (9 sites) and Cytb contained the highest variable rate (0.7%) in the complete sequences. Moreover, out of the 40 variable sites located in 10 protein-coding genes, 12 sites were nonsynonymous.

Solution of effective Hamiltonian of impurity hopping between two sites in a metal

NASA Astrophysics Data System (ADS)

Ye, Jinwu

1998-03-01

We analyze in detail all the possible fixed points of the effective Hamiltonian of a non-magnetic impurity hopping between two sites in a metal obtained by Moustakas and Fisher(MF). We find a line of non-fermi liquid fixed points which continuously interpolates between the 2-channel Kondo fixed point(2CK) and the one channel, two impurity Kondo (2IK) fixed point. There is one relevant direction with scaling dimension 1/2 and one leading irrelevant operator with dimension 3/2. There is also one marginal operator in the spin sector moving along this line. The additional non-fermi liquid fixed point found by MF has the same symmetry as the 2IK, it has two relevant directions with scaling dimension 1/2, therefore also unstable. The system is shown to flow to a line of fermi-liquid fixed points which continuously interpolates between the non-interacting fixed point and the 2 channel spin-flavor Kondo fixed point (2CSFK) discussed by the author previously. The effect of particle-hole symmetry breaking is discussed. The effective Hamiltonian in the external magnetic field is analysed. The scaling functions for the physical measurable quantities are derived in the different regimes; their predictions for the experiments are given. Finally the implications are given for a non-magnetic impurity hopping around three sites with triangular symmetry discussed by MF.

Remote sensing-based estimation of annual soil respiration at two contrasting forest sites

DOE PAGES

Gu, Lianhong; Huang, Ni; Black, T. Andrew; ...

2015-11-23

Soil respiration (R s), an important component of the global carbon cycle, can be estimated using remotely sensed data, but the accuracy of this technique has not been thoroughly investigated. In this article, we proposed a methodology for the remote estimation of annual R s at two contrasting FLUXNET forest sites (a deciduous broadleaf forest and an evergreen needleleaf forest).

Evaluation of a Single-Beam Sonar System to Map Seagrass at Two Sites in Northern Puget Sound, Washington

USGS Publications Warehouse

Stevens, Andrew W.; Lacy, Jessica R.; Finlayson, David P.; Gelfenbaum, Guy

2008-01-01

Seagrass at two sites in northern Puget Sound, Possession Point and nearby Browns Bay, was mapped using both a single-beam sonar and underwater video camera. The acoustic and underwater video data were compared to evaluate the accuracy of acoustic estimates of seagrass cover. The accuracy of the acoustic method was calculated for three classifications of seagrass observed in underwater video: bare (no seagrass), patchy seagrass, and continuous seagrass. Acoustic and underwater video methods agreed in 92 percent and 74 percent of observations made in bare and continuous areas, respectively. However, in patchy seagrass, the agreement between acoustic and underwater video was poor (43 percent). The poor agreement between the two methods in areas with patchy seagrass is likely because the two instruments were not precisely colocated. The distribution of seagrass at the two sites differed both in overall percent vegetated and in the distribution of percent cover versus depth. On the basis of acoustic data, seagrass inhabited 0.29 km2 (19 percent of total area) at Possession Point and 0.043 km2 (5 percent of total area) at the Browns Bay study site. The depth distribution at the two sites was markedly different. Whereas the majority of seagrass at Possession Point occurred between -0.5 and -1.5 m MLLW, most seagrass at Browns Bay occurred at a greater depth, between -2.25 and -3.5 m MLLW. Further investigation of the anthropogenic and natural factors causing these differences in distribution is needed.

A DNAzyme requiring two different metal ions at two distinct sites

PubMed Central

Zhou, Wenhu; Zhang, Yupei; Huang, Po-Jung Jimmy; Ding, Jinsong; Liu, Juewen

2016-01-01

Most previously reported RNA-cleaving DNAzymes require only a single divalent metal ion for catalysis. We recently reported a general trivalent lanthanide-dependent DNAzyme named Ce13d. This work shows that Ce13d requires both Na+ and a trivalent lanthanide (e.g. Ce3+), simultaneously. This discovery is facilitated by the sequence similarity between Ce13d and a recently reported Na+-specific DNAzyme, NaA43. The Ce13d cleavage rate linearly depends on the concentration of both metal ions. Sensitized Tb3+ luminescence and DMS footprinting experiments indicate that the guanines in the enzyme loop are important for Na+-binding. The Na+ dissociation constants of Ce13d measured from the cleavage activity assay, Tb3+ luminescence and DMS footprinting are 24.6, 16.3 and 47 mM, respectively. Mutation studies indicate that the role of Ce3+ might be replaced by G23 in NaA43. Ce3+ functions by stabilizing the transition state phosphorane, thus promoting cleavage. G23 competes favorably with low concentration Ce3+ (below 1 μM). The G23-to-hypoxanthine mutation suggests the N1 position of the guanine as a hydrogen bond donor. Together, Ce13d has two distinct metal binding sites, each fulfilling a different role. DNAzymes can be quite sophisticated in utilizing metal ions for catalysis and molecular recognition, similar to protein metalloenzymes. PMID:26657636

Two-site jumps in dimethyl sulfone studied by one- and two-dimensional 17O NMR spectroscopy

NASA Astrophysics Data System (ADS)

Beerwerth, J.; Storek, M.; Greim, D.; Lueg, J.; Siegel, R.; Cetinkaya, B.; Hiller, W.; Zimmermann, H.; Senker, J.; Böhmer, R.

2018-03-01

Polycrystalline dimethyl sulfone is studied using central-transition oxygen-17 exchange NMR. The quadrupolar and chemical shift tensors are determined by combining quantum chemical calculations with line shape analyses of rigid-lattice spectra measured for stationary and rotating samples at several external magnetic fields. Quantum chemical computations predict that the largest principal axes of the chemical shift anisotropy and electrical field gradient tensors enclose an angle of about 73°. This prediction is successfully tested by comparison with absorption spectra recorded at three different external magnetic fields. The experimental one-dimensional motionally narrowed spectra and the two-dimensional exchange spectrum are compatible with model calculations involving jumps of the molecules about their two-fold symmetry axis. This motion is additionally investigated by means of two-time stimulated-echo spectroscopy which allows for a determination of motional correlation functions over a wider temperature range than previously reported using carbon and deuteron NMR. On the basis of suitable second-order quadrupolar frequency distributions, sin-sin stimulated-echo amplitudes are calculated for a two-site model in the limit of vanishing evolution time and compared with experimental findings. The present study thus establishes oxygen-17 NMR as a powerful method that will be particularly useful for the study of solids and liquids devoid of nuclei governed by first-order anisotropies.

Using Remotely Sensed Data for Documentation of Archaeological Sites in Northeastern Mesopotamia

NASA Astrophysics Data System (ADS)

Matoušková, E.; Starková, L.; Pavelka, K.; Nováček, K.; Šedina, J.; Faltýnová, M.; Housarová, E.

2016-06-01

This paper introduces two archaeological sites documented during the MULINEM (The Medieval Urban Landscape in Northeastern Mesopotamia) project. This project investigates the Late Sasanian and Islamic urban network in the land of Erbil, a historic province of Hidyab (Adiabene) that is located in northern Iraq. The investigated sites are the two deserted cities of Makhmúr al-Quadíma and Al-Hadítha. It is assumed that these two sites used to form large cities with high business and cultural importance in the medieval period. The archaeological locations are endangered by various threats.The Al-Hadítha site seems to be under the control of the „Islamic state" at the moment and Makhmúr al-Quadíma is located just next to the town of new Makhmúr that expands rapidly and without complex urban plans. Documentation of the archaeological sites has been done by using remotely sensed methods together with in-situ measurements (where available). FORMOSAT-2 data that has been gained through a research announcement: Free FORMOSAT-2 satellite imagery and when combined with other sources (recent and historical data) it provides a powerful documentation tool. In-situ RPAS measurements and a DTM creation furnish a new source of highly valuable information. Influence of the political and security situation in Al-Hadítha will be analysed.

Development of the SAFE Checklist Tool for Assessing Site-Level Threats to Child Protection: Use of Delphi Methods and Application to Two Sites in India

PubMed Central

Betancourt, Theresa S.; Zuilkowski, Stephanie S.; Ravichandran, Arathi; Einhorn, Honora; Arora, Nikita; Bhattacharya Chakravarty, Aruna; Brennan, Robert T.

2015-01-01

Background The child protection community is increasingly focused on developing tools to assess threats to child protection and the basic security needs and rights of children and families living in adverse circumstances. Although tremendous advances have been made to improve measurement of individual child health status or household functioning for use in low-resource settings, little attention has been paid to a more diverse array of settings in which many children in adversity spend time and how context contributes to threats to child protection. The SAFE model posits that insecurity in any of the following fundamental domains threatens security in the others: Safety/freedom from harm; Access to basic physiological needs and healthcare; Family and connection to others; Education and economic security. Site-level tools are needed in order to monitor the conditions that can dramatically undermine or support healthy child growth, development and emotional and behavioral health. From refugee camps and orphanages to schools and housing complexes, site-level threats exist that are not well captured by commonly used measures of child health and well-being or assessments of single households (e.g., SDQ, HOME). Methods The present study presents a methodology and the development of a scale for assessing site-level child protection threats in various settings of adversity. A modified Delphi panel process was enhanced with two stages of expert review in core content areas as well as review by experts in instrument development, and field pilot testing. Results Field testing in two diverse sites in India—a construction site and a railway station—revealed that the resulting SAFE instrument was sensitive to the differences between the sites from the standpoint of core child protection issues. PMID:26540159

Two classes of binding sites for [3H]substance P in rat cerebral cortex.

PubMed

Geraghty, D P; Burcher, E

1993-01-22

The binding characteristics of [3H]substance P ([3H]SP) were investigated in membranes prepared from rat cerebral cortex. Binding of [3H]SP reached equilibrium after 50 min at 25 degrees C and was saturable at 8 nM. Saturation data could be resolved into high affinity (equilibrium dissociation constant, Kd, 0.22 nM) and low affinity sites (Kd, 2.65 nM). The low affinity sites were more numerous than the high affinity sites, with a ratio of 4:1. The non-hydrolyzable GTP analogue GppNHp had no effect on binding, indicating that the high and low affinity sites are not guanine nucleotide-regulated states of the same (NK-1) receptor. The low affinity sites are unlikely to represent NK-3 receptors since coincubation with the selective NK-3 receptor agonist senktide did not alter the biphasic nature of [3H]SP binding. The rank order of potency for inhibition of [3H]SP (2 nM) binding was SP > or = [Sar9, Met(O2)11]-SP > or = physalaemin > SP(3-11) > NP gamma = [Ala3]-SP > or = SP(4-11) > or = NPK > or = SP(5-11) > or = NKB approximately NKA > SP(1-9), compatible with binding to an NK-1 site. N-terminal fragments and non-amidated analogues were ineffective competitors for [3H]SP binding. However, competition data for several peptides including substance P (SP) and the NK-1 selective agonist [Sar9, Met(O2)11]-SP could be resolved into two components.(ABSTRACT TRUNCATED AT 250 WORDS)

SIMULATIONS OF TWO-WELL TRACER TESTS IN STRATIFIED AQUIFERS AT THE CHALK RIVER AND THE MOBILE SITES

EPA Science Inventory

A simulation of two-well injection-withdrawal tracer tests in stratified granular aquifers is presented for two widely separated sites substantially different in terms of vertical distributions of hydraulic conductivity, well spacings, flow rates, test durations and tracer travel...

Rapid and efficient introduction of a foreign gene into bacterial artificial chromosome-cloned varicella vaccine by Tn7-mediated site-specific transposition

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

Somboonthum, Pranee; Koshizuka, Tetsuo; Okamoto, Shigefumi

2010-06-20

Using a rapid and reliable system based on Tn7-mediated site-specific transposition, we have successfully constructed a recombinant Oka varicella vaccine (vOka) expressing the mumps virus (MuV) fusion protein (F). The backbone of the vector was our previously reported vOka-BAC (bacterial artificial chromosome) genome. We inserted the transposon Tn7 attachment sequence, LacZ{alpha}-mini-attTn7, into the region between ORF12 and ORF13 to generate a vOka-BAC-Tn genome. The MuV-F expressing cassette was transposed into the vOka-BAC genome at the mini-attTn7 transposition site. MuV-F protein was expressed in recombinant virus, rvOka-F infected cells. In addition, the MuV-F protein was cleaved in the rvOka-F infected cellsmore » as in MuV-infected cells. The growth of rvOka-F was similar to that of the original recombinant vOka without the F gene. Thus, we show that Tn7-mediated transposition is an efficient method for introducing a foreign gene expression cassette into the vOka-BAC genome as a live virus vector.« less

The cost-effectiveness of rapid HIV testing in substance abuse treatment: results of a randomized trial.

PubMed

Schackman, Bruce R; Metsch, Lisa R; Colfax, Grant N; Leff, Jared A; Wong, Angela; Scott, Callie A; Feaster, Daniel J; Gooden, Lauren; Matheson, Tim; Haynes, Louise F; Paltiel, A David; Walensky, Rochelle P

2013-02-01

The President's National HIV/AIDS Strategy calls for coupling HIV screening and prevention services with substance abuse treatment programs. Fewer than half of US community-based substance abuse treatment programs make HIV testing available on-site or through referral. We measured the cost-effectiveness of three HIV testing strategies evaluated in a randomized trial conducted in 12 community-based substance abuse treatment programs in 2009: off-site testing referral, on-site rapid testing with information only, on-site rapid testing with risk-reduction counseling. Data from the trial included patient demographics, prior testing history, test acceptance and receipt of results, undiagnosed HIV prevalence (0.4%) and program costs. The Cost-Effectiveness of Preventing AIDS Complications (CEPAC) computer simulation model was used to project life expectancy, lifetime costs, and quality-adjusted life years (QALYs) for HIV-infected individuals. Incremental cost-effectiveness ratios (2009 US $/QALY) were calculated after adding costs of testing HIV-uninfected individuals; costs and QALYs were discounted at 3% annually. Referral for off-site testing is less efficient (dominated) compared to offering on-site testing with information only. The cost-effectiveness ratio for on-site testing with information is $60,300/QALY in the base case, or $76,300/QALY with 0.1% undiagnosed HIV prevalence. HIV risk-reduction counseling costs $36 per person more without additional benefit. A strategy of on-site rapid HIV testing offer with information only in substance abuse treatment programs increases life expectancy at a cost-effectiveness ratio <$100,000/QALY. Policymakers and substance abuse treatment leaders should seek funding to implement on-site rapid HIV testing in substance abuse treatment programs for those not recently tested. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

The Cost-effectiveness of Rapid HIV Testing in Substance Abuse Treatment: Results of a Randomized Trial*

PubMed Central

Schackman, Bruce R.; Metsch, Lisa R.; Colfax, Grant N.; Leff, Jared A.; Wong, Angela; Scott, Callie A.; Feaster, Daniel J.; Gooden, Lauren; Matheson, Tim; Haynes, Louise F.; Paltiel, A. David; Walensky, Rochelle P.

2012-01-01

BACKGROUND The President’s National HIV/AIDS Strategy calls for coupling HIV screening and prevention services with substance abuse treatment programs. Fewer than half of US community-based substance abuse treatment programs make HIV testing available on-site or through referral. METHODS We measured the cost-effectiveness of three HIV testing strategies evaluated in a randomized trial conducted in 12 community-based substance abuse treatment programs in 2009: off-site testing referral, on-site rapid testing with information only, on-site rapid testing with risk reduction counseling. Data from the trial included patient demographics, prior testing history, test acceptance and receipt of results, undiagnosed HIV prevalence (0.4%) and program costs. The Cost Effectiveness of Preventing AIDS Complications (CEPAC) computer simulation model was used to project life expectancy, lifetime costs, and quality-adjusted life years (QALYs) for HIV-infected individuals. Incremental cost-effectiveness ratios (2009 US $/QALY) were calculated after adding costs of testing HIV-uninfected individuals; costs and QALYs were discounted at 3% annually. RESULTS Referral for off-site testing is less efficient (dominated) compared to offering on-site testing with information only. The cost-effectiveness ratio for on-site testing with information is $60,300/QALY in the base case, or $76,300/QALY with 0.1% undiagnosed HIV prevalence. HIV risk-reduction counseling costs $36 per person more without additional benefit. CONCLUSIONS A strategy of on-site rapid HIV testing offer with information only in substance abuse treatment programs increases life expectancy at a cost-effectiveness ratio <$100,000/QALY. Policymakers and substance abuse treatment leaders should seek funding to implement on-site rapid HIV testing in substance abuse treatment programs for those not recently tested. PMID:22971593

Role of Anopheles culicifacies s.l. and An. pulcherrimus in malaria transmission in Ghassreghand (Baluchistan), Iran.

PubMed

Zaim, M; Subbarao, S K; Manouchehri, A V; Cochrane, A H

1993-03-01

A 2-site immunoradiometric assay (IRMA) was performed on the head and thorax of Anopheles culicifacies s.l. and An. pulcherrimus females, the 2 most common anopheline species in the District of Ghassreghand (Baluchistan, Iran), collected during the 2 peak malaria transmission seasons (May and September-October 1991). Positive IRMA results revealed the 2 species as potential vectors of malaria in this highly endemic district. This finding serves as the first report on natural infection of An. pulcherrimus in Iran and is the second on natural infection of An. culicifacies since the previous report of 1959.

Rapid response systems.

PubMed

Lyons, Patrick G; Edelson, Dana P; Churpek, Matthew M

2018-07-01

Rapid response systems are commonly employed by hospitals to identify and respond to deteriorating patients outside of the intensive care unit. Controversy exists about the benefits of rapid response systems. We aimed to review the current state of the rapid response literature, including evolving aspects of afferent (risk detection) and efferent (intervention) arms, outcome measurement, process improvement, and implementation. Articles written in English and published in PubMed. Rapid response systems are heterogeneous, with important differences among afferent and efferent arms. Clinically meaningful outcomes may include unexpected mortality, in-hospital cardiac arrest, length of stay, cost, and processes of care at end of life. Both positive and negative interventional studies have been published, although the two largest randomized trials involving rapid response systems - the Medical Early Response and Intervention Trial (MERIT) and the Effect of a Pediatric Early Warning System on All-Cause Mortality in Hospitalized Pediatric Patients (EPOCH) trial - did not find a mortality benefit with these systems, albeit with important limitations. Advances in monitoring technologies, risk assessment strategies, and behavioral ergonomics may offer opportunities for improvement. Rapid responses may improve some meaningful outcomes, although these findings remain controversial. These systems may also improve care for patients at the end of life. Rapid response systems are expected to continue evolving with novel developments in monitoring technologies, risk prediction informatics, and work in human factors. Copyright © 2018 Elsevier B.V. All rights reserved.

[Rapid prototyping: a very promising method].

PubMed

Haverman, T M; Karagozoglu, K H; Prins, H-J; Schulten, E A J M; Forouzanfar, T

2013-03-01

Rapid prototyping is a method which makes it possible to produce a three-dimensional model based on two-dimensional imaging. Various rapid prototyping methods are available for modelling, such as stereolithography, selective laser sintering, direct laser metal sintering, two-photon polymerization, laminated object manufacturing, three-dimensional printing, three-dimensional plotting, polyjet inkjet technology,fused deposition modelling, vacuum casting and milling. The various methods currently being used in the biomedical sector differ in production, materials and properties of the three-dimensional model which is produced. Rapid prototyping is mainly usedforpreoperative planning, simulation, education, and research into and development of bioengineering possibilities.

Antigenic mapping of an H9N2 avian influenza virus reveals two discrete antigenic sites and a novel mechanism of immune escape.

PubMed

Peacock, Thomas; Reddy, Kolli; James, Joe; Adamiak, Beata; Barclay, Wendy; Shelton, Holly; Iqbal, Munir

2016-01-07

H9N2 avian influenza virus is a major cause of poultry production loss across Asia leading to the wide use of vaccines. Efficacy of vaccines is often compromised due to the rapid emergence of antigenic variants. To improve the effectiveness of vaccines in the field, a better understanding of the antigenic epitopes of the major antigen, hemagglutinin, is required. To address this, a panel of nine monoclonal antibodies were generated against a contemporary Pakistani H9N2 isolate, which represents a major Asian H9N2 viral lineage. Antibodies were characterized in detail and used to select a total of 26 unique 'escape' mutants with substitutions across nine different amino acid residues in hemagglutinin including seven that have not been described as antigenic determinants for H9N2 viruses before. Competition assays and structural mapping revealed two novel, discrete antigenic sites "H9-A" and "H9-B". Additionally, a second subset of escape mutants contained amino acid deletions within the hemagglutinin receptor binding site. This constitutes a novel method of escape for group 1 hemagglutinins and could represent an alternative means for H9N2 viruses to overcome vaccine induced immunity. These results will guide surveillance efforts for arising antigenic variants as well as evidence based vaccine seed selection and vaccine design.

Antigenic mapping of an H9N2 avian influenza virus reveals two discrete antigenic sites and a novel mechanism of immune escape

PubMed Central

Peacock, Thomas; Reddy, Kolli; James, Joe; Adamiak, Beata; Barclay, Wendy; Shelton, Holly; Iqbal, Munir

2016-01-01

H9N2 avian influenza virus is a major cause of poultry production loss across Asia leading to the wide use of vaccines. Efficacy of vaccines is often compromised due to the rapid emergence of antigenic variants. To improve the effectiveness of vaccines in the field, a better understanding of the antigenic epitopes of the major antigen, hemagglutinin, is required. To address this, a panel of nine monoclonal antibodies were generated against a contemporary Pakistani H9N2 isolate, which represents a major Asian H9N2 viral lineage. Antibodies were characterized in detail and used to select a total of 26 unique ‘escape’ mutants with substitutions across nine different amino acid residues in hemagglutinin including seven that have not been described as antigenic determinants for H9N2 viruses before. Competition assays and structural mapping revealed two novel, discrete antigenic sites “H9-A” and “H9-B”. Additionally, a second subset of escape mutants contained amino acid deletions within the hemagglutinin receptor binding site. This constitutes a novel method of escape for group 1 hemagglutinins and could represent an alternative means for H9N2 viruses to overcome vaccine induced immunity. These results will guide surveillance efforts for arising antigenic variants as well as evidence based vaccine seed selection and vaccine design. PMID:26738561

Rapid Authentication of Ginkgo biloba Herbal Products Using the Recombinase Polymerase Amplification Assay.

PubMed

Liu, Yang; Wang, Xiao-Yue; Wei, Xue-Min; Gao, Zi-Tong; Han, Jian-Ping

2018-05-22

Species adulteration in herbal products (HPs) exposes consumers to health risks. Chemical and morphological methods have their own deficiencies when dealing with the detection of species containing the same active compounds in HPs. In this study, we developed a rapid identification method using the recombinase polymerase amplification (RPA) assay to detect two species, Ginkgo biloba and Sophora japonica (as adulteration), in Ginkgo biloba HPs. Among 36 Ginkgo biloba HP samples, 34 were found to have Ginkgo biloba sequences, and 9 were found to have Sophora japonica sequences. During the authentication process, the RPA-LFS assay showed a higher specificity, sensitivity and efficiency than PCR-based methods. We initially applied the RPA-LSF technique to detect plant species in HPs, demonstrating that this assay can be developed into an efficient tool for the rapid on-site authentication of plant species in Ginkgo biloba HPs.

Post-Fledging Dispersal of King Penguins (Aptenodytes patagonicus) from Two Breeding Sites in the South Atlantic

PubMed Central

Pütz, Klemens; Trathan, Phil N.; Pedrana, Julieta; Collins, Martin A.; Poncet, Sally; Lüthi, Benno

2014-01-01

Most studies concerning the foraging ecology of marine vertebrates are limited to breeding adults, although other life history stages might comprise half the total population. For penguins, little is known about juvenile dispersal, a period when individuals may be susceptible to increased mortality given their naïve foraging behaviour. Therefore, we used satellite telemetry to study king penguin fledglings (n = 18) from two sites in the Southwest Atlantic in December 2007. The two sites differed with respect to climate and proximity to the Antarctic Polar Front (APF), a key oceanographic feature generally thought to be important for king penguin foraging success. Accordingly, birds from both sites foraged predominantly in the vicinity of the APF. Eight king penguins were tracked for periods greater than 120 days; seven of these (three from the Falkland Islands and four from South Georgia) migrated into the Pacific. Only one bird from the Falkland Islands moved into the Indian Ocean, visiting the northern limit of the winter pack-ice. Three others from the Falkland Islands migrated to the eastern coast of Tierra del Fuego before travelling south. Derived tracking parameters describing their migratory behaviour showed no significant differences between sites. Nevertheless, generalized linear habitat modelling revealed that juveniles from the Falkland Islands spent more time in comparatively shallow waters with low sea surface temperature, sea surface height and chlorophyll variability. Birds from South Georgia spent more time in deeper waters with low sea surface temperature and sea surface height, but high concentrations of chlorophyll. Our results indicate that inexperienced king penguins, irrespective of the location of their natal site in relation to the position of the APF, develop their foraging skills progressively over time, including specific adaptations to the environment around their prospective breeding site. PMID:24828545

Post-fledging dispersal of king penguins (Aptenodytes patagonicus) from two breeding sites in the South Atlantic.

PubMed

Pütz, Klemens; Trathan, Phil N; Pedrana, Julieta; Collins, Martin A; Poncet, Sally; Lüthi, Benno

2014-01-01

Most studies concerning the foraging ecology of marine vertebrates are limited to breeding adults, although other life history stages might comprise half the total population. For penguins, little is known about juvenile dispersal, a period when individuals may be susceptible to increased mortality given their naïve foraging behaviour. Therefore, we used satellite telemetry to study king penguin fledglings (n = 18) from two sites in the Southwest Atlantic in December 2007. The two sites differed with respect to climate and proximity to the Antarctic Polar Front (APF), a key oceanographic feature generally thought to be important for king penguin foraging success. Accordingly, birds from both sites foraged predominantly in the vicinity of the APF. Eight king penguins were tracked for periods greater than 120 days; seven of these (three from the Falkland Islands and four from South Georgia) migrated into the Pacific. Only one bird from the Falkland Islands moved into the Indian Ocean, visiting the northern limit of the winter pack-ice. Three others from the Falkland Islands migrated to the eastern coast of Tierra del Fuego before travelling south. Derived tracking parameters describing their migratory behaviour showed no significant differences between sites. Nevertheless, generalized linear habitat modelling revealed that juveniles from the Falkland Islands spent more time in comparatively shallow waters with low sea surface temperature, sea surface height and chlorophyll variability. Birds from South Georgia spent more time in deeper waters with low sea surface temperature and sea surface height, but high concentrations of chlorophyll. Our results indicate that inexperienced king penguins, irrespective of the location of their natal site in relation to the position of the APF, develop their foraging skills progressively over time, including specific adaptations to the environment around their prospective breeding site.

Rapid, transient, and highly localized induction of plastidial ω-3 fatty acid desaturase mRNA at fungal infection sites in Petroselinum crispum

PubMed Central

Kirsch, Christoph; Takamiya-Wik, Monica; Reinold, Susanne; Hahlbrock, Klaus; Somssich, Imre E.

1997-01-01

Parsley (Petroselinum crispum) plants and suspension-cultured cells have been used extensively for studies of non-host-resistance mechanisms in plant/pathogen interactions. We now show that treatment of cultured parsley cells with a defined peptide elicitor of fungal origin causes rapid and large changes in the levels of various unsaturated fatty acids. While linoleic acid decreased and linolenic acid increased steadily for several hours, comparatively sharp increases in oleic acid followed a biphasic time course. In contrast, the overall level of stearic acid remained unaffected. Using a PCR-based approach, a parsley cDNA was isolated sharing high sequence similarity with ω-3 fatty acid desaturases. Subsequent isolation and characterization of a full-length cDNA enabled its functional identification as a plastid-localized ω-3 fatty acid desaturase by complementation of the Arabidopsis thaliana fad7/8 double mutant which is low in trienoic fatty acids. ω-3 Fatty acid desaturase mRNA accumulated rapidly and transiently in elicitor-treated cultured parsley cells, protoplasts, and leaves, as well as highly localized around fungal infection sites in parsley leaf buds. These results indicate that unsaturated fatty acid metabolism is yet another component of the highly complex, transcriptionally regulated pathogen defense response in plants. PMID:9050908

The rapid transient surveyor

NASA Astrophysics Data System (ADS)

Baranec, C.; Lu, J. R.; Wright, S. A.; Tonry, J.; Tully, R. B.; Szapudi, I.; Takamiya, M.; Hunter, L.; Riddle, R.; Chen, S.; Chun, M.

2016-07-01

The Rapid Transient Surveyor (RTS) is a proposed rapid-response, high-cadence adaptive optics (AO) facility for the UH 2.2-m telescope on Maunakea. RTS will uniquely address the need for high-acuity and sensitive near-infrared spectral follow-up observations of tens of thousands of objects in mere months by combining an excellent observing site, unmatched robotic observational efficiency, and an AO system that significantly increases both sensitivity and spatial resolving power. We will initially use RTS to obtain the infrared spectra of 4,000 Type Ia supernovae identified by the Asteroid Terrestrial-Impact Last Alert System over a two year period that will be crucial to precisely measuring distances and mapping the distribution of dark matter in the z < 0.1 universe. RTS will comprise an upgraded version of the Robo-AO laser AO system and will respond quickly to target-of-opportunity events, minimizing the time between discovery and characterization. RTS will acquire simultaneous-multicolor images with an acuity of 0.07-0.10" across the entire visible spectrum (20% i'-band Strehl in median conditions) and <0.16" in the near infrared, and will detect companions at 0.5" at contrast ratio of 500. The system will include a high-efficiency prism integral field unit spectrograph: R = 70-140 over a total bandpass of 840-1830nm with an 8.7" by 6.0" field of view (0.15" spaxels). The AO correction boosts the infrared point-source sensitivity of the spectrograph against the sky background by a factor of seven for faint targets, giving the UH 2.2-m the H-band sensitivity of a 5.7-m telescope without AO.

Implementing Rapid HIV Testing With or Without Risk-Reduction Counseling in Drug Treatment Centers: Results of a Randomized Trial

PubMed Central

Feaster, Daniel J.; Gooden, Lauren; Matheson, Tim; Mandler, Raul N.; Haynes, Louise; Tross, Susan; Kyle, Tiffany; Gallup, Dianne; Kosinski, Andrzej S.; Douaihy, Antoine; Schackman, Bruce R.; Das, Moupali; Lindblad, Robert; Erickson, Sarah; Korthuis, P. Todd; Martino, Steve; Sorensen, James L.; Szapocznik, José; Walensky, Rochelle; Branson, Bernard; Colfax, Grant N.

2012-01-01

Objectives. We examined the effectiveness of risk reduction counseling and the role of on-site HIV testing in drug treatment. Methods. Between January and May 2009, we randomized 1281 HIV-negative (or status unknown) adults who reported no past-year HIV testing to (1) referral for off-site HIV testing, (2) HIV risk-reduction counseling with on-site rapid HIV testing, or (3) verbal information about testing only with on-site rapid HIV testing. Results. We defined 2 primary self-reported outcomes a priori: receipt of HIV test results and unprotected anal or vaginal intercourse episodes at 6-month follow-up. The combined on-site rapid testing participants received more HIV test results than off-site testing referral participants (P < .001; Mantel-Haenszel risk ratio = 4.52; 97.5% confidence interval [CI] = 3.57, 5.72). At 6 months, there were no significant differences in unprotected intercourse episodes between the combined on-site testing arms and the referral arm (P = .39; incidence rate ratio [IRR] = 1.04; 97.5% CI = 0.95, 1.14) or the 2 on-site testing arms (P = .81; IRR = 1.03; 97.5% CI = 0.84, 1.26). Conclusions. This study demonstrated on-site rapid HIV testing’s value in drug treatment centers and found no additional benefit from HIV sexual risk-reduction counseling. PMID:22515871

Biogenic Volatile Organic Compounds (BVOCs) and their oxidation products at two Mediterranean background sites

NASA Astrophysics Data System (ADS)

Debevec, Cecile; Sauvage, Stephane; Gros, Valerie; Sciare, Jean; Pikridas, Michael; Dusanter, Sebastien; Leonardis, Thierry; Gaudion, Vincent; Depelchin, Laurence; Fronval, Isabelle; Sarda-Esteve, Roland; Baisnee, Dominique; Vasiliadou, Emily; Savvides, Chrysanthos; Kalogridis, Cerise; Michoud, Vincent; Locoge, Nadine

2017-04-01

In the framework of the ChArMEx (Chemistry Aerosol Mediterranean Experiments) program, this work aims at providing a better characterization of the sources and fate of VOCs impacting the Mediterranean region as well as conducting a parallel between organic aerosol and gas phase composition. To reach these objectives, on-line measurements of a large number of VOCs were conducted by flame ionization detection/gas chromatography and proton transfer reaction mass spectrometry at two Mediterranean receptor sites, Cape Corsica in summer 2013 and the Cyprus Atmospheric Observatory (CAO) in March 2015. Additionally, off-line air samples were collected on cartridges. On-line submicron aerosol chemical composition was performed in parallel with an aerosol mass spectrometer. VOCs Sources were identified using positive matrix factorization (PMF) tool and discussed in previous studies (Michoud et al., submitted, Debevec et al., submitted). This work focuses on BVOCs measured at these sampling sites (especially on their levels, speciation, variability and processes). Different speciation of monoterpenes was noticed at these sites. Even if monoterpenes were mainly composed of β-pinene at both sites (34 % - 38 % of the total monoterpenes mass concentration), α-terpinene was observed in higher proportion at Cape Corsica (21 %) than CAO (2 %) while lower proportion of α-pinene was measured (Cape Corsica: 24 %, CAO: 35 %). Biogenic sources were found to be significant contributors to the VOCs concentrations observed at these sampling sites (Cape Corsica: 20%, CAO: 36 %) but have shown different variabilities. At Cape Corsica, a primary and a secondary biogenic factor were identified, both correlating with air temperature and exhibiting a clear diurnal profile. At CAO, two different biogenic factors were identified with distinct diurnal profiles, the first one driven by isoprene was correlated with air temperature and the second one, driven by monoterpenes, showed maxima during

Honokiol promotes non-rapid eye movement sleep via the benzodiazepine site of the GABA(A) receptor in mice.

PubMed

Qu, Wei-Min; Yue, Xiao-Fang; Sun, Yu; Fan, Kun; Chen, Chang-Rui; Hou, Yi-Ping; Urade, Yoshihiro; Huang, Zhi-Li

2012-10-01

Decoctions of the Chinese herb houpu contain honokiol and are used to treat a variety of mental disorders, including depression. Depression commonly presents alongside sleep disorders and sleep disturbances, which appear to be a major risk factor for depression. Here, we have evaluated the somnogenic effect of honokiol and the mechanisms involved. Honokiol was administered i.p. at 20:00 h in mice. Flumazenil, an antagonist at the benzodiazepine site of the GABA(A) receptor, was administered i.p. 15 min before honokiol. The effects of honokiol were measured by EEG and electromyogram (EMG), c-Fos expression and in vitro electrophysiology. Honokiol (10 and 20 mg·kg⁻¹) significantly shortened the sleep latency to non-rapid eye movement (non-REM, NREM) sleep and increased the amount of NREM sleep. Honokiol increased the number of state transitions from wakefulness to NREM sleep and, subsequently, from NREM sleep to wakefulness. However, honokiol had no effect on either the amount of REM sleep or EEG power density of both NREM and REM sleep. Honokiol increased c-Fos expression in ventrolateral preoptic area (VLPO) neurons, as examined by immunostaining, and excited sleep-promoting neurons in the VLPO by whole-cell patch clamping in the brain slice. Pretreatment with flumazenil abolished the somnogenic effects and activation of the VLPO neurons by honokiol. Honokiol promoted NREM sleep by modulating the benzodiazepine site of the GABA(A) receptor, suggesting potential applications in the treatment of insomnia, especially for patients who experience difficulty in falling and staying asleep. © 2012 The Authors. British Journal of Pharmacology © 2012 The British Pharmacological Society.

Scalable loading of a two-dimensional trapped-ion array

PubMed Central

Bruzewicz, Colin D.; McConnell, Robert; Chiaverini, John; Sage, Jeremy M.

2016-01-01

Two-dimensional arrays of trapped-ion qubits are attractive platforms for scalable quantum information processing. Sufficiently rapid reloading capable of sustaining a large array, however, remains a significant challenge. Here with the use of a continuous flux of pre-cooled neutral atoms from a remotely located source, we achieve fast loading of a single ion per site while maintaining long trap lifetimes and without disturbing the coherence of an ion quantum bit in an adjacent site. This demonstration satisfies all major criteria necessary for loading and reloading extensive two-dimensional arrays, as will be required for large-scale quantum information processing. Moreover, the already high loading rate can be increased by loading ions in parallel with only a concomitant increase in photo-ionization laser power and no need for additional atomic flux. PMID:27677357

Summary of nutrient and biomass data from two aspen sites in western United States

Treesearch

Robert S. Johnston; Dale L. Bartos

1977-01-01

Summary tables are presented for aboveground biomass and nutrient concentrations for 20 aspen trees (Populus tremuloides Michx.) that were sampled at two study sites in Utah and Wyoming. Trees were divided into seven components - leaves, current twigs, old twigs, deadwood (branches), branches, bark, and bole wood. Samples from each component were analyzed for nitrogen...

Rapid hiv testing in urban outreach: a strategy for improving posttest counseling rates.

PubMed

Keenan, P A; Keenan, J M

2001-12-01

In 1998, 48% of persons who had HIV testing at publicly funded sites in the United States failed to return for test results and posttest counseling. Opportunities for timely HIV therapy were lost; valuable resources were wasted. This study tested the hypothesis that rapid HIV testing enables a high percentage of high-risk outreach clients to learn their serostatus. We did on-site counseling and rapid HIV testing at community-based organizations (e.g., chemical dependency programs, homeless shelters) in North Minneapolis. The project tested 735 persons. All but one (99.9%) learned their HIV serostatus. African Americans made up 79% of subjects. Rapid testing has a role to play in HIV outreach. It is useful in populations who are at high risk of HIV infection, who currently are not accessing HIV testing, and who have high failure to return rates. Future developments in rapid testing technology will make this testing option more convenient and cost-effective.

Polyoma virus small tumor antigen pre-mRNA splicing requires cooperation between two 3' splice sites.

PubMed Central

Ge, H; Noble, J; Colgan, J; Manley, J L

1990-01-01

We have studied splicing of the polyoma virus early region pre-mRNA in vitro. This RNA is alternatively spliced in vivo to produce mRNA encoding the large, middle-sized (MTAg), and small (StAg) tumor antigens. Our primary interest was to learn how the 48-nucleotide StAg intron is excised, because the length of this intron is significantly less than the apparent minimum established for mammalian introns. Although the products of all three splices are detected in vitro, characterization of the pathway and sequence requirements of StAg splicing suggests that splicing factors interact with the precursor RNA in an unexpected way to catalyze removal of this intron. Specifically, StAg splicing uses either of two lariat branch points, one of which is located only 4 nucleotides from the 3' splice site. Furthermore, the StAg splice absolutely requires that the alternative MTAg 3' splice site, located 14 nucleotides downstream of the StAg 3' splice site, be intact. Insertion mutations that increase or decrease the quality of the MTAg pyrimidine stretch enhance or repress StAg as well as MTAg splicing, and a single-base change in the MTAg AG splice acceptor totally blocks both splices. These results demonstrate the ability of two 3' splice sites to cooperate with each other to bring about removal of a single intron. Images PMID:2159146

Influence of Clouds On The Surface Radiative Balance For Two Mediterranean Sites

NASA Astrophysics Data System (ADS)

Bortoli, D.; Costa, M. J.; Nardino, M.

Clouds strongly affect the Earth's climate influencing the surface radiative balance by reducing the incident solar radiation and increasing the downward longwave flux. Al- though the quantitative impact of clouds on the surface radiative balance is necessarily associated with great uncertainties due to the complexity and variation of the under- lying parameters, cloud radiative forcing is one of the main regulating factors of the Earth's climate. The present work aims at determining the effect of cloud coverage on the surface radiative balance, in order to contribute for a better understanding of local variations in the Mediterranean climate. Measurements of the cloud cover index (CCI) require the presence of an observer capable of quantifying cloud amounts in the sky in sight above the measurements' site. Since such measurements are not always available the cloud cover index is re- trieved using two different methodologies. On one hand the CCI is computed from the surface radiometer measurements throughout a parameterisation. On the other it is retrieved using a bi-spectral algorithm based on the METEOSAT satellite measure- ments from the visible and infrared spectral regions. Results of the CCI are compared with co-located observations to perform a general check against the available "ground truth". At the same time the CCI values obtained from both methodologies are inter- compared. Results of the CCI and their implications on the surface radiative balance are presented for the two Mediterranean sites selected, one located in Italy and the other in the south of Portugal. The cloud radiative forcing calculations show a cooling effect of the surface in presence of clouds for both sites. Moreover, a seasonal dependence is obtained, with a stronger cooling effect during summer. Acknowledgements: The work was supported by Instituto de Cooperação Científica e Tecnológica Internacional (ICCTI) - Portugal and Consiglio Nazionale delle Ricerche (CNR) - Italy

Rapid On-Site Evaluation of Fine-Needle Aspiration by Non-Cytopathologists: A Systematic Review and Meta-Analysis of Diagnostic Accuracy Studies for Adequacy Assessment.

PubMed

Pearson, Lauren; Factor, Rachel E; White, Sandra K; Walker, Brandon S; Layfield, Lester J; Schmidt, Robert L

2018-06-06

Rapid on-site evaluation (ROSE) has been shown to improve adequacy rates and reduce needle passes. ROSE is often performed by cytopathologists who have limited availability and may be costlier than alternatives. Several recent studies examined the use of alternative evaluators (AEs) for ROSE. A summary of this information could help inform guidelines regarding the use of AEs. The objective was to assess the accuracy of AEs compared to cytopathologists in assessing the adequacy of specimens during ROSE. This was a systematic review and meta-analysis. Reporting and study quality were assessed using the STARD guidelines and QUADAS-2. All steps were performed independently by two evaluators. Summary estimates were obtained using the hierarchal method in Stata v14. Heterogeneity was evaluated using Higgins' I2 statistic. The systematic review identified 13 studies that were included in the meta-analysis. Summary estimates of sensitivity and specificity for AEs were 97% (95% CI: 92-99%) and 83% (95% CI: 68-92%). There was wide variation in accuracy statistics between studies (I2 = 0.99). AEs sometimes have accuracy that is close to cytopathologists. However, there is wide variability between studies, so it is not possible to provide a broad guideline regarding the use of AEs. © 2018 S. Karger AG, Basel.

Rapid effects of corticosterone on cache recovery in mountain chickadees (Parus gambeli).

PubMed

Saldanha, C J; Schlinger, B A; Clayton, N S

2000-03-01

Environmental perturbations increase adrenal activity in several vertebrates. Increases in corticosterone may serve as a proximate trigger whereby organisms can rapidly adapt their behavior to survive environmental fluctuations. In food-caching songbirds, inclement weather may present the need to alter caching and/or retrieval behaviors to ensure food supplies. We hypothesized that corticosterone may increase the rate of caching and/or retrieval behaviors in the mountain chickadee, a food-storing songbird, and tested if these potential effects were mediated by alterations in appetite, activity, or memory for cache sites. Corticosterone or vehicle was administered to subjects 5 min prior to either caching or recovery in a naturalistic laboratory paradigm during which we recorded the number of caching events, sites visited, and seeds eaten (caching) or caches recovered, total sites visited, cache-related visits, and non-cache-related visits (recovery). Data were analyzed using nested ANOVA for treatment within sequential trial. There was no effect on any caching behaviors following treatment. However, birds treated with corticosterone during retrieval recovered more seeds and tended to visit more cache-related sites than did controls. Since groups did not differ in the number of seeds eaten or the total number of sites visited, it seems unlikely that corticosterone affected appetite or activity. Rapid surges in corticosterone may increase the efficacy of an underlying memory process for cache sites which is reflected in higher cache recovery in corticosterone-treated birds than in controls. Thus, rapid alterations in plasma corticosterone following environmental change may alter memory-reliant behaviors which promote survival in the food-caching mountain chickadee. Copyright 2000 Academic Press.

Superfund at work: Hazardous waste cleanup efforts nationwide, Spring 1993 (Harvey and Knott Drum Site, New Castle County, Delaware)

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

Not Available

From 1963 to 1969, two acres of the Harvey and Knott Drum site in New Castle County, Delaware served as an open dump and burning area for sanitary, municipal, and industrial wastes. Sludge, paint pigment, and solvents contaminated the site until the State of Delaware and the US Environmental Protection Agency (EPA) intervened in 1981. Site conditions required a combination of traditional cleanup measures. After the immediate health threats posed by the site were eliminated, EPA reached an innovative, mixed funding settlement for long-term cleanup with two parties responsible for the site contamination. The following actions highlight the success ofmore » the Superfund program: An emergency removal of contaminants reduced immediate environmental and public health effects; A rapid assessment of ground water safeguarded drinking water supplies; and The full cooperation of General Motors (GM) expedited implementation of the cleanup, valued at $3.2 million.« less

Evaluation of Two Eastern White Pine Site Index Equations at Biltmore Estate, North Carolina

Treesearch

W. Henry McNab; Bernard R. Parresol; Brian A. Ritter

2000-01-01

The accuracy of two white pine (Pinus strobus L.) polymorphic site index equations was compared with field data from three plots in a loo-year-old stand at Biltmore Estate, Asheville, NC. One equation was developed from New Hampshire data and the other from Southern Appalachian data. Tree height has been measured periodically on those plots between...

Changes in Contaminant Mass Discharge from DNAPL Source Mass Depletion: Evaluation at Two Field Sites

EPA Science Inventory

Changes in contaminant fluxes resulting from aggressive remediation of dense nonaqueous phase liquid (DNAPL) source zone were investigated at two sites, one at Hill Air Force Base (AFB), Utah, and the other at Ft. Lewis Military Reservation, WA. Passive Flux Meters (PFM) and a va...

Rapid Growth of Uropathogenic Escherichia coli during Human Urinary Tract Infection.

PubMed

Forsyth, Valerie S; Armbruster, Chelsie E; Smith, Sara N; Pirani, Ali; Springman, A Cody; Walters, Matthew S; Nielubowicz, Greta R; Himpsl, Stephanie D; Snitkin, Evan S; Mobley, Harry L T

2018-03-06

Uropathogenic Escherichia coli (UPEC) strains cause most uncomplicated urinary tract infections (UTIs). These strains are a subgroup of extraintestinal pathogenic E. coli (ExPEC) strains that infect extraintestinal sites, including urinary tract, meninges, bloodstream, lungs, and surgical sites. Here, we hypothesize that UPEC isolates adapt to and grow more rapidly within the urinary tract than other E. coli isolates and survive in that niche. To date, there has not been a reliable method available to measure their growth rate in vivo Here we used two methods: segregation of nonreplicating plasmid pGTR902, and peak-to-trough ratio (PTR), a sequencing-based method that enumerates bacterial chromosomal replication forks present during cell division. In the murine model of UTI, UPEC strain growth was robust in vivo , matching or exceeding in vitro growth rates and only slowing after reaching high CFU counts at 24 and 30 h postinoculation (hpi). In contrast, asymptomatic bacteriuria (ABU) strains tended to maintain high growth rates in vivo at 6, 24, and 30 hpi, and population densities did not increase, suggesting that host responses or elimination limited population growth. Fecal strains displayed moderate growth rates at 6 hpi but did not survive to later times. By PTR, E. coli in urine of human patients with UTIs displayed extraordinarily rapid growth during active infection, with a mean doubling time of 22.4 min. Thus, in addition to traditional virulence determinants, including adhesins, toxins, iron acquisition, and motility, very high growth rates in vivo and resistance to the innate immune response appear to be critical phenotypes of UPEC strains. IMPORTANCE Uropathogenic Escherichia coli (UPEC) strains cause most urinary tract infections in otherwise healthy women. While we understand numerous virulence factors are utilized by E. coli to colonize and persist within the urinary tract, these properties are inconsequential unless bacteria can divide

Atmospheric aerosol compositions and sources at two national background sites in northern and southern China

NASA Astrophysics Data System (ADS)

Zhu, Qiao; He, Ling-Yan; Huang, Xiao-Feng; Cao, Li-Ming; Gong, Zhao-Heng; Wang, Chuan; Zhuang, Xin; Hu, Min

2016-08-01

Although China's severe air pollution has become a focus in the field of atmospheric chemistry and the mechanisms of urban air pollution there have been researched extensively, few field sampling campaigns have been conducted at remote background sites in China, where air pollution characteristics on a larger scale are highlighted. In this study, an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS), together with an Aethalometer, was deployed at two of China's national background sites in northern (Lake Hongze site; 33.23° N, 118.33° E; altitude 21 m) and southern (Mount Wuzhi site; 18.84° N, 109.49° E; altitude 958 m) China in the spring seasons in 2011 and 2015, respectively, in order to characterize submicron aerosol composition and sources. The campaign-average PM1 concentration was 36.8 ± 19.8 µg m-3 at the northern China background (NCB) site, which was far higher than that at the southern China background (SCB) site (10.9 ± 7.8 µg m-3). Organic aerosol (OA) (27.2 %), nitrate (26.7 %), and sulfate (22.0 %) contributed the most to the PM1 mass at NCB, while OA (43.5 %) and sulfate (30.5 %) were the most abundant components of the PM1 mass at SCB, where nitrate only constituted a small fraction (4.7 %) and might have contained a significant amount of organic nitrates (5-11 %). The aerosol size distributions and organic aerosol elemental compositions all indicated very aged aerosol particles at both sites. The OA at SCB was more oxidized with a higher average oxygen to carbon (O / C) ratio (0.98) than that at NCB (0.67). Positive matrix factorization (PMF) analysis was used to classify OA into three components, including a hydrocarbon-like component (HOA, attributed to fossil fuel combustion) and two oxygenated components (OOA1 and OOA2, attributed to secondary organic aerosols from different source areas) at NCB. PMF analysis at SCB identified a semi-volatile oxygenated component (SV-OOA) and a low-volatility oxygenated

Esthetic rehabilitation of complicated crown fractures utilizing rapid orthodontic extrusion and two different restoration modalities.

PubMed

Milardovic Ortolan, Sladana; Strujic, Mihovil; Aurer, Andrej; Viskic, Josko; Bergman, Lana; Mehulic, Ketij

2012-01-01

This case report describes the management of a crown-root fractured maxillary right central incisor and a crown fractured maxillary left central incisor using two different techniques. A complex procedure was designed to manage this case including orthodontic extrusion to move the fracture line above the alveolar bone and surgical recontouring of the altered gingival margin. Finally, the right incisor was restored prosthodontically. Prosthetic treatment was based on performing a post and core, and all-ceramic crown on the extruded tooth. The left, less-damaged incisor was restored directly using composite resin. The treatment resulted in good esthetics and secured periodontal health. This case report demonstrates that a multidisciplinary treatment approach is a reliable and predictable option to save a tooth. How to cite this article: Ortolan SM, Strujic M, Aurer A, Viskic J, Bergman L, Mehulic K. Esthetic Rehabilitation of Complicated Crown Fractures Utilizing Rapid Orthodontic Extrusion and Two Different Restoration Modalities. Int J Clin Pediatr Dent 2012;5(1):64-67.

Rapid evolution of RNA editing sites in a small non-essential plastid gene

PubMed Central

Fiebig, Andreas; Stegemann, Sandra; Bock, Ralph

2004-01-01

Chloroplast RNA editing proceeds by C-to-U transitions at highly specific sites. Here, we provide a phylogenetic analysis of RNA editing in a small plastid gene, petL, encoding subunit VI of the cytochrome b6f complex. Analyzing representatives from most major groups of seed plants, we find an unexpectedly high frequency and dynamics of RNA editing. High-frequency editing has previously been observed in plastid ndh genes, which are remarkable in that their mutational inactivation does not produce an obvious mutant phenotype. In order to test the idea that reduced functional constraints allow for more flexible evolution of RNA editing sites, we have created petL knockout plants by tobacco chloroplast transformation. We find that, in the higher plant tobacco, targeted inactivation of petL does not impair plant growth under a variety of conditions markedly contrasting the important role of petL in photosynthesis in the green alga Chlamydomonas reinhardtii. Together with a low number of editing sites in plastid genes that are essential to gene expression and photosynthetic activity, these data suggest that RNA editing sites may evolve more readily in those genes whose transitory loss of function can be tolerated. Accumulated evidence for this ‘relative neutrality hypothesis for the evolution of plastid editing sites’ is discussed. PMID:15240834

Orbital ordering in FeV2O4: Spinel with two orbitally active sites

NASA Astrophysics Data System (ADS)

Sarkar, Soumyajit; Saha-Dasgupta, T.

2011-12-01

By employing first-principles electronic structure calculations, we investigate orbital ordering in FeV2O4, a spinel with orbital degrees of freedom both at Fe and V sites that exhibits two tetragonal phases, one compressed at high temperature and another elongated at low temperature. Our first-principles study shows the ferro-orbital ordering of dx2-y2 and d3z2-r2 types at Fe sites at the high- and low-temperature phases, respectively. The orbital ordering at V sites is found to consist of orbital chains running along different directions with orbitals rotated alternatively within each chain, similar to that found for MnV2O4 [S. Sarkar , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.102.216405 102, 216405 (2009)]. Further, we find that the single-ion anisotropy effect with hard and easy c axis favors the compressed and elongated tetrahedral shapes. This gives rise to magnetocrystalline anisotropy-dependent shapes, similar to that reported in the context of rare-earth-based magnetic shape memory alloys.

Two-dimensional time-resolved x-ray diffraction study of dual phase rapid solidification in steels

NASA Astrophysics Data System (ADS)

Yonemura, Mitsuharu; Osuki, Takahiro; Terasaki, Hidenori; Komizo, Yuichi; Sato, Masugu; Toyokawa, Hidenori; Nozaki, Akiko

2010-01-01

The high intensity heat source used for fusion welding creates steep thermal gradients of 100 °C/s from 1800 °C. Further, the influence of preferred orientation is important for the observation of a directional solidification that follows the dendrite growth along the ⟨100⟩ direction toward the moving heat source. In the present study, we observed the rapid solidification of weld metal at a time resolution of 0.01-0.1 s by a two-dimensional time-resolved x-ray diffraction (2DTRXRD) system for real welding. The diffraction rings were dynamically observed by 2DTRXRD with synchrotron energy of 18 keV while the arc passes over the irradiation area of the x-rays. The arc power output was 10 V-150 A, and the scan speed of the arc was 1.0 mm/s. The temperature rise in instruments was suppressed by a water-cooled copper plate under the specimen. Further, the temperature distribution of the weld metal was measured by a thermocouple and correlated with the diffraction patterns. Consequently, solidification and solid phase transformation of low carbon steels and stainless steels were observed during rapid cooling by 2DTRXRD. In the low carbon steel, the microstructure is formed in a two step process, (i) formation of crystallites and (ii) increase of crystallinity. In stainless steel, the irregular interface layer of δ/γ in the quenched metal after solidification is expected to show the easy movement of dendrites at a lower temperature. In carbide precipitation stainless steel, it is easy for NbC to grow on δ phase with a little undercooling. Further, a mistlike pattern, which differs from the halo pattern, in the fusion zone gave some indication of the possibilities to observe the nucleation and the early solidification by 2DTRXRD.

Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein.

PubMed

Hellberg, M E; Moy, G W; Vacquier, V D

2000-03-01

Male-specific proteins have increasingly been reported as targets of positive selection and are of special interest because of the role they may play in the evolution of reproductive isolation. We report the rapid interspecific divergence of cDNA encoding a major acrosomal protein of unknown function (TMAP) of sperm from five species of teguline gastropods. A mitochondrial DNA clock (calibrated by congeneric species divided by the Isthmus of Panama) estimates that these five species diverged 2-10 MYA. Inferred amino acid sequences reveal a propeptide that has diverged rapidly between species. The mature protein has diverged faster still due to high nonsynonymous substitution rates (> 25 nonsynonymous substitutions per site per 10(9) years). cDNA encoding the mature protein (89-100 residues) shows evidence of positive selection (Dn/Ds > 1) for 4 of 10 pairwise species comparisons. cDNA and predicted secondary-structure comparisons suggest that TMAP is neither orthologous nor paralogous to abalone lysin, and thus marks a second, phylogenetically independent, protein subject to strong positive selection in free-spawning marine gastropods. In addition, an internal repeat in one species (Tegula aureotincta) produces a duplicated cleavage site which results in two alternatively processed mature proteins differing by nine amino acid residues. Such alternative processing may provide a mechanism for introducing novel amino acid sequence variation at the amino-termini of proteins. Highly divergent TMAP N-termini from two other tegulines (Tegula regina and Norrisia norrisii) may have originated by such a mechanism.

Lingual palpation for porcine cysticercosis: a rapid epidemiological tool for estimating prevalence and community risk in Africa.

PubMed

Guyatt, Helen L; Fèvre, Eric M

2016-10-01

To assess the association between the prevalence of tongue cyst-positive and antigen-positive pigs across different settings in Africa, to evaluate whether examining pigs for cysts could be used as a rapid surveillance tool for identifying geographical areas with a higher probability of high transmission of cysticercosis. Published data were collated from 26 study sites across Africa that reported the prevalence of porcine cysticercosis by both lingual and serological examinations. The study sites were located in 10 countries across Africa. Seroprevalence rates ranged from 4% to 41%. Despite the varied study sites, the relationship between the two variables was highly consistent and suggests identification of tongue cysts may be useful for cysticercosis surveillance. We found that all areas with more than 10% of pigs having cysts in their tongues had at least 30% seroprevalence (PPV of 100%), although this cut-off is less reliable at predicting that an area is of low transmission (NPV of 84%). Assessing the prevalence of tongue cyst-positive pigs is a potential rapid epidemiological tool for identifying areas at high risk of cysticercosis, although further refinement and validation is required using standardised data sets. © 2016 The Authors. Tropical Medicine & International Health Published by John Wiley & Sons Ltd.

Evaluation of two commercial procedures for rapid identification of Neisseria gonorrhoeae using a reference panel of antigenically diverse gonococci.

PubMed Central

Boehm, D M; Bernhardt, M; Kurzynski, T A; Pennell, D R; Schell, R F

1990-01-01

Two commercial tests for the rapid identification of Neisseria gonorrhoeae were evaluated. Two hundred seventy-nine organisms were tested, including 202 strains of N. gonorrhoeae. The Syva MicroTrak test results were less subjective but required a fluorescence microscope. The Phadebact Monoclonal GC OMNI Test required modification of the manufacturer's interpretive instructions in order to avoid cross-reactions, but it was a practical test. Specificities of both tests were 100%. Sensitivities of the Phadebact Monoclonal GC OMNI and Syva MicroTrak tests were 100% and approximately 100%, respectively. PMID:2121792

Environmental effects of the Big Rapids dam remnant removal, Big Rapids, Michigan, 2000-02

USGS Publications Warehouse

Healy, Denis F.; Rheaume, Stephen J.; Simpson, J. Alan

2003-01-01

The U.S. Geological Survey (USGS), in cooperation with the city of Big Rapids, investigated the environmental effects of removal of a dam-foundation remnant and downstream cofferdam from the Muskegon River in Big Rapids, Mich. The USGS applied a multidiscipline approach, which determined the water quality, sediment character, and stream habitat before and after dam removal. Continuous water-quality data and discrete water-quality samples were collected, the movement of suspended and bed sediment were measured, changes in stream habitat were assessed, and streambed elevations were surveyed. Analyses of water upstream and downstream from the dam showed that the dam-foundation remnant did not affect water quality. Dissolved-oxygen concentrations downstream from the dam remnant were depressed for a short period (days) during the beginning of the dam removal, in part because of that removal effort. Sediment transport from July 2000 through March 2002 was 13,800 cubic yards more at the downstream site than the upstream site. This increase in sediment represents the remobilized sediment upstream from the dam, bank erosion when the impoundment was lowered, and contributions from small tributaries between the sites. Five habitat reaches were monitored before and after dam-remnant removal. The reaches consisted of a reference reach (A), upstream from the effects of the impoundment; the impoundment (B); and three sites below the impoundment where habitat changes were expected (C, D, and E, in downstream order). Stream-habitat assessment reaches varied in their responses to the dam-remnant removal. Reference reach A was not affected. In impoundment reach B, Great Lakes and Environmental Assessment Section (GLEAS) Procedure 51 ratings went from fair to excellent. For the three downstream reaches, reach C underwent slight habitat degradation, but ratings remained good; reach D underwent slight habitat degradation with ratings changing from excellent to good; and, in an area

Study of Aerosol Optical Properties Over Two Sites in the Foothills of the Central Himalayas

NASA Astrophysics Data System (ADS)

Rupakheti, D.; Kang, S.; Cong, Z.; Rupakheti, M.; Tripathee, L.; Panday, A. K.; Holben, B.

2018-04-01

Atmospheric aerosol possesses impacts on climate system and ecological environments, human health and agricultural productivity. The environment over Himalayas and Tibetan Plateau region are continuously degraded due to the transport of pollution from the foothills of the Himalayas; mostly the Indo-Gangetic Plain (IGP). Thus, analysis of aerosol optical properties over two sites; Lumbini and Kathmandu (the southern slope of central Himalayas) using AERONET's CIMEL sun photometer were conducted in this study. Aerosol optical depth (AOD at 500 nm), angstrom exponent (α or AE), volume size distribution (VSD), single scattering albedo (SSA) and asymmetry parameter (AP) were studied for 2013-2014 and the average AOD was found to be: 0.64 ± 0.41 (Lumbini) and 0.45 ± 0.30 (Kathmandu). The average AE was found to be: 1.25 ± 0.24 and 1.26 ± 0.18 respectively for two sites. The relation between AOD and AE was used to discriminate the aerosol types over these sites which indicated anthropogenic, mixed and biomass burning origin aerosol constituted the major aerosol types in Lumbini and Kathmandu. A clear bi-modal distribution of aerosol volume size was observed with highest volume concentration during the post-monsoon season in fine mode and pre-monsoon season in coarse mode (Lumbini) and highest value over both modes during pre-monsoon season in Kathmandu. The single scattering albedo (SSA) and asymmetry parameter (AP) analyses suggested aerosols over the Himalayan foothills sites are dominated by absorbing and anthropogenic aerosols from urban and industrial activities and biomass burning. Long-term studies are essential to understand and characterize the nature of aerosol over this research gap zone.

Longleaf pine wood and straw yields from two old-field planted sites in Georgia

Treesearch

E. David Dickens; David J. Moorhead; Bryan C. McElvany; Ray Hicks

2012-01-01

Little is known or published concerning longleaf pine’s growth rate, or wood and pine straw yields on old-field sites. Two study areas were installed in unthinned longleaf plantations established on former old-fields in Screven and Tift Counties, Georgia to address pine growth and straw yields. Soil series were delineated and replicated plots with three levels of...

Evapotranspiration of rubber ( Hevea brasiliensis ) cultivated at two plantation sites in Southeast Asia: RUBBER EVAPOTRANSPIRATION IN SE ASIA

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

Giambelluca, Thomas W.; Mudd, Ryan G.; Liu, Wen

The expansion of rubber (Hevea brasiliensis) cultivation to higher latitudes and higher elevations in southeast Asia is part of a dramatic shift in the direction of rural land cover change in the region toward more tree covered landscapes. To investigate the possible effects of increasing rubber cultivation in the region on ecosystem services including water cycling, eddy covariance towers were established to measure ecosystem fluxes within two rubber plantations, one each in Bueng Kan, northeastern Thailand, and Kampong Cham, central Cambodia. The results show that evapotranspiration (ET) at both sites is strongly related to variations in available energy and leafmore » area, and moderately controlled by soil moisture. Measured mean annual ET was 1128 and 1272 mm for the Thailand and Cambodia sites, respectively. After adjustment for energy closure, mean annual was estimated to be 1211 and 1459 mm yr at the Thailand and Cambodia sites, respectively. Based on these estimates and that of another site in Xishuangbanna, southwestern China, it appears that of rubber is higher than that of other tree dominated land covers in the region, including forest. While measurements by others in non rubber tropical ecosystems indicate that at high net radiation sites is at most only slightly higher than for sites with lower net radiation, mean annual rubber increases strongl with increasing net radiation across the three available rubber plantation observation sites. With the continued expansion of tree dominated land covers, including rubber cultivation, in southeast Asia, the possible association between commercially viable, fast growing tree crop species Giambelluca et al. Evapotranspiration of rubber (Havea brasiliensis) cultivated at two sites in southeast Asia and their relatively high water use raises concerns about potential effects on water and food security.« less

Temporal-Spatial Interaction between Reactive Oxygen Species and Abscisic Acid Regulates Rapid Systemic Acclimation in Plants[W][OPEN

PubMed Central

Suzuki, Nobuhiro; Miller, Gad; Salazar, Carolina; Mondal, Hossain A.; Shulaev, Elena; Cortes, Diego F.; Shuman, Joel L.; Luo, Xiaozhong; Shah, Jyoti; Schlauch, Karen; Shulaev, Vladimir; Mittler, Ron

2013-01-01

Being sessile organisms, plants evolved sophisticated acclimation mechanisms to cope with abiotic challenges in their environment. These are activated at the initial site of exposure to stress, as well as in systemic tissues that have not been subjected to stress (termed systemic acquired acclimation [SAA]). Although SAA is thought to play a key role in plant survival during stress, little is known about the signaling mechanisms underlying it. Here, we report that SAA in plants requires at least two different signals: an autopropagating wave of reactive oxygen species (ROS) that rapidly spreads from the initial site of exposure to the entire plant and a stress-specific signal that conveys abiotic stress specificity. We further demonstrate that SAA is stress specific and that a temporal–spatial interaction between ROS and abscisic acid regulates rapid SAA to heat stress in plants. In addition, we demonstrate that the rapid ROS signal is associated with the propagation of electric signals in Arabidopsis thaliana. Our findings unravel some of the basic signaling mechanisms underlying SAA in plants and reveal that signaling events and transcriptome and metabolome reprogramming of systemic tissues in response to abiotic stress occur at a much faster rate than previously envisioned. PMID:24038652

Tetraethylene glycol promoted two-step, one-pot rapid synthesis of indole-3-[1- 11C]acetic acid

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

Lee, Sojeong; Qu, Wenchao; Alexoff, David L.

2014-12-12

An operationally friendly, two-step, one-pot process has been developed for the rapid synthesis of carbon-11 labeled indole-3-acetic acid ([ 11]IAA or [ 11]auxin). By replacing an aprotic polar solvent with tetraethylene glycol, nucleophilic [ 11]cyanation and alkaline hydrolysis reactions were performed consecutively in a single pot without a time-consuming intermediate purification step. The entire production time for this updated procedure is 55 min, which dramatically simplifies the entire synthesis and reduces the starting radioactivity required for a whole plant imaging study.

Dual-scanning optical coherence elastography for rapid imaging of two tissue volumes (Conference Presentation)

NASA Astrophysics Data System (ADS)

Fang, Qi; Frewer, Luke; Wijesinghe, Philip; Hamzah, Juliana; Ganss, Ruth; Allen, Wes M.; Sampson, David D.; Curatolo, Andrea; Kennedy, Brendan F.

2017-02-01

In many applications of optical coherence elastography (OCE), it is necessary to rapidly acquire images in vivo, or within intraoperative timeframes, over fields-of-view far greater than can be achieved in one OCT image acquisition. For example, tumour margin assessment in breast cancer requires acquisition over linear dimensions of 4-5 centimetres in under 20 minutes. However, the majority of existing techniques are not compatible with these requirements, which may present a hurdle to the effective translation of OCE. To increase throughput, we have designed and developed an OCE system that simultaneously captures two 3D elastograms from opposite sides of a sample. The optical system comprises two interferometers: a common-path interferometer on one side of the sample and a dual-arm interferometer on the other side. This optical system is combined with scanning mechanisms and compression loading techniques to realize dual-scanning OCE. The optical signals scattered from two volumes are simultaneously detected on a single spectrometer by depth-encoding the interference signal from each interferometer. To demonstrate dual-scanning OCE, we performed measurements on tissue-mimicking phantoms containing rigid inclusions and freshly isolated samples of murine hepatocellular carcinoma, highlighting the use of this technique to visualise 3D tumour stiffness. These findings indicate that our technique holds promise for in vivo and intraoperative applications.

Monitoring Phytophthora ramorum and P. kernoviae in soil and rainwater samples collected at two sites on a cornish estate

Treesearch

David Lockley; Judith Turner; Gillian Humphries; Phil Jennings

2008-01-01

Soil samples were collected from quadrats marked out below the canopies of two rhododendrons, one infected by Phytophthora ramorum (Site 1) and the other (Site 2) infected by Phytophthora kernoviae and P. ramorum. Rainwater was collected in high-level and low level traps. Soil and rainwater were sampled at...

Rapid Two-Millisecond Interrogation of Electrochemical, Aptamer-Based Sensor Response Using Intermittent Pulse Amperometry.

PubMed

Santos-Cancel, Mirelis; Lazenby, Robert A; White, Ryan J

2018-06-22

In this manuscript, we employ the technique intermittent pulse amperometry (IPA) to interrogate equilibrium and kinetic target binding to the surface of electrochemical, aptamer-based (E-AB) sensors, achieving as fast as 2 ms time resolution. E-AB sensors comprise an electrode surface modified with a flexible nucleic acid aptamer tethered at the 3'-terminus with a redox-active molecule. The introduction of a target changes the conformation and flexibility of the nucleic acid, which alters the charge transfer rate of the appended redox molecule. Typically, changes in charge transfer rate within this class of sensor are monitored via voltammetric methods. Here, we demonstrate that the use of IPA enables the detection of changes in charge transfer rates (i.e., current) at times <100 μs after the application of a potential pulse. Changes in sensor current are quantitatively related to target analyte concentration and can be used to create binding isotherms. Furthermore, the application of IPA enables rapid probing of the electrochemical surface with a time resolution equivalent to as low as twice the applied potential pulse width, not previously demonstrated with traditional voltammetric techniques employed with E-AB sensors (alternating current, square wave, cyclic). To visualize binding, we developed false-color plots analogous to those used in the field of fast-scan cyclic voltammetry. The use of IPA is universal, as demonstrated with two representative small molecule E-AB sensors directed against the aminoglycoside antibiotic tobramycin and adenosine triphosphate (ATP). Intermittent pulse amperometry exhibits an unprecedented sub-microsecond temporal response and is a general method for measuring rapid sensor performance.

Cyclone-induced rapid creation of extreme Antarctic sea ice conditions

PubMed Central

Wang, Zhaomin; Turner, John; Sun, Bo; Li, Bingrui; Liu, Chengyan

2014-01-01

Two polar vessels, Akademik Shokalskiy and Xuelong, were trapped by thick sea ice in the Antarctic coastal region just to the west of 144°E and between 66.5°S and 67°S in late December 2013. This event demonstrated the rapid establishment of extreme Antarctic sea ice conditions on synoptic time scales. The event was associated with cyclones that developed at lower latitudes. Near the event site, cyclone-enhanced strong southeasterly katabatic winds drove large westward drifts of ice floes. In addition, the cyclones also gave southward ice drift. The arrival and grounding of Iceberg B9B in Commonwealth Bay in March 2011 led to the growth of fast ice around it, forming a northward protruding barrier. This barrier blocked the westward ice drift and hence aided sea ice consolidation on its eastern side. Similar cyclone-induced events have occurred at this site in the past after the grounding of Iceberg B9B. Future events may be predictable on synoptic time scales, if cyclone-induced strong wind events can be predicted. PMID:24937550

Dating of sediment record at two contrasting sites of the Seine River using radioactivity data and hydrological time series.

PubMed

Vrel, Anne; Boust, Dominique; Lesueur, Patrick; Deloffre, Julien; Dubrulle-Brunaud, Carole; Solier, Luc; Rozet, Marianne; Thouroude, Coralie; Cossonnet, Catherine; Thomas, Sandrine

2013-12-01

Sediment cores were collected at the outlet of the highly anthropogenized catchment of the Seine River at two contrasting sites: a flood plain of the lower Seine River and a quasi-permanently submerged harbour basin (or wet dock) in the upper tidal estuary. Analyses of artificial radionuclides ((137)Cs and plutonium isotopes), coupled with hydrological and bathymetric data, lead to a precise dating of the sediment cores collected at the two sites. (137)Cs signals originating from global fallout (early 1960s) and from the Chernobyl accident (1986) are identified, but at different levels due to the incomplete nature or variable continuity of the records. Anomalous (238)Pu concentrations found at both sites (1-2 Bq kg(-1)) are attributed to unknown industrial releases originating from upstream. Interpolating (137)Cs sediment activities under the assumption of a constant sediment rate, those releases were dated back to 1975 ± 1, thus providing a local but reliable time-marker. Age models have highlighted a very contrasting sediment filling dynamics in these two sites. This study presents the first sediment record of alpha- and gamma-emitting artificial radionuclides obtained at the outlet of the huge catchment area of the River Seine, over a period covering the last 50 years. Copyright © 2013 Elsevier Ltd. All rights reserved.

Airborne and Ground-Based Optical Characterization of Legacy Underground Nuclear Test Sites

NASA Astrophysics Data System (ADS)

Vigil, S.; Craven, J.; Anderson, D.; Dzur, R.; Schultz-Fellenz, E. S.; Sussman, A. J.

2015-12-01

Detecting, locating, and characterizing suspected underground nuclear test sites is a U.S. security priority. Currently, global underground nuclear explosion monitoring relies on seismic and infrasound sensor networks to provide rapid initial detection of potential underground nuclear tests. While seismic and infrasound might be able to generally locate potential underground nuclear tests, additional sensing methods might be required to further pinpoint test site locations. Optical remote sensing is a robust approach for site location and characterization due to the ability it provides to search large areas relatively quickly, resolve surface features in fine detail, and perform these tasks non-intrusively. Optical remote sensing provides both cultural and surface geological information about a site, for example, operational infrastructure, surface fractures. Surface geological information, when combined with known or estimated subsurface geologic information, could provide clues concerning test parameters. We have characterized two legacy nuclear test sites on the Nevada National Security Site (NNSS), U20ak and U20az using helicopter-, ground- and unmanned aerial system-based RGB imagery and light detection and ranging (lidar) systems. The multi-faceted information garnered from these different sensing modalities has allowed us to build a knowledge base of how a nuclear test site might look when sensed remotely, and the standoff distances required to resolve important site characteristics.

Explaining the appeal for immigrant men who have sex with men of a community-based rapid HIV-testing site in Montreal (Actuel sur Rue).

PubMed

Lessard, David; Lebouché, Bertrand; Engler, Kim; Thomas, Réjean; Machouf, Nimâ

2015-01-01

Immigrant men who have sex with men (MSM) are vulnerable to HIV. In the last decade, several rapid HIV-testing facilities targeting MSM have been established around the world and seem popular among immigrants. This study analyzes factors contributing to immigrant MSM's use of Actuel sur Rue (AsR), a community-based rapid HIV-testing site in Montreal's gay village, where 31% of clients are immigrants. From October 2013 to January 2014, AsR staff compiled a list of new clients born outside of Canada. With their consent, 40 immigrant MSM were reached among these new clients for a 15-minute phone survey entailing open-ended and multiple-choice questions. The survey sought immigrant MSM's reasons for visiting AsR; satisfaction with service and staff; and open comments. An inductive thematic analysis was conducted with the qualitative data, and descriptive statistics were produced with the quantitative data. The qualitative findings indicate that the main reasons for seeking an HIV test were a recent risk, routine testing, or being in a new relationship. Clients chose AsR mainly because it is easily accessible, service is fast or they heard about it from a friend. The quantitative findings indicate that rates of satisfaction were high (over 90% were satisfied about all aspects except for openings hours) and more than 80% felt comfortable while receiving services at AsR. Nevertheless, this study's findings have implications for improving services. They stress the importance of offering rapid yet comprehensive service and of taking into account immigrant MSM's concerns for confidentiality.

Access to NMR Spectroscopy for Two-Year College Students: The NMR Site at Trinity University

ERIC Educational Resources Information Center

Mills, Nancy S.; Shanklin, Michael

2011-01-01

Students at two-year colleges and small four-year colleges have often obtained their exposure to NMR spectroscopy through "canned" spectra because the cost of an NMR spectrometer, particularly a high-field spectrometer, is prohibitive in these environments. This article describes the design of a NMR site at Trinity University in which…

Experimental warming differentially affects microbial structure and activity in two contrasted moisture sites in a Sphagnum-dominated peatland.

PubMed

Delarue, Frédéric; Buttler, Alexandre; Bragazza, Luca; Grasset, Laurent; Jassey, Vincent E J; Gogo, Sébastien; Laggoun-Défarge, Fatima

2015-04-01

Several studies on the impact of climate warming have indicated that peat decomposition/mineralization will be enhanced. Most of these studies deal with the impact of experimental warming during summer when prevalent abiotic conditions are favorable to decomposition. Here, we investigated the effect of experimental air warming by open-top chambers (OTCs) on water-extractable organic matter (WEOM), microbial biomasses and enzymatic activities in two contrasted moisture sites named Bog and Fen sites, the latter considered as the wetter ones. While no or few changes in peat temperature and water content appeared under the overall effect of OTCs, we observed that air warming smoothed water content differences and led to a decrease in mean peat temperature at the warmed Bog sites. This thermal discrepancy between the two sites led to contrasting changes in microbial structure and activities: a rise in hydrolytic activity at the warmed Bog sites and a relative enhancement of bacterial biomass at the warmed Fen sites. These features were not associated with any change in WEOM properties namely carbon and sugar contents and aromaticity, suggesting that air warming did not trigger any shift in OM decomposition. Using various tools, we show that the use of single indicators of OM decomposition can lead to fallacious conclusions. Lastly, these patterns may change seasonally as a consequence of complex interactions between groundwater level and air warming, suggesting the need to improve our knowledge using a high time-resolution approach. Copyright © 2015 Elsevier B.V. All rights reserved.

Basin characteristics, history of stream gaging, and statistical summary of selected streamflow records for the Rapid Creek basin, western South Dakota

USGS Publications Warehouse

Driscoll, Daniel G.; Zogorski, John S.

1990-01-01

The report presents a summary of basin characteristics affecting streamflow, a history of the U.S. Geological Survey 's stream-gaging program, and a compilation of discharge records and statistical summaries for selected sites within the Rapid Creek basin. It is the first in a series which will investigate surface-water/groundwater relations along Rapid Creek. The summary of basin characteristics includes descriptions of the geology and hydrogeology, physiography and climate, land use and vegetation, reservoirs, and water use within the basin. A recounting of the U.S. Geological Survey 's stream-gaging program and a tabulation of historic stream-gaging stations within the basin are furnished. A compilation of monthly and annual mean discharge values for nine currently operated, long-term, continuous-record, streamflow-gaging stations on Rapid Creek is presented. The statistical summary for each site includes summary statistics on monthly and annual mean values, correlation matrix for monthly values, serial correlation for 1 year lag for monthly values, percentile rankings for monthly and annual mean values, low and high value tables, duration curves, and peak-discharge tables. Records of monthend contents for two reservoirs within the basin also are presented. (USGS)

Continuous feed, on-site composting of kitchen garbage.

PubMed

Hwang, Eung-Ju; Shin, Hang-Sik; Tay, Joo-Hwa

2002-04-01

Kitchen garbage generated at a school cafeteria was treated and stabilised in a controlled on-site composting unit for volume reduction and on-site utilisation of processed garbage. The on-site composter was fed with the garbage on a daily basis during the two-months experimental period. Compost was not removed from the unit but was entirely reused as a bulking agent in order to minimise the need for additional bulking agent and compost handling. Performance of the composter tinder this condition was investigated. Most of the easily degradable organic matter (EDM) in the garbage was biodegraded rapidly, and the final product had a low content of EDM. Lipids, total sugar, and hemi-cellulose were degraded 96%, 81%, and 66% respectively. Free air space (FAS) was higher than 0.5 all the time, so accumulation of dry matter in the unit was not significant in reducing reaction efficiency. Other reaction parameters such as pH and MC were kept within a suitable range; however, it was advisable to maintain MC at over 46%. As a result, this method of operation was able to stabilise the garbage with low sawdust demand and little compost production.

Social Networking Sites as Virtual Communities of Practice: A Mixed Method Study

ERIC Educational Resources Information Center

Davis, Lorretta J.

2010-01-01

Membership in social networking sites is increasing rapidly. Social networking sites serve many purposes including networking, communication, recruitment, and sharing knowledge. Social networking sites, public or private, may be hosted on applications such as Facebook and LinkedIn. As individuals begin to follow and participate in social…

Rainfall and cave water isotopic relationships in two South-France sites

NASA Astrophysics Data System (ADS)

Genty, D.; Labuhn, I.; Hoffmann, G.; Danis, P. A.; Mestre, O.; Bourges, F.; Wainer, K.; Massault, M.; Van Exter, S.; Régnier, E.; Orengo, Ph.; Falourd, S.; Minster, B.

2014-04-01

This article presents isotopic measurements (δ18O and δD) of precipitation and cave drip water from two sites in southern France in order to investigate the link between rainfall and seepage water, and to characterize regional rainfall isotopic variability. These data, which are among the longest series in France, come from two rainfall stations in south-west France (Le Mas 1996-2012, and Villars 1998-2012; typically under Atlantic influence), and from one station in the south-east (Orgnac 2000-2012; under both Mediterranean and Atlantic influence). Rainfall isotopic composition is compared to drip water collected under stalactites from the same sites: Villars Cave (four drip stations 1999-2012) in the south-west, and Chauvet Cave (two drip stations 2000-2012) in the south-east, near Orgnac. The study of these isotopic data sets allows the following conclusions to be drawn about the rainfall/drip water relationships and about rainfall variability: (1) the cave drip water isotopic composition does not show any significant changes since the beginning of measurements; in order to explain its isotopic signature it is necessary to integrate weighted rainfall δ18O of all months during several years, which demonstrates that, even at shallow depths (10-50 m), cave drip water is a mixture of rain water integrated over relatively long periods, which give an apparent time residence from several months to up to several years. These results have important consequences on the interpretation of proxies like speleothem fluid inclusions and tree-ring cellulose isotopic composition, which are used for paleoclimatic studies; (2) in the Villars Cave, where drip stations at two different depths were studied, lower δ18O values were observed in the lower galleries, which might be due to winter season overflows during infiltration and/or to older rain water with a different isotopic composition that reaches the lower galleries after years; (3) local precipitation is characterized by

Bioavailability, ecotoxicity, and geological characteristics of trace lead in sediments from two sites on Negro River, Uruguay, South America.

PubMed

Míguez, Diana M; Huertas, Raquel; Carrara, María V; Carnikián, Agustín; Bouvier, María E; Martínez, María J; Keel, Karen; Pioda, Carolina; Darré, Elena; Pérez, Ramiro; Viera, Santiago; Massa, Enrique

2012-04-01

Bioassays of two sites along the Rio Negro in Uruguay indicate ecotoxicity, which could be attributable to trace concentrations of lead in river sediments. Monthly samples at two sites at Baygorria and Bonete locations were analyzed for both particle size and lead. Lead was determined by atomic spectrometry in river water and sediment and particle size by sieving and sedimentation. Data showed that Baygorria's sediments have greater percentage of clay than Bonete's (20.4 and 5.8%, respectively). Lead was measurable in Baygorria's sediments, meanwhile in Bonete's, it was always below the detection limit. In water samples, lead was below detection limit at both sites. Bioassays using sub-lethal growth and survival test with Hyalella curvispina amphipod, screening with bioluminescent bacteria Photobacterium leiognathi, and acute toxicity bioassay with Pimephales promelas fish indicated toxicity at Baygorria, with much less effect at Bonete. Even though no lethal effects could be demonstrated, higher sub-lethal toxicity was found in samples from Baygorria site, showing a possible concentration of the contaminant in the clay fraction.

iSS-PseDNC: identifying splicing sites using pseudo dinucleotide composition.

PubMed

Chen, Wei; Feng, Peng-Mian; Lin, Hao; Chou, Kuo-Chen

2014-01-01

In eukaryotic genes, exons are generally interrupted by introns. Accurately removing introns and joining exons together are essential processes in eukaryotic gene expression. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapid and effective detection of splice sites that play important roles in gene structure annotation and even in RNA splicing. Although a series of computational methods were proposed for splice site identification, most of them neglected the intrinsic local structural properties. In the present study, a predictor called "iSS-PseDNC" was developed for identifying splice sites. In the new predictor, the sequences were formulated by a novel feature-vector called "pseudo dinucleotide composition" (PseDNC) into which six DNA local structural properties were incorporated. It was observed by the rigorous cross-validation tests on two benchmark datasets that the overall success rates achieved by iSS-PseDNC in identifying splice donor site and splice acceptor site were 85.45% and 87.73%, respectively. It is anticipated that iSS-PseDNC may become a useful tool for identifying splice sites and that the six DNA local structural properties described in this paper may provide novel insights for in-depth investigations into the mechanism of RNA splicing.

Simulating the Surface Relief of Nanoaerosols Obtained via the Rapid Cooling of Droplets

NASA Astrophysics Data System (ADS)

Tovbin, Yu. K.; Zaitseva, E. S.; Rabinovich, A. B.

2018-03-01

An approach is formulated that theoretically describes the structure of a rough surface of small aerosol particles obtained from a liquid droplet upon its rapid cooling. The problem consists of two stages. In the first stage, a concentration profile of the droplet-vapor transition region is calculated. In the second stage, local fractions of vacant sites and their pairs are found on the basis of this profile, and the rough structure of a frozen droplet surface transitioning to the solid state is calculated. Model parameters are the temperature of the initial droplet and those of the lateral interaction between droplet atoms. Information on vacant sites inside the region of transition allows us to identify adsorption centers and estimate the monolayer capacity, compared to that of the total space of the region of transition. The approach is oriented toward calculating adsorption isotherms on real surfaces.

Persistence of uranium groundwater plumes: contrasting mechanisms at two DOE sites in the groundwater-river interaction zone.

PubMed

Zachara, John M; Long, Philip E; Bargar, John; Davis, James A; Fox, Patricia; Fredrickson, Jim K; Freshley, Mark D; Konopka, Allan E; Liu, Chongxuan; McKinley, James P; Rockhold, Mark L; Williams, Kenneth H; Yabusaki, Steve B

2013-04-01

We examine subsurface uranium (U) plumes at two U.S. Department of Energy sites that are located near large river systems and are influenced by groundwater-river hydrologic interaction. Following surface excavation of contaminated materials, both sites were projected to naturally flush remnant uranium contamination to levels below regulatory limits (e.g., 30 μg/L or 0.126 μmol/L; U.S. EPA drinking water standard), with 10 years projected for the Hanford 300 Area (Columbia River) and 12 years for the Rifle site (Colorado River). The rate of observed uranium decrease was much lower than expected at both sites. While uncertainty remains, a comparison of current understanding suggests that the two sites have common, but also different mechanisms controlling plume persistence. At the Hanford 300 A, the persistent source is adsorbed U(VI) in the vadose zone that is released to the aquifer during spring water table excursions. The release of U(VI) from the vadose zone and its transport within the oxic, coarse-textured aquifer sediments is dominated by kinetically-limited surface complexation. Modeling implies that annual plume discharge volumes to the Columbia River are small (site, slow oxidation of naturally reduced, contaminant U(IV) in the saturated zone and a continuous influx of U(VI) from natural, up-gradient sources influence plume persistence. Rate-limited mass transfer and surface complexation also control U(VI) migration velocity in the sub-oxic Rifle groundwater. Flux of U(VI) from the vadose zone at the Rifle site may be locally important, but it is not the dominant process that sustains the plume. A wide range in microbiologic functional diversity exists at both sites. Strains of Geobacter and other metal reducing bacteria are present at low natural abundance that are capable of enzymatic U(VI) reduction in localized zones of accumulated detrital organic carbon or after organic carbon amendment. Major differences between the

Persistence of uranium groundwater plumes: Contrasting mechanisms at two DOE sites in the groundwater-river interaction zone

NASA Astrophysics Data System (ADS)

Zachara, John M.; Long, Philip E.; Bargar, John; Davis, James A.; Fox, Patricia; Fredrickson, Jim K.; Freshley, Mark D.; Konopka, Allan E.; Liu, Chongxuan; McKinley, James P.; Rockhold, Mark L.; Williams, Kenneth H.; Yabusaki, Steve B.

2013-04-01

We examine subsurface uranium (U) plumes at two U.S. Department of Energy sites that are located near large river systems and are influenced by groundwater-river hydrologic interaction. Following surface excavation of contaminated materials, both sites were projected to naturally flush remnant uranium contamination to levels below regulatory limits (e.g., 30 μg/L or 0.126 μmol/L; U.S. EPA drinking water standard), with 10 years projected for the Hanford 300 Area (Columbia River) and 12 years for the Rifle site (Colorado River). The rate of observed uranium decrease was much lower than expected at both sites. While uncertainty remains, a comparison of current understanding suggests that the two sites have common, but also different mechanisms controlling plume persistence. At the Hanford 300 A, the persistent source is adsorbed U(VI) in the vadose zone that is released to the aquifer during spring water table excursions. The release of U(VI) from the vadose zone and its transport within the oxic, coarse-textured aquifer sediments is dominated by kinetically-limited surface complexation. Modeling implies that annual plume discharge volumes to the Columbia River are small (< one pore volume). At the Rifle site, slow oxidation of naturally reduced, contaminant U(IV) in the saturated zone and a continuous influx of U(VI) from natural, up-gradient sources influence plume persistence. Rate-limited mass transfer and surface complexation also control U(VI) migration velocity in the sub-oxic Rifle groundwater. Flux of U(VI) from the vadose zone at the Rifle site may be locally important, but it is not the dominant process that sustains the plume. A wide range in microbiologic functional diversity exists at both sites. Strains of Geobacter and other metal reducing bacteria are present at low natural abundance that are capable of enzymatic U(VI) reduction in localized zones of accumulated detrital organic carbon or after organic carbon amendment. Major differences between

Cation distributions on rapidly solidified cobalt ferrite

NASA Technical Reports Server (NTRS)

De Guire, Mark R.; Kalonji, Gretchen; O'Handley, Robert C.

1990-01-01

The cation distributions in two rapidly solidified cobalt ferrites have been determined using Moessbauer spectroscopy at 4.2 K in an 8-T magnetic field. The samples were obtained by gas atomization of a Co0-Fe2O3-P2O5 melt. The degree of cation disorder in both cases was greater than is obtainable by cooling unmelted cobalt ferrite. The more rapidly cooled sample exhibited a smaller departure from the equilibrium cation distribution than did the more slowly cooled sample. This result is explained on the basis of two competing effects of rapid solidification: high cooling rate of the solid, and large undercooling.

A rapid assessment survey of invasive species of macrobenthic invertebrates in Korean waters

NASA Astrophysics Data System (ADS)

Park, Chul; Kim, Sung-Tae; Hong, Jae-Sang; Choi, Keun-Hyung

2017-09-01

Introduced species are a growing and imminent threat to living marine resources in parts of the world's oceans. The present study is a rapid assessment survey of invasive macrobenthic invertebrate species in Korean ports. We surveyed over 40 ports around Korea during the period of May 2010 March 2013. Among the sampling sites were concrete walls, docks and associated floats, bumpers, tires, and ropes which might harbor non-native species. We found 15 invasive species as follows: one Sponge, two Bryozoans, three Mollusks, one Polychaete, four Cirripedes, and four Ascidians. Three morphologically similar species, namely X. atrata, M. galloprovincialis, and X. securis were further examined for distinctions in their morphology. Although they could be reasonably distinguished based on shell shapes, significant overlap was noted so that additional analysis may be required to correctly distinguish them. Although many of the introduced species have already spread to all three coastal areas, newly arrived invasive species showed a relatively restricted range, with a serpulid polychaete Ficopomatus enigmaticus and a mytilid bivalve Xenostrobus securis found only at a few sites on the East Coast. An exception is for Balanus perforatus, which has rapidly colonized the East coast of Korea following its introduction into the region. Successful management of invasive macrobenthic invertebrates should be established in order to contain the spread of these newly arrived species.

Controlling and fine tuning the physical properties of two identical metal coordination sites in de novo designed three stranded coiled coil peptides.

PubMed

Iranzo, Olga; Chakraborty, Saumen; Hemmingsen, Lars; Pecoraro, Vincent L

2011-01-19

Herein we report how de novo designed peptides can be used to investigate whether the position of a metal site along a linear sequence that folds into a three-stranded α-helical coiled coil defines the physical properties of Cd(II) ions in either CdS(3) or CdS(3)O (O-being an exogenous water molecule) coordination environments. Peptides are presented that bind Cd(II) into two identical coordination sites that are located at different topological positions at the interior of these constructs. The peptide GRANDL16PenL19IL23PenL26I binds two Cd(II) as trigonal planar 3-coordinate CdS(3) structures whereas GRANDL12AL16CL26AL30C sequesters two Cd(II) as pseudotetrahedral 4-coordinate CdS(3)O structures. We demonstrate how for the first peptide, having a more rigid structure, the location of the identical binding sites along the linear sequence does not affect the physical properties of the two bound Cd(II). However, the sites are not completely independent as Cd(II) bound to one of the sites ((113)Cd NMR chemical shift of 681 ppm) is perturbed by the metalation state (apo or [Cd(pep)(Hpep)(2)](+) or [Cd(pep)(3)](-)) of the second center ((113)Cd NMR chemical shift of 686 ppm). GRANDL12AL16CL26AL30C shows a completely different behavior. The physical properties of the two bound Cd(II) ions indeed depend on the position of the metal center, having pK(a2) values for the equilibrium [Cd(pep)(Hpep)(2)](+) → [Cd(pep)(3)](-) + 2H(+) (corresponding to deprotonation and coordination of cysteine thiols) that range from 9.9 to 13.9. In addition, the L26AL30C site shows dynamic behavior, which is not observed for the L12AL16C site. These results indicate that for these systems one cannot simply assign a "4-coordinate structure" and assume certain physical properties for that site since important factors such as packing of the adjacent Leu, size of the intended cavity (endo vs exo) and location of the metal site play crucial roles in determining the final properties of the bound

Rapid on-site defibrillation versus community program.

PubMed

Fedoruk, J C; Paterson, D; Hlynka, M; Fung, K Y; Gobet, Michael; Currie, Wayne

2002-01-01

For patients who suffer out-of-hospital cardiac arrest, the time from collapse to initial defibrillation is the single most important factor that affects survival to hospital discharge. The purpose of this study was to compare the survival rates of cardiac arrest victims within an institution that has a rapid defibrillation program with those of its own urban community, tiered EMS system. A logistic regression analysis of a retrospective data series (n = 23) and comparative analysis to a second retrospective data series (n = 724) were gathered for the study period September 1994 to September 1999. The first data series included all persons at Casino Windsor who suffered a cardiac arrest. Data collected included: age, gender, death/survival (neurologically intact discharge), presenting rhythm (ventricular fibrillation (VF), ventricular tachycardia (VT), or other), time of collapse, time to arrival of security personnel, time to initiation of cardiopulmonary resuscitation (CPR) prior to defibrillation (when applicable), time to arrival of staff nurse, time to initial defibrillation, and time to return of spontaneous circulation (if any). Significantly, all arrests within this series were witnessed by the surveillance camera systems, allowing time of collapse to be accurately determined rather than estimated. These data were compared to those of similar events, times, and intervals for all patients in the greater Windsor area who suffered cardiac arrest. This second series was based upon the Ontario Prehospital Advanced Life Support (OPALS) Study database, as coordinated by the Clinical Epidemiology Unit of the Ottawa Hospital, University of Ottawa. The Casino Windsor had 23 cases of cardiac arrests. Of the cases, 13 (56.5%) were male and 10 (43.5%) were female. All cases (100%) were witnessed. The average of the ages was 61.1 years, of the time to initial defibrillation was 7.7 minutes, and of the time for EMS to reach the patient was 13.3 minutes. The presenting

Rapid-Sequence Serial Sexual Homicides.

PubMed

Schlesinger, Louis B; Ramirez, Stephanie; Tusa, Brittany; Jarvis, John P; Erdberg, Philip

2017-03-01

Serial sexual murderers have been described as committing homicides in a methodical manner, taking substantial time between offenses to elude the authorities. The results of our study of the temporal patterns (i.e., the length of time between homicides) of a nonrandom national sample of 44 serial sexual murderers and their 201 victims indicate that this representation may not always be accurate. Although 25 offenders (56.8%) killed with longer than a 14-day period between homicides, a sizeable subgroup was identified: 19 offenders (43.2%) who committed homicides in rapid-sequence fashion, with fewer than 14 days between all or some of the murders. Six offenders (13.6%) killed all their victims in one rapid-sequence, spree-like episode, with homicides just days apart or sometimes two murders in the same day. Thirteen offenders (29.5%) killed in one or two rapid-sequence clusters (i.e., more than one murder within a 14-day period, as well as additional homicides with greater than 14 days between each). The purpose of our study was to describe this subgroup of rapid-sequence offenders who have not been identified until now. These findings argue for accelerated forensic assessments of dangerousness and public safety when a sexual murder is detected. Psychiatric disorders with rapidly occurring symptom patterns, or even atypical mania or mood dysregulation, may serve as exemplars for understanding this extraordinary group of offenders. © 2017 American Academy of Psychiatry and the Law.

Genealogies of rapidly adapting populations

PubMed Central

Neher, Richard A.; Hallatschek, Oskar

2013-01-01

The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on the null hypothesis that natural selection is a weak or infrequent evolutionary force. However, many species, particularly pathogens, are under continuous pressure to adapt in response to changing environments. A statistical framework for inference from diversity data of such populations is currently lacking. Towards this goal, we explore the properties of genealogies in a model of continual adaptation in asexual populations. We show that lineages trace back to a small pool of highly fit ancestors, in which almost simultaneous coalescence of more than two lineages frequently occurs. Whereas such multiple mergers are unlikely under the neutral coalescent, they create a unique genetic footprint in adapting populations. The site frequency spectrum of derived neutral alleles, for example, is nonmonotonic and has a peak at high frequencies, whereas Tajima’s D becomes more and more negative with increasing sample size. Because multiple merger coalescents emerge in many models of rapid adaptation, we argue that they should be considered as a null model for adapting populations. PMID:23269838

Two standardized fractions of Gardenia jasminoides Ellis with rapid antidepressant effects are differentially associated with BDNF up-regulation in the hippocampus.

PubMed

Ren, Li; Tao, Weiwei; Zhang, Hailou; Xue, Wenda; Tang, Juanjuan; Wu, Ruyan; Xia, Baomei; Wu, Haoxing; Chen, Gang

2016-07-01

B in the hippocampus post a single administration. Two standardized fractions GJ-PE and GJ-BO exhibited comparable rapid antidepressant-like effects on the CMS mice. However, only the effects of GJ-PE was associated with BDNF signaling. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Contrasting physiological responses of two co-occurring eucalypts to seasonal drought at restored bauxite mine sites.

PubMed

Szota, Christopher; Farrell, Claire; Koch, John M; Lambers, Hans; Veneklaas, Erik J

2011-10-01

This study describes the physiological response of two co-occurring tree species (Eucalyptus marginata and Corymbia calophylla) to seasonal drought at low- and high-quality restored bauxite mine sites in south-western Australia. Seasonal changes in photosynthesis (A), stomatal conductance (g(s)), leaf water potential (ψ), leaf osmotic potential (ψ), leaf relative water content (RWC) and pressure-volume analysis were captured over an 18-month field study to (i) determine the nature and severity of physiological stress in relation to site quality and (ii) identify any physiological differences between the two species. Root system restriction at the low-quality site reduced maximum rates of gas exchange (g(s) and A) and increased water stress (midday ψ and daily RWC) in both species during drought. Both species showed high stomatal sensitivity during drought; however, E. marginata demonstrated a higher dehydration tolerance where ψ and RWC fell to -3.2 MPa and 73% compared with -2.4 MPa and 80% for C. calophylla. Corymbia calophylla showed lower g(s) and higher ψ and RWC during drought, indicating higher drought tolerance. Pressure-volume curves showed that cell-wall elasticity of E. marginata leaves increased in response to drought, while C. calophylla leaves showed lower osmotic potential at zero turgor in summer than in winter, indicating osmotic adjustment. Both species are clearly able to tolerate seasonal drought at hostile sites; however, by C. calophylla closing stomata earlier in the drought cycle, maintaining a higher water status during drought and having the additional mechanism of osmotic adjustment, it may have a greater capacity to survive extended periods of drought.

Two Mars years of surface changes seen at the Viking Landing sites

NASA Technical Reports Server (NTRS)

Guinness, E. A.; Leff, C. E.; Arvidson, R. E.

1982-01-01

An analysis of the spectrophotometric properties of the new dust deposited at the Viking Lander 1 site indicates that the new deposits are the same as the bright red material that only partially covered the site at the beginning of the mission. Certain areas of the Viking 1 site also showed an increase in contrast during the second year. The contrast increase is thought to be due to the partial removal of the recently deposited dust cover by high-velocity winds. What is more, a small soil slump occurred near the base of a boulder lying about 25 m from the lander. It is noted that whereas no obvious erosion has been detected at the Viking 2 site, periodic removal of the dust cover at this site is implied by the abundance of rocks at the site.

Rapid Spontaneously Resolving Acute Subdural Hematoma

PubMed Central

Gan, Qi; Zhao, Hexiang; Zhang, Hanmei; You, Chao

2017-01-01

Introduction: This study reports a rare patient of a rapid spontaneously resolving acute subdural hematoma. In addition, an analysis of potential clues for the phenomenon is presented with a review of the literature. Patient Presentation: A 1-year-and-2-month-old boy fell from a height of approximately 2 m. The patient was in a superficial coma with a Glasgow Coma Scale of 8 when he was transferred to the authors’ hospital. Computed tomography revealed the presence of an acute subdural hematoma with a midline shift beyond 1 cm. His guardians refused invasive interventions and chose conservative treatment. Repeat imaging after 15 hours showed the evident resolution of the hematoma and midline reversion. Progressive magnetic resonance imaging demonstrated the complete resolution of the hematoma, without redistribution to a remote site. Conclusions: Even though this phenomenon has a low incidence, the probability of a rapid spontaneously resolving acute subdural hematoma should be considered when patients present with the following characteristics: children or elderly individuals suffering from mild to moderate head trauma; stable or rapidly recovered consciousness; and simple acute subdural hematoma with a moderate thickness and a particularly low-density band in computed tomography scans. PMID:28468224

Accuracy of commercially available c-reactive protein rapid tests in the context of undifferentiated fevers in rural Laos.

PubMed

Phommasone, Koukeo; Althaus, Thomas; Souvanthong, Phonesavanh; Phakhounthong, Khansoudaphone; Soyvienvong, Laxoy; Malapheth, Phatthaphone; Mayxay, Mayfong; Pavlicek, Rebecca L; Paris, Daniel H; Dance, David; Newton, Paul; Lubell, Yoel

2016-02-04

C-Reactive Protein (CRP) has been shown to be an accurate biomarker for discriminating bacterial from viral infections in febrile patients in Southeast Asia. Here we investigate the accuracy of existing rapid qualitative and semi-quantitative tests as compared with a quantitative reference test to assess their potential for use in remote tropical settings. Blood samples were obtained from consecutive patients recruited to a prospective fever study at three sites in rural Laos. At each site, one of three rapid qualitative or semi-quantitative tests was performed, as well as a corresponding quantitative NycoCard Reader II as a reference test. We estimate the sensitivity and specificity of the three tests against a threshold of 10 mg/L and kappa values for the agreement of the two semi-quantitative tests with the results of the reference test. All three tests showed high sensitivity, specificity and kappa values as compared with the NycoCard Reader II. With a threshold of 10 mg/L the sensitivity of the tests ranged from 87-98 % and the specificity from 91-98 %. The weighted kappa values for the semi-quantitative tests were 0.7 and 0.8. The use of CRP rapid tests could offer an inexpensive and effective approach to improve the targeting of antibiotics in remote settings where health facilities are basic and laboratories are absent. This study demonstrates that accurate CRP rapid tests are commercially available; evaluations of their clinical impact and cost-effectiveness at point of care is warranted.

UTSA-74: A MOF-74 Isomer with Two Accessible Binding Sites per Metal Center for Highly Selective Gas Separation.

PubMed

Luo, Feng; Yan, Changsheng; Dang, Lilong; Krishna, Rajamani; Zhou, Wei; Wu, Hui; Dong, Xinglong; Han, Yu; Hu, Tong-Liang; O'Keeffe, Michael; Wang, Lingling; Luo, Mingbiao; Lin, Rui-Biao; Chen, Banglin

2016-05-04

A new metal-organic framework Zn2(H2O)(dobdc)·0.5(H2O) (UTSA-74, H4dobdc = 2,5-dioxido-1,4-benzenedicarboxylic acid), Zn-MOF-74/CPO-27-Zn isomer, has been synthesized and structurally characterized. It has a novel four coordinated fgl topology with one-dimensional channels of about 8.0 Å. Unlike metal sites in the well-established MOF-74 with a rod-packing structure in which each of them is in a five coordinate square pyramidal coordination geometry, there are two different Zn(2+) sites within the binuclear secondary building units in UTSA-74 in which one of them (Zn1) is in a tetrahedral while another (Zn2) in an octahedral coordination geometry. After activation, the two axial water molecules on Zn2 sites can be removed, generating UTSA-74a with two accessible gas binding sites per Zn2 ion. Accordingly, UTSA-74a takes up a moderately high and comparable amount of acetylene (145 cm(3)/cm(3)) to Zn-MOF-74. Interestingly, the accessible Zn(2+) sites in UTSA-74a are bridged by carbon dioxide molecules instead of being terminally bound in Zn-MOF-74, so UTSA-74a adsorbs a much smaller amount of carbon dioxide (90 cm(3)/cm(3)) than Zn-MOF-74 (146 cm(3)/cm(3)) at room temperature and 1 bar, leading to a superior MOF material for highly selective C2H2/CO2 separation. X-ray crystal structures, gas sorption isotherms, molecular modeling, and simulated and experimental breakthroughs comprehensively support this result.

Metagenome sequencing of the microbial community of two Brazilian anthropogenic Amazon dark earth sites, Brazil.

PubMed

Lemos, Leandro Nascimento; de Souza, Rosineide Cardoso; de Souza Cannavan, Fabiana; Patricio, André; Pylro, Victor Satler; Hanada, Rogério Eiji; Mui, Tsai Siu

2016-12-01

The Anthropogenic Amazon Dark Earth soil is considered one of the world's most fertile soils. These soils differs from conventional Amazon soils because its higher organic content concentration. Here we describe the metagenome sequencing of microbial communities of two sites of Anthropogenic Amazon Dark Earth soils from Amazon Rainforest, Brazil. The raw sequence data are stored under Short Read Accession number: PRJNA344917.

Two classes of cholesterol binding sites for the β2AR revealed by thermostability and NMR.

PubMed

Gater, Deborah L; Saurel, Olivier; Iordanov, Iordan; Liu, Wei; Cherezov, Vadim; Milon, Alain

2014-11-18

Cholesterol binding to G protein-coupled receptors (GPCRs) and modulation of their activities in membranes is a fundamental issue for understanding their function. Despite the identification of cholesterol binding sites in high-resolution x-ray structures of the ?2 adrenergic receptor (β2AR) and other GPCRs, the binding affinity of cholesterol for this receptor and exchange rates between the free and bound cholesterol remain unknown. In this study we report the existence of two classes of cholesterol binding sites in β2AR. By analyzing the β2AR unfolding temperature in lipidic cubic phase (LCP) as a function of cholesterol concentration we observed high-affinity cooperative binding of cholesterol with sub-nM affinity constant. In contrast, saturation transfer difference (STD) NMR experiments revealed the existence of a second class of cholesterol binding sites, in fast exchange on the STD NMR timescale. Titration of the STD signal as a function of cholesterol concentration provided a lower limit of 100 mM for their dissociation constant. However, these binding sites are specific for both cholesterol and β2AR, as shown with control experiments using ergosterol and a control membrane protein (KpOmpA). We postulate that this specificity is mediated by the high-affinity bound cholesterol molecules and propose the formation of transient cholesterol clusters around the high-affinity binding sites.

A multiplexed microfluidic toolbox for the rapid optimization of affinity-driven partition in aqueous two phase systems.

PubMed

Bras, Eduardo J S; Soares, Ruben R G; Azevedo, Ana M; Fernandes, Pedro; Arévalo-Rodríguez, Miguel; Chu, Virginia; Conde, João P; Aires-Barros, M Raquel

2017-09-15

Antibodies and other protein products such as interferons and cytokines are biopharmaceuticals of critical importance which, in order to be safely administered, have to be thoroughly purified in a cost effective and efficient manner. The use of aqueous two-phase extraction (ATPE) is a viable option for this purification, but these systems are difficult to model and optimization procedures require lengthy and expensive screening processes. Here, a methodology for the rapid screening of antibody extraction conditions using a microfluidic channel-based toolbox is presented. A first microfluidic structure allows a simple negative-pressure driven rapid screening of up to 8 extraction conditions simultaneously, using less than 20μL of each phase-forming solution per experiment, while a second microfluidic structure allows the integration of multi-step extraction protocols based on the results obtained with the first device. In this paper, this microfluidic toolbox was used to demonstrate the potential of LYTAG fusion proteins used as affinity tags to optimize the partitioning of antibodies in ATPE processes, where a maximum partition coefficient (K) of 9.2 in a PEG 3350/phosphate system was obtained for the antibody extraction in the presence of the LYTAG-Z dual ligand. This represents an increase of approx. 3.7 fold when compared with the same conditions without the affinity molecule (K=2.5). Overall, this miniaturized and versatile approach allowed the rapid optimization of molecule partition followed by a proof-of-concept demonstration of an integrated back extraction procedure, both of which are critical procedures towards obtaining high purity biopharmaceuticals using ATPE. Copyright © 2017 Elsevier B.V. All rights reserved.

Electronic Cigarette Marketing Online: a Multi-Site, Multi-Product Comparison.

PubMed

Chu, Kar-Hai; Sidhu, Anupreet K; Valente, Thomas W

2015-01-01

Electronic cigarette awareness and use has been increasing rapidly. E-cigarette brands have utilized social networking sites to promote their products, as the growth of the e-cigarette industry has paralleled that of Web 2.0. These online platforms are cost-effective and have unique technological features and user demographics that can be attractive for selective marketing. The popularity of multiple sites also poses a risk of exposure to social networks where e-cigarette brands might not have a presence. To examine the marketing strategies of leading e-cigarette brands on multiple social networking sites, and to identify how affordances of the digital media are used to their advantage. Secondary analyses include determining if any brands are benefitting from site demographics, and exploring cross-site diffusion of marketing content through multi-site users. We collected data from two e-cigarette brands from four social networking sites over approximately 2.5 years. Content analysis is used to search for themes, population targeting, marketing strategies, and cross-site spread of messages. Twitter appeared to be the most frequently used social networking site for interacting directly with product users. Facebook supported informational broadcasts, such as announcements regarding political legislation. E-cigarette brands also differed in their approaches to their users, from informal conversations to direct product marketing. E-cigarette makers use different strategies to market their product and engage their users. There was no evidence of direct targeting of vulnerable populations, but the affordances of the different sites are exploited to best broadcast context-specific messages. We developed a viable method to study cross-site diffusion, although additional refinement is needed to account for how different types of digital media are used.

Rapid All-Sky Transient Discovery and Analysis with Evryscope

NASA Astrophysics Data System (ADS)

Corbett, Henry T.; Law, Nicholas; Fors, Octavi; Ratzloff, Jeff; Goeke, Erin; Howard, Ward S.

2018-01-01

The Evryscope is an array of 24 small telescopes on a common mount, capable of observing the entire visible sky down to g' ~ 16 with a two-minute cadence. Each exposure covers 8000 square degrees over 691 MPix and requires minimal readout time, providing 97% continuous coverage of the night sky. The system's large field of view and rapid cadence enable exploration of a previously inaccessible parameter space of bright and fast transients, including nearby microlensing events, supernovae, and kilonovae GW counterparts. The first instrument, located at CTIO in Chile, was deployed in mid-2015 and is currently in production creating multi-year light curves with percent-level precision. A second identical system is on track for deployment at Mount Laguna Observatory in California in early 2018. Once operational, the two sites will provide simultaneous two-color photometry over a 4000 square degree overlapping region accessible to both instruments, operating as a combined discovery and follow-up network for transient phenomena on all nearby stars and many nearby galaxies. I will present recent science results from the Evryscope and an overview of our data reduction pipeline.

The Rapid Benefit Indicators Approach: A Process for Assessing the Social Benefits of Ecological Restoration

EPA Science Inventory

The Rapid Benefit Indicators (RBI) Approach is an easy-to-use process for assessing restoration sites using non-monetary benefit indicators. The RBI uses readily-available data to estimate and quantify benefits to people around an ecological restoration site. It is a five step as...

Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein.

PubMed

Velmurugu, Yogambigai; Vivas, Paula; Connolly, Mitchell; Kuznetsov, Serguei V; Rice, Phoebe A; Ansari, Anjum

2018-02-28

The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a μs-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (∼100 μs) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1-10 ms) step is accelerated ∼5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is non-specific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.

Probing numerical Laplace inversion methods for two and three-site molecular exchange between interconnected pore structures.

PubMed

Silletta, Emilia V; Franzoni, María B; Monti, Gustavo A; Acosta, Rodolfo H

2018-01-01

Two-dimension (2D) Nuclear Magnetic Resonance relaxometry experiments are a powerful tool extensively used to probe the interaction among different pore structures, mostly in inorganic systems. The analysis of the collected experimental data generally consists of a 2D numerical inversion of time-domain data where T 2 -T 2 maps are generated. Through the years, different algorithms for the numerical inversion have been proposed. In this paper, two different algorithms for numerical inversion are tested and compared under different conditions of exchange dynamics; the method based on Butler-Reeds-Dawson (BRD) algorithm and the fast-iterative shrinkage-thresholding algorithm (FISTA) method. By constructing a theoretical model, the algorithms were tested for a two- and three-site porous media, varying the exchange rates parameters, the pore sizes and the signal to noise ratio. In order to test the methods under realistic experimental conditions, a challenging organic system was chosen. The molecular exchange rates of water confined in hierarchical porous polymeric networks were obtained, for a two- and three-site porous media. Data processed with the BRD method was found to be accurate only under certain conditions of the exchange parameters, while data processed with the FISTA method is precise for all the studied parameters, except when SNR conditions are extreme. Copyright © 2017 Elsevier Inc. All rights reserved.

'Test n Treat (TnT)': a cluster-randomised feasibility trial of frequent, rapid-testing and same-day, on-site treatment to reduce rates of chlamydia in high-risk further education college students: statistical analysis plan.

PubMed

Phillips, Rachel; Oakeshott, Pippa; Kerry-Barnard, Sarah; Reid, Fiona

2018-06-05

There are high rates of sexually transmitted infections (STIs) in ethnically diverse, sexually active students aged 16-24 years attending London further education (FE) colleges. However, uptake of chlamydia screening remains low. The TnT study aims to assess the feasibility of conducting a future trial in FE colleges to investigate if frequent, rapid, on-site testing and treatment (TnT) reduces chlamydia rates. This article presents the statistical analysis plan for the main study publication as approved and signed off by the Trial Management Group prior to the first data extraction for the final report. TnT is a cluster-randomised feasibility trial conducted over 7 months with parallel qualitative and economic assessments. Colleges will be randomly allocated into the intervention (TnT) or the control group (no TnT). Six FE colleges in London will be included. At each college for 2 days, 80 consecutive sexually active students aged 16-24 years (total 480 students across all six colleges) will be recruited from public areas and asked to provide baseline samples. One and 4 months after recruitment intervention colleges will be visited on two consecutive days by the TnT team where participating students will be texted and invited to come for same-day, on-site, rapid chlamydia testing and, if positive, treatment. Participants in the control colleges will receive 'thank you' texts 1 and 4 months after recruitment. Seven months after recruitment, participants from both groups will be invited to complete questionnaires and provide samples for TnT. All samples will be tested, and same-day treatment offered to participants with positive results. Key feasibility outcomes include: recruitment rates, testing and treatment uptake rates (at 1 and 4 months) and follow-up rates (at 7 months). ISRCTN 58038795 . Registered on 31 August 2016.

Site characterization in densely fractured dolomite: comparison of methods.

PubMed

Muldoon, Maureen; Bradbury, Ken R

2005-01-01

One of the challenges in characterizing fractured-rock aquifers is determining whether the equivalent porous medium approximation is valid at the problem scale. Detailed hydrogeologic characterization completed at a small study site in a densely fractured dolomite has yielded an extensive data set that was used to evaluate the utility of the continuum and discrete-fracture approaches to aquifer characterization. There are two near-vertical sets of fractures at the site; near-horizontal bedding-plane partings constitute a third fracture set. Eighteen boreholes, including five coreholes, were drilled to a depth of approximately 10.6 m. Borehole geophysical logs revealed several laterally extensive horizontal fractures and dissolution zones. Flowmeter and short-interval packer testing identified which of these features were hydraulically important. A monitoring system, consisting of short-interval piezometers and multilevel samplers, was designed to monitor four horizontal fractures and two dissolution zones. The resulting network consisted of >70 sampling points and allowed detailed monitoring of head distributions in three dimensions. Comparison of distributions of hydraulic head and hydraulic conductivity determined by these two approaches suggests that even in a densely fractured-carbonate aquifer, a characterization approach using traditional long-interval monitoring wells is inadequate to characterize ground water movement for the purposes of regulatory monitoring or site remediation. In addition, traditional multiwell pumping tests yield an average or bulk hydraulic conductivity that is not adequate for predicting rapid ground water travel times through the fracture network, and the pumping test response does not appear to be an adequate tool for assessing whether the porous medium approximation is valid.

A novel AVPR2 splice site mutation leads to partial X-linked nephrogenic diabetes insipidus in two brothers.

PubMed

Schernthaner-Reiter, Marie Helene; Adams, David; Trivellin, Giampaolo; Ramnitz, Mary Scott; Raygada, Margarita; Golas, Gretchen; Faucz, Fabio R; Nilsson, Ola; Nella, Aikaterini A; Dileepan, Kavitha; Lodish, Maya; Lee, Paul; Tifft, Cynthia; Markello, Thomas; Gahl, William; Stratakis, Constantine A

2016-05-01

X-linked nephrogenic diabetes insipidus (NDI, OMIM#304800) is caused by mutations in the arginine vasopressin (AVP, OMIM*192340) receptor type 2 (AVPR2, OMIM*300538) gene. A 20-month-old boy and his 8-year-old brother presented with polyuria, polydipsia, and failure to thrive. Both boys demonstrated partial DDAVP (1-desamino-8-D AVP or desmopressin) responses; thus, NDI diagnosis was delayed. While routine sequencing of AVPR2 showed a potential splice site variant, it was not until exome sequencing confirmed the AVPR2 splice site variant and did not reveal any more likely candidates that the patients' diagnosis was made and proper treatment was instituted. Both patients were hemizygous for two AVPR2 variants predicted in silico to affect AVPR2 messenger RNA (mRNA) splicing. A minigene assay revealed that the novel AVPR2 c.276A>G mutation creates a novel splice acceptor site leading to 5' truncation of AVPR2 exon 2 in HEK293 human kidney cells. Both patients have been treated with high-dose DDAVP with a remarkable improvement of their symptoms and accelerated linear growth and weight gain. We present here a unique case of partial X-linked NDI due to an AVPR2 splice site mutation; patients with diabetes insipidus of unknown etiology may harbor splice site mutations that are initially underestimated in their pathogenicity on sequence analysis. • X-linked nephrogenic diabetes insipidus is caused by AVPR2 mutations, and disease severity can vary depending on the functional effect of the mutation. What is New: • We demonstrate here that a splice site mutation in AVPR2 leads to partial X-linked NDI in two brothers. • Treatment with high-dose DDAVP led to improvement of polyuria and polydipsia, weight gain, and growth.

A scoping review of rapid review methods.

PubMed

Tricco, Andrea C; Antony, Jesmin; Zarin, Wasifa; Strifler, Lisa; Ghassemi, Marco; Ivory, John; Perrier, Laure; Hutton, Brian; Moher, David; Straus, Sharon E

2015-09-16

Rapid reviews are a form of knowledge synthesis in which components of the systematic review process are simplified or omitted to produce information in a timely manner. Although numerous centers are conducting rapid reviews internationally, few studies have examined the methodological characteristics of rapid reviews. We aimed to examine articles, books, and reports that evaluated, compared, used or described rapid reviews or methods through a scoping review. MEDLINE, EMBASE, the Cochrane Library, internet websites of rapid review producers, and reference lists were searched to identify articles for inclusion. Two reviewers independently screened literature search results and abstracted data from included studies. Descriptive analysis was conducted. We included 100 articles plus one companion report that were published between 1997 and 2013. The studies were categorized as 84 application papers, seven development papers, six impact papers, and four comparison papers (one was included in two categories). The rapid reviews were conducted between 1 and 12 months, predominantly in Europe (58 %) and North America (20 %). The included studies failed to report 6 % to 73 % of the specific systematic review steps examined. Fifty unique rapid review methods were identified; 16 methods occurred more than once. Streamlined methods that were used in the 82 rapid reviews included limiting the literature search to published literature (24 %) or one database (2 %), limiting inclusion criteria by date (68 %) or language (49 %), having one person screen and another verify or screen excluded studies (6 %), having one person abstract data and another verify (23 %), not conducting risk of bias/quality appraisal (7 %) or having only one reviewer conduct the quality appraisal (7 %), and presenting results as a narrative summary (78 %). Four case studies were identified that compared the results of rapid reviews to systematic reviews. Three studies found that the conclusions between

Long-Range Rapidity Correlations in Heavy-Light Ion Collisions

NASA Astrophysics Data System (ADS)

Kovchegov, Yuri; Wertepny, Douglas

2013-04-01

We study two-particle long-range rapidity correlations arising in the early stages of heavy ion collisions in the saturation/Color Glass Condensate framework, assuming for simplicity that one colliding nucleus is much larger than the other. We calculate the two-gluon production cross section while including all-order saturation effects in the heavy nucleus with the lowest-order rescattering in the lighter nucleus. We find four types of correlations in the two-gluon production cross section: (i) geometric correlations, (ii) HBT correlations, (iii) back-to-back correlations, and (iv) near-side azimuthal correlations which are long-range in rapidity. The geometric correlations (i) are due to the fact that nucleons are correlated by simply being confined within the same nucleus and may lead to long-range rapidity correlations for the produced particles without strong azimuthal angle dependence. Somewhat surprisingly, long-range rapidity correlations (iii) and (iv) have exactly the same amplitudes along with azimuthal and rapidity shapes: one centered around δφ=π with the other one centered around δφ=0 (here δφ is the azimuthal angle between the two produced gluons). This prediction is in agreement with the recent ALICE p+Pb data.

Cross-section, velocity, and bedload data at two erosion sites on the Tanana River near Fairbanks, Alaska, 1979

USGS Publications Warehouse

Burrows, Robert L.

1980-01-01

In an effort to relate river processes to vertical and lateral erosion at two sites on the Tanana River in the vicinity of Fairbanks, Alaska, measurements of depth, velocity, and bedload-transport rates were made at several sections at each site. To facilitate comparison of the river processes and ongoing erosion, compilation and graphic presentation of the velocity distributions and bedload-transport rates are presented in conjunction with cross-section configuration immediately adjacent to the area of erosion. Dry sieve analyses of the bedload samples give particle-size distribution. Approximately 85 to 95% of the material in transport at both sites was in the sand range (>0.062 millimeter <2.0 millimeter). (USGS)

Rapidly growing non-tuberculous mycobacteria infection of prosthetic knee joints: A report of two cases.

PubMed

Kim, Manyoung; Ha, Chul-Won; Jang, Jae Won; Park, Yong-Beom

2017-08-01

Non-tuberculous mycobacteria (NTM) cause prosthetic knee joint infections in rare cases. Infections with rapidly growing non-tuberculous mycobacteria (RGNTM) are difficult to treat due to their aggressive clinical behavior and resistance to antibiotics. Infections of a prosthetic knee joint by RGNTM have rarely been reported. A standard of treatment has not yet been established because of the rarity of the condition. In previous reports, diagnoses of RGNTM infections in prosthetic knee joints took a long time to reach because the condition was not suspected, due to its rarity. In addition, it is difficult to identify RGNTM in the lab because special identification tests are needed. In previous reports, after treatment for RGNTM prosthetic infections, knee prostheses could not be re-implanted in all cases but one, resulting in arthrodesis or resection arthroplasty; this was most likely due to the aggressiveness of these organisms. In the present report, two cases of prosthetic knee joint infection caused by RGNTM (Mycobacterium abscessus) are described that were successfully treated, and in which prosthetic joints were finally reimplanted in two-stage revision surgery. Copyright © 2017 Elsevier B.V. All rights reserved.

Adiabatically modeling quantum gates with two-site Heisenberg spins chain: Noise vs interferometry

NASA Astrophysics Data System (ADS)

Jipdi, M. N.; Tchoffo, M.; Fai, L. C.

2018-02-01

We study the Landau Zener (LZ) dynamics of a two-site Heisenberg spin chain assisted with noise and focus on the implementation of logic gates via the resulting quantum interference. We present the evidence of the quantum interference phenomenon in triplet spin states and confirm that, three-level systems mimic Landau-Zener-Stückelberg (LZS) interferometers with occupancies dependent on the effective phase. It emerges that, the critical parameters tailoring the system are obtained for constructive interferences where the two sets of the chain are found to be maximally entangled. Our findings demonstrate that the enhancement of the magnetic field strength suppresses noise effects; consequently, the noise severely impacts the occurrence of quantum interference for weak magnetic fields while for strong fields, quantum interference subsists and allows the modeling of universal sets of quantum gates.

Rapid Suppression of Onchocerca volvulus Transmission in Two Communities of the Southern Chiapas Focus, Mexico, Achieved by Quarterly Treatments with Mectizan

PubMed Central

Rodríguez-Pérez, Mario A.; Lutzow-Steiner, Miguel A.; Segura-Cabrera, Aldo; Lizarazo-Ortega, Cristian; Domínguez-Vázquez, Alfredo; Sauerbrey, Mauricio; Richards, Frank; Unnasch, Thomas R.; Hassan, Hassan K.; Hernández-Hernández, Raymundo

2008-01-01

The impact of quarterly Mectizan (ivermectin) treatments on transmission, microfiladermia, and ocular lesions was evaluated in two formerly hyperendemic communities (Las Golondrinas and Las Nubes II) located in the main endemic focus for onchocerciasis in Southern Chiapas, Mexico. The data suggest that Onchocerca volvulus transmission has been suppressed after elimination of microfiladermia in these two communities. Increasing the frequency of Mectizan treatment to four times per year appears to have resulted in the rapid suppression of transmission in communities with residual transmission. PMID:18689630

Randomized Trial of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration With and Without Rapid On-site Evaluation for Lung Cancer Genotyping.

PubMed

Trisolini, Rocco; Cancellieri, Alessandra; Tinelli, Carmine; de Biase, Dario; Valentini, Ilaria; Casadei, Gianpiero; Paioli, Daniela; Ferrari, Franco; Gordini, Giovanni; Patelli, Marco; Tallini, Giovanni

2015-12-01

Experts and scientific society guidelines recommend that rapid on-site evaluation (ROSE) be used with endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) to optimize lung cancer genotyping, but no comparative trial has been carried out to confirm and quantify its usefulness. To assess the influence of ROSE on the yield of EBUS-TBNA for a multigene molecular analysis of lung cancer samples, consecutive patients with suspected or known advanced lung cancer were randomized to undergo EBUS-TBNA without ROSE (EBUS arm) or with ROSE (ROSE arm). The primary end point was the rate of the successful accomplishment of the institution's clinical protocol for molecular profiling of nonsquamous non-small cell lung cancer (EGFR and KRAS testing, followed by ALK testing for tumors with EGFR and KRAS wild-type status). Complete genotyping was achieved in 108 of 126 patients (85.7%) (90.8% in the ROSE arm vs 80.3% in the EBUS arm, P = .09). The patients in the ROSE arm were less likely to have samples that could be used only for pathologic diagnosis because of minimal tumor burden (0 vs 6, P = .05), and were more likely to have the bronchoscopy terminated after a single biopsy site (58.9% vs 44.1%, P = .01). ROSE prevents the need for a repeat invasive diagnostic procedure aimed at molecular profiling in at least one out of 10 patients with advanced lung cancer and significantly reduces the risk of retrieving samples that can be used only for pathologic subtyping because of minimal tumor burden. ClinicalTrials.gov; No.: NCT01799382; URL: www.clinicaltrials.gov.

Program Director as Webmaster? Analysis of 131 Anesthesiology Department Web Sites and Program Director Web Site Involvement and Opinion Survey.

PubMed

Daneshpayeh, Negin; Lee, Howard; Berger, Jeffrey

2013-01-01

The last formal review of academic anesthesiology department Web sites (ADWs) for content was conducted in 2009. ADWs have been rated as very important by medical students in researching residency training programs; however, the rapid evolution of sites require that descriptive statistics must be more current to be considered reliable. We set out to provide an updated overview of ADW content and to better understand residency program directors' (PD) role and comfort with ADWs. Two independent reviewers (ND and HL) analyzed all 131 Accreditation Council for Graduate Medical Education (ACGME) accredited ADWs. A binary system (Yes/No) was used to determine which features were present. Reviewer reliability was confirmed with inter-rater reliability and percentage agreement calculation. Additionally, a blinded electronic survey (Survey Monkey, Portland, OR) was sent to anesthesiology residency PDs via electronic mail investigating the audiences for ADWs, the frequency of updates and the degree of PD involvement. 13% of anesthesiology departments still lack a Web site with a homepage with links to the residency program and educational offerings (18% in 2009). Only half (55%) of Web sites contain information for medical students, including clerkship information. Furthermore, programs rarely contain up-to-date calendars (13%), accreditation cycle lengths (11%), accreditation dates (7%) or board pass rates (6%). The PD survey, completed by 42 of 131 PDs, noted a correlation (r = 0.36) between the number of years as PD and the frequency of Web site updates - less experienced PDs appear to update their sites more frequently (p = 0.03). Although 86% of PDs regarded a Web site as "very" important in recruitment, only 9% felt "very" comfortable with the skills required to advertise and market a Web site. Despite the overall increase in ADW content since 2009, privacy concerns, limited resources and time constraints may prevent PDs from providing the most up-to-date Web sites for

Centrifuge-less dispersive liquid-liquid microextraction base on the solidification of switchable solvent for rapid on-site extraction of four pyrethroid insecticides in water samples.

PubMed

Hu, Lu; Wang, Huazi; Qian, Heng; Liu, Chaoran; Lu, Runhua; Zhang, Sanbing; Zhou, Wenfeng; Gao, Haixiang; Xu, Donghui

2016-11-11

An on-site dispersive liquid liquid microextraction base on the solidification of switchable solvent has been developed as a simple, rapid and eco-friendly sample extraction method for the fast determination of pyrethroid insecticides in aqueous samples using high-performance liquid chromatography with ultraviolet detection. In this extraction method, medium-chain saturated fatty acids (n≥10), which can rapidly solidify at low temperatures (<20°C), were investigated as switchable hydrophilic solvents. The fatty acids were converted into the hydrophilic form by adding sodium hydroxide. Microdroplets of the fatty acids were generated when injected into an acidic sample that had been pretreated by the addition of sulfuric acid. The formed cloudy solution was cooled to a low temperature to turn the fatty acids into a solid, which was then separated by filtration, thus avoiding the time-consuming step of centrifugation. The microextraction process was performed in a 10mL syringe and the pretreatment process could thus be finished in 5min. No external energy resources were required in this method, which makes it a potential method for on-site extraction. The optimal experimental parameters were as follows: 350μL of decanoic acid (1mol/L) was used as the extraction solvent, 150μL of sulfuric acid (2mol/L) was used to decrease the pH of the samples, no salt was added, and the temperature of the samples was in the range of 20-40°C. Finally, the sample was cooled in an ice bath for three minutes. Under these optimal conditions, good responses for four pyrethroid insecticides were obtained in the concentration ranges of 1-500μg/L, with coefficients of determination greater than 0.9993. The recoveries of the four pyrethroid insecticides ranged from 84.7 to 95.3%, with relative standard deviations ranging from 1.6 to 4.6%. The limits of detection based on a signal-to-noise ratio of 3 were in the range of 0.24-0.68μg/L, and the enrichment factors were in the range of 121

A two-site filtration model for silica nanoaggregate mobility in porous media under high salinity conditions

NASA Astrophysics Data System (ADS)

Taghavy, Amir; Kim, Ijung; Huh, Chun; DiCarlo, David A.

2018-06-01

A variable-viscosity colloid transport simulator is developed to model the mobility behavior of surface-engineered nanosilica aggregates (nSiO2) under high salinity conditions. A two-site (2S) filtration approach was incorporated to account for heterogeneous particle-collector surface interactions. 2S model was then implemented along with the conventional clean bed filtration (CFT) and maximum retention capacity (MRC) particle filtration models to simulate the results of a series of column tests conducted in brine (8% wt. NaCl and 2% wt. CaCl2)-saturated Ottawa sand columns at various pore velocities (7 to 71 m/day). Simulation results reveal the superiority of the MRC and 2S model classes over CFT model with respect to numerical performance criteria; a general decrease of normalized sum of squared residuals (ca. 20-90% reduction) and an enhanced degree of normality of model residuals were detected for 2S and MRC over CFT in all simulated experiments. Based on our findings, conformance with theories underpinning colloid deposition in porous media was the ultimate factor that set 2S and MRC model classes apart in terms of explaining the observed mobility trends. MRC and 2S models were evaluated based on the scaling of the fitted maximum retention capacity parameter with variation of experimental conditions. Two subclasses of 2S that consider a mix of favorable and unfavorable attachment sites with irreversible attachment to favorable sites (with and without physical straining effects) were found most consistent with filtration theory and shadow zone predictions, yielding theoretical conformity indices of 0.6 and higher, the highest among all implemented models. An explanation for such irreversible favorable deposition sites on the surface of silica nanoaggregates might be a partial depletion of stabilizing steric forces that had led to the formation of these aggregates.

Growth and nutrition response of young sweetgum plantations to repeated nitrogen fertilization on two site types

Treesearch

D. Andrew Scott; James A. Burger; Donald J. Kaczmarek; Michael B. Kane

2004-01-01

Short-rotation intensive tree culture is being investigated in the southern United States as a method of producing hardwood fiber, but little is known about the early productivity and nutritional needs of these systems, especially on different site types. We studied the growth and foliar nutrition response of two sweetgum (Liquidambar styraciflua L...

Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics

PubMed Central

Li, Tang; Chamberlin, Stephen G; Caraco, M Daniel; Liberles, David A; Gaucher, Eric A; Benner, Steven A

2006-01-01

Background The exchange of nucleotides at synonymous sites in a gene encoding a protein is believed to have little impact on the fitness of a host organism. This should be especially true for synonymous transitions, where a pyrimidine nucleotide is replaced by another pyrimidine, or a purine is replaced by another purine. This suggests that transition redundant exchange (TREx) processes at the third position of conserved two-fold codon systems might offer the best approximation for a neutral molecular clock, serving to examine, within coding regions, theories that require neutrality, determine whether transition rate constants differ within genes in a single lineage, and correlate dates of events recorded in genomes with dates in the geological and paleontological records. To date, TREx analysis of the yeast genome has recognized correlated duplications that established a new metabolic strategies in fungi, and supported analyses of functional change in aromatases in pigs. TREx dating has limitations, however. Multiple transitions at synonymous sites may cause equilibration and loss of information. Further, to be useful to correlate events in the genomic record, different genes within a genome must suffer transitions at similar rates. Results A formalism to analyze divergence at two fold redundant codon systems is presented. This formalism exploits two-state approach-to-equilibrium kinetics from chemistry. This formalism captures, in a single equation, the possibility of multiple substitutions at individual sites, avoiding any need to "correct" for these. The formalism also connects specific rate constants for transitions to specific approximations in an underlying evolutionary model, including assumptions that transition rate constants are invariant at different sites, in different genes, in different lineages, and at different times. Therefore, the formalism supports analyses that evaluate these approximations. Transitions at synonymous sites within two

Hydrologic characteristics of low-impact stormwater control measures at two sites in northeastern Ohio, 2008-13

USGS Publications Warehouse

Darner, Robert A.; Shuster, William D.; Dumouchelle, Denise H.

2015-01-01

This report updates and examines hydrologic data gathered to characterize the performance of two stormwater-control measure (SCM) sites in the Chagrin River watershed, Ohio. At the Sterncrest Drive site, roadside bioswales and rain gardens were used to alleviate drainage problems in this residential neighborhood area. At the Washington Street site, a treatment train (including a pervious-paver system, rain garden, and bioswales) was used to reduce and delay stormwater runoff at a small business development. Selected metrics were used to demonstrate SCM system performance with regard to stormwater-management objectives at each site. Rain-garden overflow-frequency data collected at the Sterncrest Drive site during 2008–13 were used to characterize system sensitivity to rainfall characteristics. Approximately 70 percent of storms exceeding 0.75 inches during 3 hours or more resulted in overflows. Drainage-design features that may restrict flow through the system were identified. Overall, the data and local observations confirmed the continued success of the SCM at the Sterncrest Drive site in preventing roadway closure due to flooding. The additional years of data collected at the Washington Street site indicated that a previous analysis of increased runoff removal, based on only the first 2 years (2009–10) of data, provided premature conclusions. With 5 years of data (2009–13) and adjusting for changes in rainfall characteristics, it appears that the percentage of runoff removed by the system is decreasing; however, the lag time (time from onset of rainfall to runoff) has remained nearly constant. The annual mean percent removal for 2010–13 ranged from 55 to 37 percent with an overall mean of 45 percent, and this does meet the project objective of reducing runoff from the business complex. One possible explanation for the combination of increased volume of runoff and no change in the timing of runoff is the preferential flow paths developed in the SCM

Microbial community characterization and functional gene quantification in RDX-degrading microcosms derived from sediment and groundwater at two naval sites.

PubMed

Wilson, Fernanda Paes; Cupples, Alison M

2016-08-01

The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has long been recognized as a problematic environmental pollutant, and efforts to remediate contaminated soils, sediments, and groundwater have been going on for decades. In recent years, much interest has focused on using bioremediation to clean up these sites. The current study investigated the microorganisms (16S rRNA genes, Illumina) and functional genes (xenA, xenB, and xplA) linked to RDX biodegradation in microcosms composed of sediment or groundwater from two Navy sites. For this, experiments included sediment samples from three depths (5 to 30 ft) from two wells located in one Navy site. In addition, the groundwater upstream and downstream of an emulsified oil biobarrier was examined from another Navy site. Further, for the groundwater experiments, the effect of glucose addition was explored. For the sediment experiments, the most enriched phylotypes during RDX degradation varied over time, by depth and well locations. However, several trends were noted, including the enrichment of Pseudomonas, Rhodococcus, Arthrobacter, and Sporolactobacillus in the sediment microcosms. For the groundwater-based experiments, Pseudomonas, unclassified Rhodocyclaceae, Sphingomonas, and Rhodococcus were also highly abundant during RDX degradation. The abundance of both xplA and xenA significantly increased during RDX degradation compared to the control microcosms for many treatments (both groundwater and sediment microcosms). In a limited number of microcosms, the copy number of the xenB gene increased. Phylotype data were correlated with functional gene data to highlight potentially important biomarkers for RDX biodegradation at these two Navy sites.

Rapid versus standard intravenous rehydration in paediatric gastroenteritis: pragmatic blinded randomised clinical trial

PubMed Central

Parkin, Patricia C; Willan, Andrew R; Schuh, Suzanne

2011-01-01

Objective To determine if rapid rather than standard intravenous rehydration results in improved hydration and clinical outcomes when administered to children with gastroenteritis. Design Single centre, two arm, parallel randomised pragmatic controlled trial. Blocked randomisation stratified by site. Participants, caregivers, outcome assessors, investigators, and statisticians were blinded to the treatment assignment. Setting Paediatric emergency department in a tertiary care centre in Toronto, Canada. Participants 226 children aged 3 months to 11 years; complete follow-up was obtained on 223 (99%). Eligible children were aged over 90 days, had a diagnosis of dehydration secondary to gastroenteritis, had not responded to oral rehydration, and had been prescribed intravenous rehydration. Children were excluded if they weighed less than 5 kg or more than 33 kg, required fluid restriction, had a suspected surgical condition, or had an insurmountable language barrier. Children were also excluded if they had a history of a chronic systemic disease, abdominal surgery, bilious or bloody vomit, hypotension, or hypoglycaemia or hyperglycaemia. Interventions Rapid (60 mL/kg) or standard (20 mL/kg) rehydration with 0.9% saline over an hour; subsequent fluids administered according to protocol. Main outcome measures Primary outcome: clinical rehydration, assessed with a validated scale, two hours after the start of treatment. Secondary outcomes: prolonged treatment, mean clinical dehydration scores over the four hour study period, time to discharge, repeat visits to emergency department, adequate oral intake, and physician’s comfort with discharge. Data from all randomised patients were included in an intention to treat analysis. Results 114 patients were randomised to rapid rehydration and 112 to standard. One child was withdrawn because of severe hyponatraemia at baseline. There was no evidence of a difference between the rapid and standard rehydration groups in the

XIAP inhibits caspase-3 and -7 using two binding sites: evolutionarily conserved mechanism of IAPs

PubMed Central

Scott, Fiona L; Denault, Jean-Bernard; Riedl, Stefan J; Shin, Hwain; Renatus, Martin; Salvesen, Guy S

2005-01-01

The X-linked inhibitor of apoptosis protein (XIAP) uses its second baculovirus IAP repeat domain (BIR2) to inhibit the apoptotic executioner caspase-3 and -7. Structural studies have demonstrated that it is not the BIR2 domain itself but a segment N-terminal to it that directly targets the activity of these caspases. These studies failed to demonstrate a role of the BIR2 domain in inhibition. We used site-directed mutagenesis of BIR2 and its linker to determine the mechanism of executioner caspase inhibition by XIAP. We show that the BIR2 domain contributes substantially to inhibition of executioner caspases. A surface groove on BIR2, which also binds to Smac/DIABLO, interacts with a neoepitope generated at the N-terminus of the caspase small subunit following activation. Therefore, BIR2 uses a two-site interaction mechanism to achieve high specificity and potency for inhibition. Moreover, for caspase-7, the precise location of the activating cleavage is critical for subsequent inhibition. Since apical caspases utilize this cleavage site differently, we predict that the origin of the death stimulus should dictate the efficiency of inhibition by XIAP. PMID:15650747

Impact of Canadian wildfire smoke on air quality at two rural sites in NY State

NASA Astrophysics Data System (ADS)

Dutkiewicz, Vincent A.; Husain, Liaquat; Roychowdhury, Utpal K.; Demerjian, Kenneth L.

2011-04-01

We report high concentrations of black carbon aerosols (BC), present at two rural sites in New York during the last week in May 2010, that are linked to wildfire activity. At Mayville BC from wood smoke was recorded for a total of 20 h from three separate episodes, mean concentration was 1400 ng m -3. These three short events contributed 13% of the BC burden during the month of May. At Whiteface Mountain high concentrations of BC, carbon monoxide gas (CO), and fine particulate matter mass (PM 2.5) are reported from a heavy smoke event that impacted the Adirondack region of the State on May 31, 2010. PM 2.5 mass recorded at the Lodge site (600 m above mean sea level) was 150 μg m -3 at 8:30 am EST and the 24-h mean was almost twice the USEPA limits while CO concentration exceeded 1000 ppb and BC concentration reached 9600 ng m -3. The event was delayed several hours at the Summit site (1500 m above mean sea level) but at 5:45 pm BC concentration reached 1600 ng m -3 and CO was 317 ppbv. Detailed temporal profiles and correlations are presented.

Two signaling molecules share a phosphotyrosine-containing binding site in the platelet-derived growth factor receptor.

PubMed

Nishimura, R; Li, W; Kashishian, A; Mondino, A; Zhou, M; Cooper, J; Schlessinger, J

1993-11-01

Autophosphorylation sites of growth factor receptors with tyrosine kinase activity function as specific binding sites for Src homology 2 (SH2) domains of signaling molecules. This interaction appears to be a crucial step in a mechanism by which receptor tyrosine kinases relay signals to downstream signaling pathways. Nck is a widely expressed protein consisting exclusively of SH2 and SH3 domains, the overexpression of which causes cell transformation. It has been shown that various growth factors stimulate the phosphorylation of Nck and its association with autophosphorylated growth factor receptors. A panel of platelet-derived growth factor (PDGF) receptor mutations at tyrosine residues has been used to identify the Nck binding site. Here we show that mutation at Tyr-751 of the PDGF beta-receptor eliminates Nck binding both in vitro and in living cells. Moreover, the Y751F PDGF receptor mutant failed to mediate PDGF-stimulated phosphorylation of Nck in intact cells. A phosphorylated Tyr-751 is also required for binding of phosphatidylinositol-3 kinase to the PDGF receptor. Hence, the SH2 domains of p85 and Nck share a binding site in the PDGF receptor. Competition experiments with different phosphopeptides derived from the PDGF receptor suggest that binding of Nck and p85 is influenced by different residues around Tyr-751. Thus, a single tyrosine autophosphorylation site is able to link the PDGF receptor to two distinct SH2 domain-containing signaling molecules.

Restriction-Site-Specific PCR as a Rapid Test To Detect Enterohemorrhagic Escherichia coli O157:H7 Strains in Environmental Samples

PubMed Central

Kimura, Richard; Mandrell, Robert E.; Galland, John C.; Hyatt, Doreene; Riley, Lee W.

2000-01-01

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is an important food-borne pathogen in industrialized countries. We developed a rapid and simple test for detecting E. coli O157:H7 using a method based on restriction site polymorphisms. Restriction-site-specific PCR (RSS-PCR) involves the amplification of DNA fragments using primers based on specific restriction enzyme recognition sequences, without the use of endonucleases, to generate a set of amplicons that yield “fingerprint” patterns when resolved electrophoretically on an agarose gel. The method was evaluated in a blinded study of E. coli isolates obtained from environmental samples collected at beef cattle feedyards. The 54 isolates were all initially identified by a commonly used polyclonal antibody test as belonging to O157:H7 serotype. They were retested by anti-O157 and anti-H7 monoclonal antibody enzyme-linked immunosorbent assay (ELISA). The RSS-PCR method identified all 28 isolates that were shown to be E. coli O157:H7 by the monoclonal antibody ELISA as belonging to the O157:H7 serotype. Of the remaining 26 ELISA-confirmed non-O157:H7 strains, the method classified 25 strains as non-O157:H7. The specificity of the RSS-PCR results correlated better with the monoclonal antibody ELISA than with the polyclonal antibody latex agglutination tests. The RSS-PCR method may be a useful test to distinguish E. coli O157:H7 from a large number of E. coli isolates from environmental samples. PMID:10831431

An approach for evaluating the repeatability of rapid wetland assessment methods: The effects of training and experience

EPA Science Inventory

We sampled 92 wetlands from four different basins in the United States to quantify observer repeatability in rapid wetland condition assessment using the Delaware Rapid Assessment Protocol (DERAP). In the Inland Bays basin of Delaware, 58 wetland sites were sampled by multiple ob...

Neurons with two sites of synaptic integration learn invariant representations.

PubMed

Körding, K P; König, P

2001-12-01

Neurons in mammalian cerebral cortex combine specific responses with respect to some stimulus features with invariant responses to other stimulus features. For example, in primary visual cortex, complex cells code for orientation of a contour but ignore its position to a certain degree. In higher areas, such as the inferotemporal cortex, translation-invariant, rotation-invariant, and even view point-invariant responses can be observed. Such properties are of obvious interest to artificial systems performing tasks like pattern recognition. It remains to be resolved how such response properties develop in biological systems. Here we present an unsupervised learning rule that addresses this problem. It is based on a neuron model with two sites of synaptic integration, allowing qualitatively different effects of input to basal and apical dendritic trees, respectively. Without supervision, the system learns to extract invariance properties using temporal or spatial continuity of stimuli. Furthermore, top-down information can be smoothly integrated in the same framework. Thus, this model lends a physiological implementation to approaches of unsupervised learning of invariant-response properties.

Rapid Airplane Parametric Input Design (RAPID)

NASA Technical Reports Server (NTRS)

Smith, Robert E.

1995-01-01

RAPID is a methodology and software system to define a class of airplane configurations and directly evaluate surface grids, volume grids, and grid sensitivity on and about the configurations. A distinguishing characteristic which separates RAPID from other airplane surface modellers is that the output grids and grid sensitivity are directly applicable in CFD analysis. A small set of design parameters and grid control parameters govern the process which is incorporated into interactive software for 'real time' visual analysis and into batch software for the application of optimization technology. The computed surface grids and volume grids are suitable for a wide range of Computational Fluid Dynamics (CFD) simulation. The general airplane configuration has wing, fuselage, horizontal tail, and vertical tail components. The double-delta wing and tail components are manifested by solving a fourth order partial differential equation (PDE) subject to Dirichlet and Neumann boundary conditions. The design parameters are incorporated into the boundary conditions and therefore govern the shapes of the surfaces. The PDE solution yields a smooth transition between boundaries. Surface grids suitable for CFD calculation are created by establishing an H-type topology about the configuration and incorporating grid spacing functions in the PDE equation for the lifting components and the fuselage definition equations. User specified grid parameters govern the location and degree of grid concentration. A two-block volume grid about a configuration is calculated using the Control Point Form (CPF) technique. The interactive software, which runs on Silicon Graphics IRIS workstations, allows design parameters to be continuously varied and the resulting surface grid to be observed in real time. The batch software computes both the surface and volume grids and also computes the sensitivity of the output grid with respect to the input design parameters by applying the precompiler tool

Differences between nipher and slter shielded rain gages at two Colorado deposition monitoring sites

USGS Publications Warehouse

Bigelow, David S.; Denning, A. Scott

1990-01-01

In the last decade the United States and Canada have made significant progress in establishing spatial ad temporal estimates of atmospheric deposition throughout North America. Fundamental to the wet-deposition portion of these estimates is the accurate and precise measurement of precipitation amount. Goodison and others (I-3) have reported on a new type of shielded snow gage known as the Canadian MSC Nipher shielded snow gage. Because this shielded snow gage has been shown to be superior to other precipitation gages for the estimation of snowfall amount, its design was adapted to the Universal Belfort precipitation gage (4), the dominant precipitation gage used at deposition monitoring sites in the United States. Favorable results taken from monitoring sites using this modified Nipher shielded snow gage (3-6) have prompted the U.S. Environmental Protection Agency and the Electric Power Research Institute to adopt the Nipher shielded Belfort gage as a standard piece of equipment in the Acid MODES and Operational Evaluation Network (OEN) monitoring programs and to propose that is be included as a standard snow gage in other North American deposition monitoring programs. This communication details preliminary results from two of nine NADP/NTN deposition monitoring sites selected by the Environmental Protection Agency to compare Nipher shielded Belfort precipitation gage volumes to volumes obtained from the standard Belfort gage used in the NADP/NTN monitoring program.

Site Area Boundaries

EPA Pesticide Factsheets

This dataset consists of site boundaries from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times and were combined into one region-wide layer. Thus far the sources include:1. California Gulch (Irrigated Meadows) - ESAT Contractor.2. Manning Canyon - U.S. EPA Region 8; ESAT Contractor.3. Rapid City Small Arms Range - U.S. EPA Region 8; ESAT Contractor.4. Animas River/Cement Creek - U.S. EPA Region 8; ESAT Contractor.5. Monticello Mill Tailings (USDOE) - USDOE; ESAT Contractor.6. Pinon Canyon - USDOD.7. Rock Flats Industrial Park - U.S. EPA Region 8.8. Bountiful/Woods Cross - U.S. EPA Region 8.9. Lincoln Park - U.S. EPA Region 8.10. Marshall Landfill - U.S. EPA Region 8.11. U.S. Magnesium - Pacific Western Technologies Inc.

Theory of hard diffraction and rapidity gaps

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

Del Duca, V.

1996-02-01

In this talk we review the models describing the hard diffractive production of jets or more generally high-mass states in presence of rapidity gaps in hadron-hadron and lepton-hadron collisions. By rapidity gaps we mean regions on the lego plot in (pseudo)-rapidity and azimuthal angle where no hadrons are produced, between the jet(s) and an elastically scattered hadron (single hard diffraction) or between two jets (double hard diffraction). {copyright} {ital 1996 American Institute of Physics.}

Thermal regime of active layer at two lithologically contrasting sites on James Ross Island, Antarctic Peninsula.

NASA Astrophysics Data System (ADS)

Hrbáček, Filip; Nývlt, Daniel; Láska, Kamil

2016-04-01

Antarctic Peninsula region (AP) represents one of the most rapidly warming parts of our planet in the last 50 years. Despite increasing research activities along both western and eastern sides of AP in last decades, there is still a lot of gaps in our knowledge relating to permafrost, active layer and its thermal and physical properties. This study brings new results of active layer monitoring on James Ross Island, which is the largest island in northern AP. Its northern part, Ulu Peninsula, is the largest ice-free area (more than 200 km2) in the region. Due its large area, we focused this study on sites located in different lithologies, which would affect local thermal regime of active layer. Study site (1) at Abernethy Flats area (41 m a.s.l.) lies ~7 km from northern coast. Lithologically is formed by disintegrated Cretaceous calcareous sandstones and siltstones of the Santa Marta Formation. Study site (2) is located at the northern slopes of Berry Hill (56 m a.s.l.), about 0.4 km from northern coastline. Lithology is composed of muddy to intermediate diamictites, tuffaceous siltstones to fine grained sandstones of the Mendel Formation. Data of air temperature at 2 meters above ground and the active layer temperatures at 75 cm deep profiles were obtained from both sites in period 1 January 2012 to 31 December 2014. Small differences were found when comparing mean air temperatures and active temperatures at 5 and 75 cm depth in the period 2012-2014. While the mean air temperatures varied between -7.7 °C and -7.0 °C, the mean ground temperatures fluctuated between -6.6 °C and -6.1 °C at 5 cm and -6.9 °C and -6.0 °C at 75 cm at Abernethy Flats and Berry Hill slopes respectively. Even though ground temperature differences along the profiles weren't pronounced during thawing seasons, the maximum active layer thickness was significantly larger at Berry Hill slopes (80 to 82 cm) than at Abernethy Flats (52 to 64 cm). We assume this differences are affected by

D Modelling and Rapid Prototyping for Cardiovascular Surgical Planning - Two Case Studies

NASA Astrophysics Data System (ADS)

Nocerino, E.; Remondino, F.; Uccheddu, F.; Gallo, M.; Gerosa, G.

2016-06-01

In the last years, cardiovascular diagnosis, surgical planning and intervention have taken advantages from 3D modelling and rapid prototyping techniques. The starting data for the whole process is represented by medical imagery, in particular, but not exclusively, computed tomography (CT) or multi-slice CT (MCT) and magnetic resonance imaging (MRI). On the medical imagery, regions of interest, i.e. heart chambers, valves, aorta, coronary vessels, etc., are segmented and converted into 3D models, which can be finally converted in physical replicas through 3D printing procedure. In this work, an overview on modern approaches for automatic and semiautomatic segmentation of medical imagery for 3D surface model generation is provided. The issue of accuracy check of surface models is also addressed, together with the critical aspects of converting digital models into physical replicas through 3D printing techniques. A patient-specific 3D modelling and printing procedure (Figure 1), for surgical planning in case of complex heart diseases was developed. The procedure was applied to two case studies, for which MCT scans of the chest are available. In the article, a detailed description on the implemented patient-specific modelling procedure is provided, along with a general discussion on the potentiality and future developments of personalized 3D modelling and printing for surgical planning and surgeons practice.

Target-mediated drug disposition model for drugs with two binding sites that bind to a target with one binding site.

PubMed

Gibiansky, Leonid; Gibiansky, Ekaterina

2017-10-01

The paper extended the TMDD model to drugs with two identical binding sites (2-1 TMDD). The quasi-steady-state (2-1 QSS), quasi-equilibrium (2-1 QE), irreversible binding (2-1 IB), and Michaelis-Menten (2-1 MM) approximations of the model were derived. Using simulations, the 2-1 QSS approximation was compared with the full 2-1 TMDD model. As expected and similarly to the standard TMDD for monoclonal antibodies (mAb), 2-1 QSS predictions were nearly identical to 2-1 TMDD predictions, except for times of fast changes following initiation of dosing, when equilibrium has not yet been reached. To illustrate properties of new equations and approximations, several variations of population PK data for mAbs with soluble (slow elimination of the complex) or membrane-bound (fast elimination of the complex) targets were simulated from a full 2-1 TMDD model and fitted to 2-1 TMDD models, to its approximations, and to the standard (1-1) QSS model. For a mAb with a soluble target, it was demonstrated that the 2-1 QSS model provided nearly identical description of the observed (simulated) free drug and total target concentrations, although there was some minor bias in predictions of unobserved free target concentrations. The standard QSS approximation also provided a good description of the observed data, but was not able to distinguish between free drug concentrations (with no target attached and both binding site free) and partially bound drug concentrations (with one of the binding sites occupied by the target). For a mAb with a membrane-bound target, the 2-1 MM approximation adequately described the data. The 2-1 QSS approximation converged 10 times faster than the full 2-1 TMDD, and its run time was comparable with the standard QSS model.

Plasticity within non-cerebellar pathways rapidly shapes motor performance in vivo.

PubMed

Mitchell, Diana E; Della Santina, Charles C; Cullen, Kathleen E

2016-05-09

Although cerebellar mechanisms are vital to maintain accuracy during complex movements and to calibrate simple reflexes, recent in vitro studies have called into question the widely held view that synaptic changes within cerebellar pathways exclusively guide alterations in motor performance. Here we investigate the vestibulo-ocular reflex (VOR) circuitry by applying temporally precise activation of vestibular afferents in awake-behaving monkeys to link plasticity at different neural sites with changes in motor performance. Behaviourally relevant activation patterns produce rapid attenuation of direct pathway VOR neurons, but not their nerve input. Changes in the strength of this pathway are sufficient to induce a lasting decrease in the evoked VOR. In addition, indirect brainstem pathways display complementary nearly instantaneous changes, contributing to compensating for the reduced sensitivity of primary VOR neurons. Taken together, our data provide evidence that multiple sites of plasticity within VOR pathways can rapidly shape motor performance in vivo.

RAPID METHOD FOR DETERMINATION OF RADIOSTRONTIUM IN EMERGENCY MILK SAMPLES

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

Maxwell, S.; Culligan, B.

2008-07-17

A new rapid separation method for radiostrontium in emergency milk samples was developed at the Savannah River Site (SRS) Environmental Bioassay Laboratory (Aiken, SC, USA) that will allow rapid separation and measurement of Sr-90 within 8 hours. The new method uses calcium phosphate precipitation, nitric acid dissolution of the precipitate to coagulate residual fat/proteins and a rapid strontium separation using Sr Resin (Eichrom Technologies, Darien, IL, USA) with vacuum-assisted flow rates. The method is much faster than previous method that use calcination or cation exchange pretreatment, has excellent chemical recovery, and effectively removes beta interferences. When a 100 ml samplemore » aliquot is used, the method has a detection limit of 0.5 Bq/L, well below generic emergency action levels.« less

Infection dynamics of pandemic 2009 H1N1 influenza virus in a two-site swine herd.

PubMed

Allerson, M W; Davies, P R; Gramer, M R; Torremorell, M

2014-12-01

Influenza A viruses are common causes of respiratory disease in pigs and can be transmitted among multiple host species, including humans. The current lack of published information on infection dynamics of influenza viruses within swine herds hinders the ability to make informed animal health, biosecurity and surveillance programme decisions. The objectives of this serial cross-sectional study were to describe the infection dynamics of influenza virus in a two-site swine system by estimating the prevalence of influenza virus in animal subpopulations at the swine breeding herd and describing the temporal pattern of infection in a selected cohort of growing pigs weaned from the breeding herd. Nasal swab and blood samples were collected at approximately 30-day intervals from the swine breeding herd (Site 1) known to be infected with pandemic 2009 H1N1 influenza virus. Sows, gilts and neonatal pigs were sampled at each sampling event, and samples were tested for influenza virus genome using matrix gene RRT-PCR. Influenza virus was detected in neonatal pigs, but was not detected in sow or gilt populations via RRT-PCR. A virus genetically similar to that detected in the neonatal pig population at Site 1 was also detected at the wean-to-finish site (Site 2), presumably following transportation of infected weaned pigs. Longitudinal sampling of nasal swabs and oral fluids revealed that influenza virus persisted in the growing pigs at Site 2 for at least 69 days. The occurrence of influenza virus in neonatal pigs, but not breeding females, at Site 1 emphasizes the potential for virus maintenance in this dynamic subpopulation, the importance of including this subpopulation in surveillance programmes and the potential transport of influenza virus between sites via the movement of weaned pigs. © 2013 Blackwell Verlag GmbH.

Rapid-mix and chemical quench studies of ferredoxin-reduced stearoyl-acyl carrier protein desaturase.

PubMed

Lyle, Karen S; Haas, Jeffrey A; Fox, Brian G

2003-05-20

Stearoyl-ACP Delta9 desaturase (Delta9D) catalyzes the NADPH- and O(2)-dependent insertion of a cis double bond between the C9 and C10 positions of stearoyl-ACP (18:0-ACP) to produce oleoyl-ACP (18:1-ACP). This work revealed the ability of reduced [2Fe-2S] ferredoxin (Fd) to act as a catalytically competent electron donor during the rapid conversion of 18:0-ACP into 18:1-ACP. Experiments on the order of addition for substrate and reduced Fd showed high conversion of 18:0-ACP to 18:1-ACP (approximately 95% per Delta9D active site in a single turnover) when 18:0-ACP was added prior to reduced Fd. Reactions of the prereduced enzyme-substrate complex with O(2) and the oxidized enzyme-substrate complex with reduced Fd were studied by rapid-mix and chemical quench methods. For reaction of the prereduced enzyme-substrate complex, an exponential burst phase (k(burst) = 95 s(-1)) of product formation accounted for approximately 90% of the turnover expected for one subunit in the dimeric protein. This rapid phase was followed by a slower phase (k(linear) = 4.0 s(-1)) of product formation corresponding to the turnover expected from the second subunit. For reaction of the oxidized enzyme-substrate complex with excess reduced Fd, a slower, linear rate (k(obsd) = 3.4 s(-1)) of product formation was observed over approximately 1.5 turnovers per Delta9D active site potentially corresponding to a third phase of reaction. An analysis of the deuterium isotope effect on the two rapid-mix reaction sequences revealed only a modest effect on k(burst) ((D)k(burst) approximately 1.5) and k(linear) (D)k(linear) approximately 1.4), indicating C-H bond cleavage does not contribute significantly to the rate-limiting steps of pre-steady-state catalysis. These results were used to assemble and evaluate a minimal kinetic model for Delta9D catalysis.

Electronic Cigarette Marketing Online: a Multi-Site, Multi-Product Comparison

PubMed Central

Sidhu, Anupreet K; Valente, Thomas W

2015-01-01

Background Electronic cigarette awareness and use has been increasing rapidly. E-cigarette brands have utilized social networking sites to promote their products, as the growth of the e-cigarette industry has paralleled that of Web 2.0. These online platforms are cost-effective and have unique technological features and user demographics that can be attractive for selective marketing. The popularity of multiple sites also poses a risk of exposure to social networks where e-cigarette brands might not have a presence. Objective To examine the marketing strategies of leading e-cigarette brands on multiple social networking sites, and to identify how affordances of the digital media are used to their advantage. Secondary analyses include determining if any brands are benefitting from site demographics, and exploring cross-site diffusion of marketing content through multi-site users. Methods We collected data from two e-cigarette brands from four social networking sites over approximately 2.5 years. Content analysis is used to search for themes, population targeting, marketing strategies, and cross-site spread of messages. Results Twitter appeared to be the most frequently used social networking site for interacting directly with product users. Facebook supported informational broadcasts, such as announcements regarding political legislation. E-cigarette brands also differed in their approaches to their users, from informal conversations to direct product marketing. Conclusions E-cigarette makers use different strategies to market their product and engage their users. There was no evidence of direct targeting of vulnerable populations, but the affordances of the different sites are exploited to best broadcast context-specific messages. We developed a viable method to study cross-site diffusion, although additional refinement is needed to account for how different types of digital media are used. PMID:27227129

Aminoalcohols as Probes of the Two-subsite Active Site of Beta-D-xylosidase from Selenomonas ruminantium

USDA-ARS?s Scientific Manuscript database

Catalysis and inhibitor binding by the GH43 beta-xylosidase are governed by the protonation state of catalytic base (D14, pKa 5.0) and catalytic acid (E186, pKa 7.2) which reside in subsite -1 of the two-subsite active site. Cationic aminoalcohols are shown to bind exclusively to subsite -1 of the ...

A density functional theory for colloids with two multiple bonding associating sites.

PubMed

Haghmoradi, Amin; Wang, Le; Chapman, Walter G

2016-06-22

Wertheim's multi-density formalism is extended for patchy colloidal fluids with two multiple bonding patches. The theory is developed as a density functional theory to predict the properties of an associating inhomogeneous fluid. The equation of state developed for this fluid depends on the size of the patch, and includes formation of cyclic, branched and linear clusters of associated species. The theory predicts the density profile and the fractions of colloids in different bonding states versus the distance from one wall as a function of bulk density and temperature. The predictions from our theory are compared with previous results for a confined fluid with four single bonding association sites. Also, comparison between the present theory and Monte Carlo simulation indicates a good agreement.

Geochemical effects of rapid sedimentation in aquatic systems: Minimal diagenesis and the preservation of historical metal signatures

USGS Publications Warehouse

Callender, E.

2000-01-01

Rapid sedimentation exerts a pronounced influence on early sedimentary diagenesis in that there is insufficient time for a sediment particle to equilibrate in any one sediment layer before that layer may be displaced vertically by another layer. These sedimentation patterns are common in surface-water reservoirs whose sedimentation rates (1-10 cm yr-1) are several orders of magnitude greater than those for natural lakes (0.01-0.5 cm yr-1). Two examples of the effects of rapid sedimentation on geochemical metal signatures are presented here. Interstitial-water data (Fe) from two sites in the Cheyenne River Embayment of Lake Oahe on the Missouri River illustrate the effects of changing sedimentation rates on dissolved species. Rapid burial during high-flow yrs appears to limit early sedimentary diagenesis to aerobic respiration. Solid-phase metal data (Pb) from a site in Pueblo Reservoir on the upper Arkansas River in Colorado appear to record historical releases by flooding of abandoned mine sites upstream in Leadville, Colorado. Interstitial-water ammonia and ferrous Fe data indicate that at least one interval at depth in the sediment where solid metal concentrations peak is a zone of minimal diagenesis. The principal diagenetic reactions that occur in these sediments are aerobic respiration and the reduction of Mn and Fe oxides. Under slower sedimentation conditions, there is sufficient time for particulate organic matter to decompose and create a diagenetic environment where metal oxides may not be stable. The quasi-steady-state interstitial Fe profiles from Tidal Potomac River sediments are an example of such a situation. This occurs primarily because the residence time of particles in the surficial sediment column is long enough to allow benthic organisms and bacteria to perform their metabolic functions. When faster sedimentation prevails, there is less time for these metabolic reactions to occur since the organisms do not occupy a sediment layer for any

Rapid forest clearing in a Myanmar proposed national park threatens two newly discovered species of geckos (Gekkonidae: Cyrtodactylus)

PubMed Central

Oswald, Patrick; Thura, Myint Kyaw; LaJeunesse Connette, Katherine J.; Grindley, Mark E.; Songer, Melissa; Zug, George R.; Mulcahy, Daniel G.

2017-01-01

Myanmar’s recent transition from military rule towards a more democratic government has largely ended decades of political and economic isolation. Although Myanmar remains heavily forested, increased development in recent years has been accompanied by exceptionally high rates of forest loss. In this study, we document the rapid progression of deforestation in and around the proposed Lenya National Park, which includes some of the largest remaining areas of lowland evergreen rainforest in mainland Southeast Asia. The globally unique forests in this area are rich in biodiversity and remain a critical stronghold for many threatened and endangered species, including large charismatic fauna such as tiger and Asian elephant. We also conducted a rapid assessment survey of the herpetofauna of the proposed national park, which resulted in the discovery of two new species of bent-toed geckos, genus Cyrtodactylus. We describe these new species, C. lenya sp. nov. and C. payarhtanensis sp. nov., which were found in association with karst (i.e., limestone) rock formations within mature lowland wet evergreen forest. The two species were discovered less than 35 km apart and are each known from only a single locality. Because of the isolated nature of the karst formations in the proposed Lenya National Park, these geckos likely have geographical ranges restricted to the proposed protected area and are threatened by approaching deforestation. Although lowland evergreen rainforest has vanished from most of continental Southeast Asia, Myanmar can still take decisive action to preserve one of the most biodiverse places on Earth. PMID:28403189

Rapid response learning of brand logo priming: Evidence that brand priming is not dominated by rapid response learning.

PubMed

Boehm, Stephan G; Smith, Ciaran; Muench, Niklas; Noble, Kirsty; Atherton, Catherine

2017-08-31

Repetition priming increases the accuracy and speed of responses to repeatedly processed stimuli. Repetition priming can result from two complementary sources: rapid response learning and facilitation within perceptual and conceptual networks. In conceptual classification tasks, rapid response learning dominates priming of object recognition, but it does not dominate priming of person recognition. This suggests that the relative engagement of network facilitation and rapid response learning depends on the stimulus domain. Here, we addressed the importance of the stimulus domain for rapid response learning by investigating priming in another domain, brands. In three experiments, participants performed conceptual decisions for brand logos. Strong priming was present, but it was not dominated by rapid response learning. These findings add further support to the importance of the stimulus domain for the relative importance of network facilitation and rapid response learning, and they indicate that brand priming is more similar to person recognition priming than object recognition priming, perhaps because priming of both brands and persons requires individuation.

Erwinia amylovora loop-mediated isothermal amplification (LAMP) assay for rapid pathogen detection and on-site diagnosis of fire blight.

PubMed

Bühlmann, Andreas; Pothier, Joël F; Rezzonico, Fabio; Smits, Theo H M; Andreou, Michael; Boonham, Neil; Duffy, Brion; Frey, Jürg E

2013-03-01

Several molecular methods have been developed for the detection of Erwinia amylovora, the causal agent of fire blight in pear and apple, but none are truly applicable for on-site use in the field. We developed a fast, reliable and field applicable detection method using a novel target on the E. amylovora chromosome that we identified by applying a comparative genomic pipeline. The target coding sequences (CDSs) are both uniquely specific for and all-inclusive of E. amylovora genotypes. This avoids potential false negatives that can occur with most commonly used methods based on amplification of plasmid gene targets, which can vary among strains. Loop-mediated isothermal AMPlification (LAMP) with OptiGene Genie II chemistry and instrumentation proved to be an exceptionally rapid (under 15 min) and robust method for detecting E. amylovora in orchards, as well as simple to use in the plant diagnostic laboratory. Comparative validation results using plant samples from inoculated greenhouse trials and from natural field infections (of regional and temporal diverse origin) showed that our LAMP had an equivalent or greater performance regarding sensitivity, specificity, speed and simplicity than real-time PCR (TaqMan), other LAMP assays, immunoassays and plating, demonstrating its utility for routine testing. Copyright © 2012 Elsevier B.V. All rights reserved.

Calpha methylation in molecular recognition. Application to substance P and the two neurokinin-1 receptor binding sites.

PubMed

Sagan, S; Lequin, O; Frank, F; Convert, O; Ayoub, M; Lavielle, S; Chassaing, G

2001-05-01

Two binding sites NK-1M (major, more abundant) and NK-1m (minor) are associated with the neurokinin-1 receptor. For the first time with a bioactive peptide, the Calpha methylation constraint, shown to be a helix stabiliser in model peptides, was systematically used to probe the molecular requirements of NK-1M and NK-1m binding sites and the previously postulated bioactive helical conformation of substance P (SP). Seven Calpha methylated analogues of the undecapeptide SP (from position 5-11) have been assayed for their affinities and their potencies to stimulate second messenger production. The consequences of Calpha methylation on the structure of SP have been analysed by circular dichroism and nuclear magnetic resonance combined with restrained molecular dynamics. The decreased potencies of six out of these seven Calpha methylated SP analogues do not allow the identification of any clear-cut differences in the structural requirements between the two binding sites. Strikingly, the most active analogue, [alphaMeMet5]SP, leads to variable subnanomolar affinity and potency when interacting with the NK-1m binding site. The conformational analyses show that the structural consequences associated with Calpha methylation of SP are sequence dependent. Moreover, a single Calpha methylation is not sufficient by itself to drastically stabilize a helical structure even pre-existing in solution, except when Gly9 is substituted by an alpha-aminoisobutyric acid. Furthermore, Calpha methylation of residues 5 and 6 of SP in the middle of the postulated helix does not stabilize, but decreases (to different extents) the stability of the helical structure previously observed in the 4-8 domain of other potent SP analogues.

Membrane fusion triggers rapid degradation of two gamete-specific, fusion-essential proteins in a membrane block to polygamy in Chlamydomonas.

PubMed

Liu, Yanjie; Misamore, Michael J; Snell, William J

2010-05-01

The plasma membranes of gametes are specialized for fusion, yet, once fusion occurs, in many organisms the new zygote becomes incapable of further membrane fusion reactions. The molecular mechanisms that underlie this loss of fusion capacity (block to polygamy) remain unknown. During fertilization in the green alga Chlamydomonas, the plus gamete-specific membrane protein FUS1 is required for adhesion between the apically localized sites on the plasma membranes of plus and minus gametes that are specialized for fusion, and the minus-specific membrane protein HAP2 is essential for completion of the membrane fusion reaction. HAP2 (GCS1) family members are also required for fertilization in Arabidopsis, and for the membrane fusion reaction in the malaria organism Plasmodium berghei. Here, we tested whether Chlamydomonas gamete fusion triggers alterations in FUS1 and HAP2 and renders the plasma membranes of the cells incapable of subsequent fusion. We find that, even though the fusogenic sites support multi-cell adhesions, triploid zygotes are rare, indicating a fusion-triggered block to the membrane fusion reaction. Consistent with the extinction of fusogenic capacity, both FUS1 and HAP2 are degraded upon fusion. The rapid, fusion-triggered cleavage of HAP2 in zygotes is distinct from degradation occurring during constitutive turnover in gametes. Thus, gamete fusion triggers specific degradation of fusion-essential proteins and renders the zygote incapable of fusion. Our results provide the first molecular explanation for a membrane block to polygamy in any organism.

Rapid Population Growth and Human Carrying Capacity: Two Perspectives. World Bank Staff Working Papers No. 690 and Population and Development Series No. 15.

ERIC Educational Resources Information Center

Mahar, Dennis J., Ed.; And Others

Two perspectives on carrying capacity and population growth are examined. The first perspective, "Carrying Capacity and Rapid Population Growth: Definition, Cases, and Consequences" (Robert Muscat), explores the possible meanings of the idea of carrying capacity under developing country conditions, looks at historical and present-day cases of…

Hydrologic Characteristics of Low-Impact Stormwater Control Measures at Two Sites in Northeastern Ohio, 2008-13 (USGS Scientific Investigations Report 2015-5030)

EPA Science Inventory

This report updates and examines hydrologic data gathered to characterize the performance of two stormwater control measures (SCM) sites in the Chagrin River watershed, Ohio. At the Sterncrest Drive site, roadside bioswales and rain gardens were used to alleviate drainage problem...

MEASUREMENT OF BIOAVAILABLE IRON AT TWO HAZARDOUS WASTE SITES

EPA Science Inventory

In the past, the concentrations of iron II in monitoring wells has been used to evaluate natural attenuation processes at hazardous waste sites. Changes in the aqueous concentrations of electron acceptors/products are important to the evaluation of natural biological attenuation...

Half-of-the-sites reactivity of outer-membrane phospholipase A against an active-site-directed inhibitor.

PubMed

Ubarretxena-Belandia, I; Cox, R C; Dijkman, R; Egmond, M R; Verheij, H M; Dekker, N

1999-03-01

The reaction of a novel active-site-directed phospholipase A1 inhibitor with the outer-membrane phospholipase A (OMPLA) was investigated. The inhibitor 1-p-nitrophenyl-octylphosphonate-2-tridecylcarbamoyl-3-et hanesulfonyl -amino-3-deoxy-sn-glycerol irreversibly inactivated OMPLA. The inhibition reaction did not require the cofactor calcium or an unprotonated active-site His142. The inhibition of the enzyme solubilized in hexadecylphosphocholine micelles was characterized by a rapid (t1/2 = 20 min) and complete loss of enzymatic activity, concurrent with the covalent modification of 50% of the active-site serines, as judged from the amount of p-nitrophenolate (PNP) released. Modification of the remaining 50% occurred at a much lower rate, indicative of half-of-the-sites reactivity against the inhibitor of this dimeric enzyme. Inhibition of monomeric OMPLA solubilized in hexadecyl-N,N-dimethyl-1-ammonio-3-propanesulfonate resulted in an equimolar monophasic release of PNP, concurrent with the loss of enzymatic activity (t1/2 = 14 min). The half-of-the-sites reactivity is discussed in view of the dimeric nature of this enzyme.

Botulinum neurotoxin serotype D attacks neurons via two carbohydrate-binding sites in a ganglioside-dependent manner.

PubMed

Strotmeier, Jasmin; Lee, Kwangkook; Völker, Anne K; Mahrhold, Stefan; Zong, Yinong; Zeiser, Johannes; Zhou, Jie; Pich, Andreas; Bigalke, Hans; Binz, Thomas; Rummel, Andreas; Jin, Rongsheng

2010-10-15

The extraordinarily high toxicity of botulinum neurotoxins primarily results from their specific binding and uptake into neurons. At motor neurons, the seven BoNT (botulinum neurotoxin) serotypes A-G inhibit acetylcholine release leading to flaccid paralysis. Uptake of BoNT/A, B, E, F and G requires a dual interaction with gangliosides and the synaptic vesicle proteins synaptotagmin or SV2 (synaptic vesicle glycoprotein 2), whereas little is known about the cell entry mechanisms of the serotypes C and D, which display the lowest amino acid sequence identity compared with the other five serotypes. In the present study we demonstrate that the neurotoxicity of BoNT/D depends on the presence of gangliosides by employing phrenic nerve hemidiaphragm preparations derived from mice expressing the gangliosides GM3, GM2, GM1 and GD1a, or only GM3 [a description of our use of ganglioside nomenclature is given in Svennerholm (1994) Prog. Brain Res. 101, XI-XIV]. High-resolution crystal structures of the 50 kDa cell-binding domain of BoNT/D alone and in complex with sialic acid, as well as biological analyses of single-site BoNT/D mutants identified two carbohydrate-binding sites. One site is located at a position previously identified in BoNT/A, B, E, F and G, but is lacking the conserved SXWY motif. The other site, co-ordinating one molecule of sialic acid, resembles the second ganglioside-binding pocket (the sialic-acid-binding site) of TeNT (tetanus neurotoxin).

A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter.

PubMed

Isalan, M; Klug, A; Choo, Y

2001-07-01

DNA-binding domains with predetermined sequence specificity are engineered by selection of zinc finger modules using phage display, allowing the construction of customized transcription factors. Despite remarkable progress in this field, the available protein-engineering methods are deficient in many respects, thus hampering the applicability of the technique. Here we present a rapid and convenient method that can be used to design zinc finger proteins against a variety of DNA-binding sites. This is based on a pair of pre-made zinc finger phage-display libraries, which are used in parallel to select two DNA-binding domains each of which recognizes given 5 base pair sequences, and whose products are recombined to produce a single protein that recognizes a composite (9 base pair) site of predefined sequence. Engineering using this system can be completed in less than two weeks and yields proteins that bind sequence-specifically to DNA with Kd values in the nanomolar range. To illustrate the technique, we have selected seven different proteins to bind various regions of the human immunodeficiency virus 1 (HIV-1) promoter.

Rapid road repair vehicle

DOEpatents

Mara, Leo M.

1999-01-01

Disclosed are improvments to a rapid road repair vehicle comprising an improved cleaning device arrangement, two dispensing arrays for filling defects more rapidly and efficiently, an array of pre-heaters to heat the road way surface in order to help the repair material better bond to the repaired surface, a means for detecting, measuring, and computing the number, location and volume of each of the detected surface imperfection, and a computer means schema for controlling the operation of the plurality of vehicle subsystems. The improved vehicle is, therefore, better able to perform its intended function of filling surface imperfections while moving over those surfaces at near normal traffic speeds.

A process to estimate net infiltration using a site-scale water-budget approach, Rainier Mesa, Nevada National Security Site, Nevada, 2002–05

USGS Publications Warehouse

Smith, David W.; Moreo, Michael T.; Garcia, C. Amanda; Halford, Keith J.; Fenelon, Joseph M.

2017-08-29

This report documents a process used to estimate net infiltration from precipitation, evapotranspiration (ET), and soil data acquired at two sites on Rainier Mesa. Rainier Mesa is a groundwater recharge area within the Nevada National Security Site where recharged water flows through bedrock fractures to a deep (450 meters) water table. The U.S. Geological Survey operated two ET stations on Rainier Mesa from 2002 to 2005 at sites characterized by pinyon-juniper and scrub-brush vegetative cover. Precipitation and ET data were corrected to remove measurement biases and gap-filled to develop continuous datasets. Net infiltration (percolation below the root zone) and changes in root-zone water storage were estimated using a monthly water-balance model.Site-scale water-budget results indicate that the heavily-fractured welded-tuff bedrock underlying thin (<40 centimeters) topsoil is a critical water source for vegetation during dry periods. Annual precipitation during the study period ranged from fourth lowest (182 millimeters [mm]) to second highest (708 mm) on record (record = 55 years). Annual ET exceeded precipitation during dry years, indicating that the fractured-bedrock reservoir capacity is sufficient to meet atmospheric-evaporative demands and to sustain vegetation through extended dry periods. Net infiltration (82 mm) was simulated during the wet year after the reservoir was rapidly filled to capacity. These results support previous conclusions that preferential fracture flow was induced, resulting in an episodic recharge pulse that was detected in nearby monitoring wells. The occurrence of net infiltration only during the wet year is consistent with detections of water-level rises in nearby monitoring wells that occur only following wet years.

Mapping Natech risk due to earthquakes using RAPID-N

NASA Astrophysics Data System (ADS)

Girgin, Serkan; Krausmann, Elisabeth

2013-04-01

Natural hazard-triggered technological accidents (so-called Natech accidents) at hazardous installations are an emerging risk with possibly serious consequences due to the potential for release of hazardous materials, fires or explosions. For the reduction of Natech risk, one of the highest priority needs is the identification of Natech-prone areas and the systematic assessment of Natech risks. With hardly any Natech risk maps existing within the EU the European Commission's Joint Research Centre has developed a Natech risk analysis and mapping tool called RAPID-N, that estimates the overall risk of natural-hazard impact to industrial installations and its possible consequences. The results are presented as risk summary reports and interactive risk maps which can be used for decision making. Currently, RAPID-N focuses on Natech risk due to earthquakes at industrial installations. However, it will be extended to also analyse and map Natech risk due to floods in the near future. The RAPID-N methodology is based on the estimation of on-site natural hazard parameters, use of fragility curves to determine damage probabilities of plant units for various damage states, and the calculation of spatial extent, severity, and probability of Natech events potentially triggered by the natural hazard. The methodology was implemented as a web-based risk assessment and mapping software tool which allows easy data entry, rapid local or regional risk assessment and mapping. RAPID-N features an innovative property estimation framework to calculate on-site natural hazard parameters, industrial plant and plant unit characteristics, and hazardous substance properties. Custom damage states and fragility curves can be defined for different types of plant units. Conditional relationships can be specified between damage states and Natech risk states, which describe probable Natech event scenarios. Natech consequences are assessed using a custom implementation of U.S. EPA's Risk Management

Solution of the effective Hamiltonian of impurity hopping between two sites in a metal

NASA Astrophysics Data System (ADS)

Ye, Jinwu

1997-07-01

We analyze in detail all the possible fixed points of the effective Hamiltonian of a nonmagnetic impurity hopping between two sites in a metal obtained by Moustakas and Fisher (MF). We find a line of non-Fermi liquid fixed points which continuously interpolates between the two-channel Kondo fixed point (2CK) and the one-channel, two-impurity Kondo (2IK) fixed point. There is one relevant direction with scaling dimension 12 and one leading irrelevant operator with dimension 32. There is also one marginal operator in the spin sector moving along this line. The marginal operator, combined with the leading irrelevant operator, will generate the relevant operator. For the general position on this line, the leading low-temperature exponents of the specific heat, the hopping susceptibility and the electron conductivity Cimp,χhimp,σ(T) are the same as those of the 2CK, but the finite-size spectrum depends on the position on the line. No universal ratios can be formed from the amplitudes of the three quantities except at the 2CK point on this line where the universal ratios can be formed. At the 2IK point on this line, σ(T)~2σu(1+aT3/2), no universal ratio can be formed either. The additional non-Fermi-liquid fixed point found by MF has the same symmetry as the 2IK, it has two relevant directions with scaling dimension 12, and is therefore also unstable. The leading low-temperature behaviors are Cimp~T,χhimp~lnT,σ(T)~2σu(1+aT3/2) no universal ratios can be formed. The system is shown to flow to a line of Fermi-liquid fixed points which continuously interpolates between the noninteracting fixed point and the two-channel spin-flavor Kondo fixed point discussed by the author previously. The effect of particle-hole symmetry breaking is discussed. The effective Hamiltonian in the external magnetic field is analyzed. The scaling functions for the physical measurable quantities are derived in the different regimes; their predictions for the experiments are given. Finally

Analysis of the interactions between GMF and Arp2/3 complex in two binding sites by molecular dynamics simulation.

PubMed

Popinako, A; Antonov, M; Dibrova, D; Chemeris, A; Sokolova, O S

2018-02-05

The Arp2/3 complex plays a key role in nucleating actin filaments branching. The glia maturation factor (GMF) competes with activators for interacting with the Arp2/3 complex and initiates the debranching of actin filaments. In this study, we performed a comparative analysis of interactions between GMF and the Arp2/3 complex and identified new amino acid residues involved in GMF binding to the Arp2/3 complex at two separate sites, revealed by X-ray and single particle EM techniques. Using molecular dynamics simulations we demonstrated the quantitative and qualitative changes in hydrogen bonds upon binding with GMF. We identified the specific amino acid residues in GMF and Arp2/3 complex that stabilize the interactions and estimated the mean force profile for the GMF using umbrella sampling. Phylogenetic and structural analyses of the recently defined GMF binding site on the Arp3 subunit indicate a new mechanism for Arp2/3 complex inactivation that involves interactions between the Arp2/3 complex and GMF at two binding sites. Copyright © 2018 Elsevier Inc. All rights reserved.

High pressure stopped-flow apparatus for the rapid mixing and subsequent study of two fluids under high hydrostatic pressures

NASA Astrophysics Data System (ADS)

Karan, Daniel M.; Macey, Robert I.

1980-08-01

A stopped-flow apparatus is described for the rapid mixing and subsequent study of two dissimilar fluids under pressures up to 1200 bar. The device consists of two identical pressure chambers which contain the two fluids, a third pressure chamber which contains gas to maintain the pressure in the system, an optical port for photometric observation, and various connections. The device has been used to measure reaction times on the order of a hundred milliseconds to tens of seconds, using a maximum of 2 ml of each reagent per experimental determination. The dead time is found to be 5-25 ms with minium average flow velocities of 2.0 m/s. The construction and operation of the device are described and examples of water transport data in red blood cells and the bromophenolblue indicated chemical reaction of NaHCO3 and HCl under pressure are presented.

Pyrrole-Based Antitubulin Agents: Two Distinct Binding Modalities are Predicted for C-2 Analogs in the Colchicine Site.

PubMed

Da, Chenxiao; Telang, Nakul; Barelli, Peter; Jia, Xin; Gupton, John T; Mooberry, Susan L; Kellogg, Glen E

2012-01-12

3,5-dibromo-4-(3,4-dimethoxyphenyl)-1H-pyrrole-2-carboxylic acid ethyl ester is a promising antitubulin lead agent that targets the colchicine site of tubulin. C-2 analogs were synthesized and tested for microtubule depolymerizing and antiproliferative activity. Molecular modeling studies using both GOLD docking and HINT (Hydropathic INTeraction) scoring revealed two distinct binding modes that explain the structural-activity relationships and are in accord with the structural basis of colchicine binding to tubulin. The binding mode of higher activity compounds is buried deeper in the site and overlaps well with rings A and C of colchicine, while the lower activity binding mode shows fewer critical contacts with tubulin. The model distinguishes highly active compounds from those with weaker activities and provides novel insights into the colchicine site and compound design.

Site characterization in densely fractured dolomite: Comparison of methods

USGS Publications Warehouse

Muldoon, M.; Bradbury, K.R.

2005-01-01

One of the challenges in characterizing fractured-rock aquifers is determining whether the equivalent porous medium approximation is valid at the problem scale. Detailed hydrogeologic characterization completed at a small study site in a densely fractured dolomite has yielded an extensive data set that was used to evaluate the utility of the continuum and discrete-fracture approaches to aquifer characterization. There are two near-vertical sets of fractures at the site; near-horizontal bedding-plane partings constitute a third fracture set. Eighteen boreholes, including five coreholes, were drilled to a depth of ???10.6 m. Borehole geophysical logs revealed several laterally extensive horizontal fractures and dissolution zones. Flowmeter and short-interval packer testing identified which of these features were hydraulically important. A monitoring system, consisting of short-interval piezometers and multilevel samplers, was designed to monitor four horizontal fractures and two dissolution zones. The resulting network consisted of >70 sampling points and allowed detailed monitoring of head distributions in three dimensions. Comparison of distributions of hydraulic head - and hydraulic conductivity determined by these two approaches suggests that even in a densely fractured-carbonate aquifer, a characterization approach using traditional long-interval monitoring wells is inadequate to characterize ground water movement for the purposes of regulatory monitoring or site remediation. In addition, traditional multiwell pumping tests yield an average or bulk hydraulic conductivity that is not adequate for predicting rapid ground water travel times through the fracture network, and the pumping test response does not appear to be an adequate tool for assessing whether the porous medium approximation is valid. Copyright ?? 2005 National Ground Water Association.

The genomic landscape of rapid repeated evolutionary ...

EPA Pesticide Factsheets

Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor–based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediatinggenes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversityhas likely been a crucial substrate for selective sweeps to propel rapid adaptation. This manuscript describes genomic evaluations that contribute to our understanding of the ecological and evolutionary risks associated with chronic contaminant exposures to wildlife populations. Here, we assessed genetic patterns associated with long-term response to an important class of highly toxic environmental pollutants. Specifically, chemical-specific tolerance has rapidly and repeatedly evolved in an estuarine fish species resident to estuaries of the Atlantic U.S. coast. We used laboratory studies to ch

[Pseudomonas folliculitis outbreaks associated with swimming pools or whirlpools in two guest-room sites in the northern region of Israel].

PubMed

Cohen-Dar, Michal; DiCastro, Noa; Grotto, Itamar

2012-07-01

In summer 2010-2011 two outbreaks of Pseudomonas foliculitis occurred among bathers who used the swimming pools or whirlpools in two guest-room sites. The source of the infection was traced to the swimming pools or whirlpools, which had not been chlorinated and monitored routinely. Of 40 bathers, 25 (62.5%) developed Pseudomonas folliculitis 2-4 days after exposure. Typically the rash began as a pruritic erythematous papule on the buttocks, axilla, and extremities, with fever, adenopathy and otitis externa. In the culture of the pustules and bacterial examination grew Pseudomonas aeroginosa. Pseudomonas folliculitis was first described by McCausland and Cox in 1975. To the best of our knowledge, this is the first description of outbreaks in swimming pools or whirlpools in guest-room sites in Israel. This article describes the epidemiological and environmental health investigation of the two outbreaks. With the rising popularity of swimming pools and whirlpools in guest-room sites, physicians in the community and the emergency rooms may encounter this disease. We urge their real time report to the public health offices, in charge of the epidemiological inquires, aiming to prevent the occurrence of new cases or improper treatment of similar cases.

Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils†

PubMed Central

Wang, Ya-Juan; Leadbetter, Jared Renton

2005-01-01

Signal degradation impacts all communications. Although acyl-homoserine lactone (acyl-HSL) quorum-sensing signals are known to be degraded by defined laboratory cultures, little is known about their stability in nature. Here, we show that acyl-HSLs are biodegraded in soils sampled from diverse U.S. sites and by termite hindgut contents. When amended to samples at physiologically relevant concentrations, 14C-labeled acyl-HSLs were mineralized to 14CO2 rapidly and, at most sites examined, without lag. A lag-free turf soil activity was characterized in further detail. Heating or irradiation of the soil prior to the addition of radiolabel abolished mineralization, whereas protein synthesis inhibitors did not. Mineralization exhibited an apparent Km of 1.5 μM acyl-HSL, ca. 1,000-fold lower than that reported for a purified acyl-HSL lactonase. Under optimal conditions, acyl-HSL degradation proceeded at a rate of 13.4 nmol · h−1 · g of fresh weight soil−1. Bioassays established that the final extent of signal inactivation was greater than for its full conversion to CO2 but that the two processes were well coupled kinetically. A most probable number of 4.6 × 105 cells · g of turf soil−1 degraded physiologically relevant amounts of hexanoyl-[1-14C]HSL to 14CO2. It would take chemical lactonolysis months to match the level of signal decay achieved in days by the observed biological activity. Rapid decay might serve either to quiet signal cross talk that might otherwise occur between spatially separated microbial aggregates or as a full system reset. Depending on the context, biological signal decay might either promote or complicate cellular communications and the accuracy of population density-based controls on gene expression in species-rich ecosystems. PMID:15746331

Complementation analysis of mutants of nitric oxide synthase reveals that the active site requires two hemes.

PubMed Central

Xie, Q W; Leung, M; Fuortes, M; Sassa, S; Nathan, C

1996-01-01

For catalytic activity, nitric oxide synthases (NOSs) must be dimeric. Previous work revealed that the requirements for stable dimerization included binding of tetrahydrobiopterin (BH4), arginine, and heme. Here we asked what function is served by dimerization. We assessed the ability of individually inactive mutants of mouse inducible NOS (iNOS; NOS2), each deficient in binding a particular cofactor or cosubstrate, to complement each other by generating NO upon cotransfection into human epithelial cells. The ability of the mutants to homodimerize was gauged by gel filtration and/or PAGE under partially denaturing conditions, both followed by immunoblot. Their ability to heterodimerize was assessed by coimmunoprecipitation. Heterodimers that contained only one COOH-terminal hemimer and only one BH4-binding site could both form and function, even though the NADPH-, FAD-, and FMN-binding domains (in the COOH-terminal hemimer) and the BH4-binding sites (in the NH2-terminal hemimer) were contributed by opposite chains. Heterodimers that contained only one heme-binding site (Cys-194) could also form, either in cis or in trans to the nucleotide-binding domains. However, for NO production, both chains had to bind heme. Thus, NO production by iNOS requires dimerization because the active site requires two hemes. Images Fig. 2 Fig. 3 Fig. 4 Fig. 7 PMID:8643499

Bioremediation techniques-classification based on site of application: principles, advantages, limitations and prospects.

PubMed

Azubuike, Christopher Chibueze; Chikere, Chioma Blaise; Okpokwasili, Gideon Chijioke

2016-11-01

Environmental pollution has been on the rise in the past few decades owing to increased human activities on energy reservoirs, unsafe agricultural practices and rapid industrialization. Amongst the pollutants that are of environmental and public health concerns due to their toxicities are: heavy metals, nuclear wastes, pesticides, green house gases, and hydrocarbons. Remediation of polluted sites using microbial process (bioremediation) has proven effective and reliable due to its eco-friendly features. Bioremediation can either be carried out ex situ or in situ, depending on several factors, which include but not limited to cost, site characteristics, type and concentration of pollutants. Generally, ex situ techniques apparently are more expensive compared to in situ techniques as a result of additional cost attributable to excavation. However, cost of on-site installation of equipment, and inability to effectively visualize and control the subsurface of polluted sites are of major concerns when carrying out in situ bioremediation. Therefore, choosing appropriate bioremediation technique, which will effectively reduce pollutant concentrations to an innocuous state, is crucial for a successful bioremediation project. Furthermore, the two major approaches to enhance bioremediation are biostimulation and bioaugmentation provided that environmental factors, which determine the success of bioremediation, are maintained at optimal range. This review provides more insight into the two major bioremediation techniques, their principles, advantages, limitations and prospects.

A two-helix motif positions the active site of lysophosphatidic acid acyltransferase for catalysis within the membrane bilayer

PubMed Central

Robertson, Rosanna M.; Yao, Jiangwei; Gajewski, Stefan; Kumar, Gyanendra; Martin, Erik W.; Rock, Charles O.; White, Stephen W.

2017-01-01

Phosphatidic acid is the central intermediate in membrane phospholipid synthesis and is generated by two acyltransferases in a pathway conserved in all life forms. The second step in this pathway is catalyzed by 1-acyl-sn-glycero-3-phosphate acyltransferase, called PlsC in bacteria. The crystal structure of PlsC from Thermotoga maritima reveals an unusual hydrophobic/aromatic N-terminal two-helix motif linked to an acyltransferase αβ domain that contains the catalytic HX4D motif. PlsC dictates the acyl chain composition of the 2-position of phospholipids, and the acyl chain selectivity ‘ruler’ is an appropriately placed and closed hydrophobic tunnel. This was confirmed by site-directed mutagenesis and membrane composition analysis of Escherichia coli cells expressing the mutated proteins. MD simulations reveal that the two-helix motif represents a novel substructure that firmly anchors the protein to one leaflet of the membrane. This binding mode allows the PlsC active site to acylate lysophospholipids within the membrane bilayer using soluble acyl donors. PMID:28714993

Plasticity within non-cerebellar pathways rapidly shapes motor performance in vivo

PubMed Central

Mitchell, Diana E.; Della Santina, Charles C.; Cullen, Kathleen E.

2016-01-01

Although cerebellar mechanisms are vital to maintain accuracy during complex movements and to calibrate simple reflexes, recent in vitro studies have called into question the widely held view that synaptic changes within cerebellar pathways exclusively guide alterations in motor performance. Here we investigate the vestibulo-ocular reflex (VOR) circuitry by applying temporally precise activation of vestibular afferents in awake-behaving monkeys to link plasticity at different neural sites with changes in motor performance. Behaviourally relevant activation patterns produce rapid attenuation of direct pathway VOR neurons, but not their nerve input. Changes in the strength of this pathway are sufficient to induce a lasting decrease in the evoked VOR. In addition, indirect brainstem pathways display complementary nearly instantaneous changes, contributing to compensating for the reduced sensitivity of primary VOR neurons. Taken together, our data provide evidence that multiple sites of plasticity within VOR pathways can rapidly shape motor performance in vivo. PMID:27157829

Prediction of allosteric sites on protein surfaces with an elastic-network-model-based thermodynamic method.

PubMed

Su, Ji Guo; Qi, Li Sheng; Li, Chun Hua; Zhu, Yan Ying; Du, Hui Jing; Hou, Yan Xue; Hao, Rui; Wang, Ji Hua

2014-08-01

Allostery is a rapid and efficient way in many biological processes to regulate protein functions, where binding of an effector at the allosteric site alters the activity and function at a distant active site. Allosteric regulation of protein biological functions provides a promising strategy for novel drug design. However, how to effectively identify the allosteric sites remains one of the major challenges for allosteric drug design. In the present work, a thermodynamic method based on the elastic network model was proposed to predict the allosteric sites on the protein surface. In our method, the thermodynamic coupling between the allosteric and active sites was considered, and then the allosteric sites were identified as those where the binding of an effector molecule induces a large change in the binding free energy of the protein with its ligand. Using the proposed method, two proteins, i.e., the 70 kD heat shock protein (Hsp70) and GluA2 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor, were studied and the allosteric sites on the protein surface were successfully identified. The predicted results are consistent with the available experimental data, which indicates that our method is a simple yet effective approach for the identification of allosteric sites on proteins.

Prediction of allosteric sites on protein surfaces with an elastic-network-model-based thermodynamic method

NASA Astrophysics Data System (ADS)

Su, Ji Guo; Qi, Li Sheng; Li, Chun Hua; Zhu, Yan Ying; Du, Hui Jing; Hou, Yan Xue; Hao, Rui; Wang, Ji Hua

2014-08-01

Allostery is a rapid and efficient way in many biological processes to regulate protein functions, where binding of an effector at the allosteric site alters the activity and function at a distant active site. Allosteric regulation of protein biological functions provides a promising strategy for novel drug design. However, how to effectively identify the allosteric sites remains one of the major challenges for allosteric drug design. In the present work, a thermodynamic method based on the elastic network model was proposed to predict the allosteric sites on the protein surface. In our method, the thermodynamic coupling between the allosteric and active sites was considered, and then the allosteric sites were identified as those where the binding of an effector molecule induces a large change in the binding free energy of the protein with its ligand. Using the proposed method, two proteins, i.e., the 70 kD heat shock protein (Hsp70) and GluA2 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor, were studied and the allosteric sites on the protein surface were successfully identified. The predicted results are consistent with the available experimental data, which indicates that our method is a simple yet effective approach for the identification of allosteric sites on proteins.

Relationships between airborne fungal spore concentration of Cladosporium and the summer climate at two sites in Britain

NASA Astrophysics Data System (ADS)

Hollins, P. D.; Kettlewell, P. S.; Atkinson, M. D.; Stephenson, D. B.; Corden, J. M.; Millington, W. M.; Mullins, J.

Cladosporium conidia have been shown to be important aeroallergens in many regions throughout the world, but annual spore concentrations vary considerably between years. Understanding these annual fluctuations may be of value in the clinical management of allergies. This study investigates the number of days in summer when spore concentration exceeds the allergenic threshold in relation to regional temperature and precipitation at two sites in England and Wales over 27 years. Results indicate that number of days in summer when the Cladosporium spores are above the allergenic concentration is positively correlated with regional temperature and negatively correlated with precipitation for both sites over the study period. Further analysis used a winter North Atlantic Oscillation index to explore the potential for long-range forecasting of the aeroallergen. For both spore measurement sites, a positive correlation exists between the winter North Atlantic Oscillation index and the number of days in summer above the allergenic threshold for Cladosporium spore concentration.

Mutational Analysis of Escherichia coli MoeA: Two Functional Activities Map to the Active Site Cleft

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

Nichols,J.; Xiang, S.; Schindelin, H.

2007-01-01

The molybdenum cofactor is ubiquitous in nature, and the pathway for Moco biosynthesis is conserved in all three domains of life. Recent work has helped to illuminate one of the most enigmatic steps in Moco biosynthesis, ligation of metal to molybdopterin (the organic component of the cofactor) to form the active cofactor. In Escherichia coli, the MoeA protein mediates ligation of Mo to molybdopterin while the MogA protein enhances this process in an ATP-dependent manner. The X-ray crystal structures for both proteins have been previously described as well as two essential MogA residues, Asp49 and Asp82. Here we describe amore » detailed mutational analysis of the MoeA protein. Variants of conserved residues at the putative active site of MoeA were analyzed for a loss of function in two different, previously described assays, one employing moeA{sup -} crude extracts and the other utilizing a defined system. Oddly, no correlation was observed between the activity in the two assays. In fact, our results showed a general trend toward an inverse relationship between the activity in each assay. Moco binding studies indicated a strong correlation between a variant's ability to bind Moco and its activity in the purified component assay. Crystal structures of the functionally characterized MoeA variants revealed no major structural changes, indicating that the functional differences observed are not due to disruption of the protein structure. On the basis of these results, two different functional areas were assigned to regions at or near the MoeA active site cleft.« less

Applications of rapid prototyping technology in maxillofacial prosthetics.

PubMed

Sykes, Leanne M; Parrott, Andrew M; Owen, C Peter; Snaddon, Donald R

2004-01-01

The purpose of this study was to compare the accuracy, required time, and potential advantages of rapid prototyping technology with traditional methods in the manufacture of wax patterns for two facial prostheses. Two clinical situations were investigated: the production of an auricular prosthesis and the duplication of an existing maxillary prosthesis, using a conventional and a rapid prototyping method for each. Conventional wax patterns were created from impressions taken of a patient's remaining ear and an oral prosthesis. For the rapid prototyping method, a cast of the ear and the original maxillary prosthesis were scanned, and rapid prototyping was used to construct the wax patterns. For the auricular prosthesis, both patterns were refined clinically and then flasked and processed in silicone using routine procedures. Twenty-six independent observers evaluated these patterns by comparing them to the cast of the patient's remaining ear. For the duplication procedure, both wax patterns were scanned and compared to scans of the original prosthesis by generating color error maps to highlight volumetric changes. There was a significant difference in opinions for the two auricular prostheses with regard to shape and esthetic appeal, where the hand-carved prosthesis was found to be of poorer quality. The color error maps showed higher errors with the conventional duplication process compared with the rapid prototyping method. The main advantage of rapid prototyping is the ability to produce physical models using digital methods instead of traditional impression techniques. The disadvantage of equipment costs could be overcome by establishing a centralized service.

Mapping and analysis of phosphorylation sites: a quick guide for cell biologists

PubMed Central

Dephoure, Noah; Gould, Kathleen L.; Gygi, Steven P.; Kellogg, Douglas R.

2013-01-01

A mechanistic understanding of signaling networks requires identification and analysis of phosphorylation sites. Mass spectrometry offers a rapid and highly sensitive approach to mapping phosphorylation sites. However, mass spectrometry has significant limitations that must be considered when planning to carry out phosphorylation-site mapping. Here we provide an overview of key information that should be taken into consideration before beginning phosphorylation-site analysis, as well as a step-by-step guide for carrying out successful experiments. PMID:23447708

Orchestrating rapid long-distance signaling in plants with Ca2+ , ROS and electrical signals.

PubMed

Choi, Won-Gyu; Miller, Gad; Wallace, Ian; Harper, Jeffrey; Mittler, Ron; Gilroy, Simon

2017-05-01

Plants show a rapid systemic response to a wide range of environmental stresses, where the signals from the site of stimulus perception are transmitted to distal organs to elicit plant-wide responses. A wide range of signaling molecules are trafficked through the plant, but a trio of potentially interacting messengers, reactive oxygen species (ROS), Ca 2+ and electrical signaling ('trio signaling') appear to form a network supporting rapid signal transmission. The molecular components underlying this rapid communication are beginning to be identified, such as the ROS producing NAPDH oxidase RBOHD, the ion channel two pore channel 1 (TPC1), and glutamate receptor-like channels GLR3.3 and GLR3.6. The plant cell wall presents a plant-specific route for possible propagation of signals from cell to cell. However, the degree to which the cell wall limits information exchange between cells via transfer of small molecules through an extracellular route, or whether it provides an environment to facilitate transmission of regulators such as ROS or H + remains to be determined. Similarly, the role of plasmodesmata as both conduits and gatekeepers for the propagation of rapid cell-to-cell signaling remains a key open question. Regardless of how signals move from cell to cell, they help prepare distant parts of the plant for impending challenges from specific biotic or abiotic stresses. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Methodology using a portable X-ray fluorescence device for on-site and rapid evaluation of heavy-atom contamination in wounds: a model study for application to plutonium contamination.

PubMed

Yoshii, Hiroshi; Yanagihara, Kouta; Imaseki, Hitoshi; Hamano, Tsuyoshi; Yamanishi, Hirokuni; Inagaki, Masayo; Sakai, Yasuhiro; Sugiura, Nobuyuki; Kurihara, Osamu; Sakai, Kazuo

2014-01-01

Workers decommissioning the Fukushima-Daiichi nuclear power plant damaged from the Great East Japan Earthquake and resulting tsunami are at risk of injury with possible contamination from radioactive heavy atoms including actinides, such as plutonium. We propose a new methodology for on-site and rapid evaluation of heavy-atom contamination in wounds using a portable X-ray fluorescence (XRF) device. In the present study, stable lead was used as the model contaminant substitute for radioactive heavy atoms. First, the wound model was developed by placing a liquid blood phantom on an epoxy resin wound phantom contaminated with lead. Next, the correlation between the concentration of contaminant and the XRF peak intensity was formulated considering the thickness of blood exiting the wound. Methods to determine the minimum detection limit (MDL) of contaminants at any maximal equivalent dose to the wound by XRF measurement were also established. For example, in this system, at a maximal equivalent dose of 16.5 mSv to the wound and blood thickness of 0.5 mm, the MDL value for lead was 1.2 ppm (3.1 nmol). The radioactivity of 239Pu corresponding to 3.1 nmol is 1.7 kBq, which is lower than the radioactivity of 239Pu contaminating puncture wounds in previous severe accidents. In conclusion, the established methodology could be beneficial for future development of a method to evaluate plutonium contamination in wounds. Highlights: Methodology for evaluation of heavy-atom contamination in a wound was established. A portable X-ray fluorescence device enables on-site, rapid and direct evaluation. This method is expected to be used for evaluation of plutonium contamination in wounds.

The dead do not lie: using skeletal remains for rapid assessment of historical small-mammal community baselines

PubMed Central

Terry, Rebecca C.

2010-01-01

Conservation and restoration efforts are often hindered by a lack of historical baselines that pre-date intense anthropogenic environmental change. In this paper I document that natural accumulations of skeletal remains represent a potential source of high-quality data on the historical composition and structure of small-mammal communities. I do so by assessing the fidelity of modern, decadal and centennial-scale time-averaged samples of skeletal remains (concentrated by raptor predation) to the living small-mammal communities from which they are derived. To test the power of skeletal remains to reveal baseline shifts, I employ the design of a natural experiment, comparing two taphonomically similar Great Basin cave localities in areas where anthropogenic land-use practices have diverged within the last century. I find relative stasis at the undisturbed site, but document rapid restructuring of the small-mammal community at the site subjected to recent disturbance. I independently validate this result using historical trapping records to show that dead remains accurately capture both the magnitude and direction of this baseline shift. Surveys of skeletal remains therefore provide a simple, powerful and rapid alternative approach for gaining insight into the historical structure and dynamics of modern small-mammal communities. PMID:20031992

A novel GMO biosensor for rapid ultrasensitive and simultaneous detection of multiple DNA components in GMO products.

PubMed

Huang, Lin; Zheng, Lei; Chen, Yinji; Xue, Feng; Cheng, Lin; Adeloju, Samuel B; Chen, Wei

2015-04-15

Since the introduction of genetically modified organisms (GMOs), there has been on-going and continuous concern and debates on the commercialization of products derived from GMOs. There is an urgent need for development of highly efficient analytical methods for rapid and high throughput screening of GMOs components, as required for appropriate labeling of GMO-derived foods, as well as for on-site inspection and import/export quarantine. In this study, we describe, for the first time, a multi-labeling based electrochemical biosensor for simultaneous detection of multiple DNA components of GMO products on the same sensing interface. Two-round signal amplification was applied by using both an exonuclease enzyme catalytic reaction and gold nanoparticle-based bio-barcode related strategies, respectively. Simultaneous multiple detections of different DNA components of GMOs were successfully achieved with satisfied sensitivity using this electrochemical biosensor. Furthermore, the robustness and effectiveness of the proposed approach was successfully demonstrated by application to various GMO products, including locally obtained and confirmed commercial GMO seeds and transgenetic plants. The proposed electrochemical biosensor demonstrated unique merits that promise to gain more interest in its use for rapid and on-site simultaneous multiple screening of different components of GMO products. Copyright © 2014 Elsevier B.V. All rights reserved.

Study on accumulation ability of two lichen species Hypogymnia physodes and Usnea hirta at iron-steel factory site, Turkey.

PubMed

Cansaran-Duman, Demet

2011-11-01

The use of biological responses to contaminant exposure by lichen species has become a useful tool in environmental quality evaluation and risk assesment. Lichen Hypogymnia physodes and Usnea hirta samples were collected in 2006 from 10 sites around iron-steel factory in Karabük, Turkey. H. physodes and U. hirta samples from Yenice forest were used as a control. The aim of present study was to evaluate the bioaccumulation ability and to determine the environmental impact of an iron-steel factory in Karabük. Seven elements (Zn, Cu, Mn, Fe, Pb, Ni, Cr and Cd) were analysed by atomic absorption spectrometry (AAS). The analytical results were compared statistically by using SPSS. As expected, the study area (Yenice forest, Karabük) chosen as control site (site no 11) showed significantly lower impact in comparison to other site (site no 1-10). Compared with the two lichen species, H. physodes showed highest metal accumulating capacity while U. hirta showed lowest. These criteria attested the best suitability for H. physodes, followed by U. hirta.

Development and Validation of Rapid Assessment Indices for Condition of Coastal Wetlands in Southern New England USA

EPA Science Inventory

The goals of this study were to develop and validate a Rapid Assessment Method (RAM) for assessing the condition of coastal wetlands in New England, USA. Eighty-one coastal wetland sites were assessed; nested within these were ten reference sites which were previously assessed us...

A rapid generation of adenovirus vector with a genetic modification in hexon protein.

PubMed

Di, Bingyan; Mao, Qinwen; Zhao, Junli; Li, Xing; Wang, Dongyang; Xia, Haibin

2012-02-10

The generation of hexon-modified adenovirus vector has proven difficult. In this paper, we developed a novel method for rapid generation of hexon-modified adenoviral vector via one step ligation in vitro followed by quick white/blue color screening. The new system has the following features. First, eGFP expression driven by the CMV promoter in E1 region functions as a reporter to evaluate the tropism of hexon-modified adenovirus in vitro. Second, it has two unique restriction enzyme sites with sticky ends located in the hexon HVR5 region. Third, a lacZ expression cassette under the control of plac promoter is placed between the two restriction enzyme sites, which allows recombinants to be selected using blue/white screening. To prove the principle of the method, genetically modified adenoviruses were successfully produced by insertion of NGR, RGD or Tat PTD peptide into hexon HVR5. Furthermore, the transduction efficiency of the Tat PTD modified virus was shown to be a significant enhancement in A172 and CHO-K1 cells. In conclusion, the novel system makes the production of truly retargeted vectors more promising, which would be of substantial benefit for cancer gene therapy. Copyright © 2012 Elsevier B.V. All rights reserved.

Tracking performance with two breathing oxygen concentrations after high altitude rapid decompression

NASA Technical Reports Server (NTRS)

Nesthus, Thomas E.; Schiflett, Samuel G.; Oakley, Carolyn J.

1992-01-01

Current military aircraft Liquid Oxygen (LOX) systems supply 99.5 pct. gaseous Aviator's Breathing Oxygen (ABO) to aircrew. Newer Molecular Sieve Oxygen Generation Systems (MSOGS) supply breathing gas concentration of 93 to 95 pct. O2. The margin is compared of hypoxia protection afforded by ABO and MSOGS breathing gas after a 5 psi differential rapid decompression (RD) in a hypobaric research chamber. The barometric pressures equivalent to the altitudes of 46000, 52000, 56000, and 60000 ft were achieved from respective base altitudes in 1 to 1.5 s decompressions. During each exposure, subjects remained at the simulated peak altitude breathing either 100 or 94 pct. O2 with positive pressure for 60 s, followed by a rapid descent to 40000 ft. Subjects used the Tactical Life Support System (TLSS) for high altitude protection. Subcritical tracking task performance on the Performance Evaluation Device (PED) provided psychomotor test measures. Overall tracking task performance results showed no differences between the MSOGS breathing O2 concentration of 94 pct. and ABO. Significance RMS error differences were found between the ground level and base altitude trials compared to peak altitude trials. The high positive breathing pressures occurring at the peak altitudes explained the differences.

Virtual directions in paleomagnetism: A global and rapid approach to evaluate the NRM components.

NASA Astrophysics Data System (ADS)

Ramón, Maria J.; Pueyo, Emilio L.; Oliva-Urcia, Belén; Larrasoaña, Juan C.

2017-02-01

We introduce a method and software to process demagnetization data for a rapid and integrative estimation of characteristic remanent magnetization (ChRM) components. The virtual directions (VIDI) of a paleomagnetic site are “all” possible directions that can be calculated from a given demagnetization routine of “n” steps (being m the number of specimens in the site). If the ChRM can be defined for a site, it will be represented in the VIDI set. Directions can be calculated for successive steps using principal component analysis, both anchored to the origin (resultant virtual directions RVD; m * (n2+n)/2) and not anchored (difference virtual directions DVD; m * (n2-n)/2). The number of directions per specimen (n2) is very large and will enhance all ChRM components with noisy regions where two components were fitted together (mixing their unblocking intervals). In the same way, resultant and difference virtual circles (RVC, DVC) are calculated. Virtual directions and circles are a global and objective approach to unravel different natural remanent magnetization (NRM) components for a paleomagnetic site without any assumption. To better constrain the stable components, some filters can be applied, such as establishing an upper boundary to the MAD, removing samples with anomalous intensities, or stating a minimum number of demagnetization steps (objective filters) or selecting a given unblocking interval (subjective but based on the expertise). On the other hand, the VPD program also allows the application of standard approaches (classic PCA fitting of directions a circles) and other ancillary methods (stacking routine, linearity spectrum analysis) giving an objective, global and robust idea of the demagnetization structure with minimal assumptions. Application of the VIDI method to natural cases (outcrops in the Pyrenees and u-channel data from a Roman dam infill in northern Spain) and their comparison to other approaches (classic end-point, demagnetization

Can rapid assessment protocols be used to judge sediment impairment in gravel-bed streams? A commentary

Treesearch

Thomas E. Lisle; John M. Buffington; Peter R. Wilcock; Kristin Bunte

2015-01-01

Land management agencies commonly use rapid assessments to evaluate the impairment of gravel-bed streams by sediment inputs from anthropogenic sources. We question whether rapid assessment can be used to reliably judge sediment impairment at a site or in a region. Beyond the challenges of repeatable and accurate sampling, we argue that a single metric or protocol is...

Pyrrole-Based Antitubulin Agents: Two Distinct Binding Modalities Are Predicted for C-2 Analogues in the Colchicine Site

PubMed Central

2011-01-01

3,5-Dibromo-4-(3,4-dimethoxyphenyl)-1H-pyrrole-2-carboxylic acid ethyl ester is a promising antitubulin lead agent that targets the colchicine site of tubulin. C-2 analogues were synthesized and tested for microtubule depolymerizing and antiproliferative activity. Molecular modeling studies using both GOLD docking and HINT (Hydropathic INTeraction) scoring revealed two distinct binding modes that explain the structure–activity relationships and are in accord with the structural basis of colchicine binding to tubulin. The binding mode of higher activity compounds is buried deeper in the site and overlaps well with rings A and C of colchicine, while the lower activity binding mode shows fewer critical contacts with tubulin. The model distinguishes highly active compounds from those with weaker activities and provides novel insights into the colchicine site and compound design. PMID:22611477

Structure of Urtica dioica agglutinin isolectin I: dimer formation mediated by two zinc ions bound at the sugar-binding site.

PubMed

Harata, K; Schubert, W D; Muraki, M

2001-11-01

Ultica dioica agglutinin, a plant lectin from the stinging nettle, consists of a total of seven individual isolectins. One of these structures, isolectin I, was determined at 1.9 A resolution by the X-ray method. The crystals belong to the space group P2(1) and the asymmetric unit contains two molecules related by local twofold symmetry. The molecule consists of two hevein-like chitin-binding domains lacking distinct secondary structure, but four disulfide bonds in each domain maintain the tertiary structure. The backbone structure of the two independent molecules is essentially identical and this is similarly true of the sugar-binding sites. In the crystal, the C-terminal domains bind Zn(2+) ions at the sugar-binding site. Owing to their location near a pseudo-twofold axis, the two zinc ions link the two independent molecules in a tail-to-tail arrangement: thus, His47 of molecule 1 and His67 of molecule 2 coordinate the first zinc ion, while the second zinc ion links Asp75 of molecule 1 and His47 of molecule 2.

Benthic habitat characterization and distribution from two representative sites of the deep-water SML Coral Province (Mediterranean)

NASA Astrophysics Data System (ADS)

Vertino, A.; Savini, A.; Rosso, A.; Di Geronimo, I.; Mastrototaro, F.; Sanfilippo, R.; Gay, G.; Etiope, G.

2010-03-01

Two sites (MS04 and MS06) from the Santa Maria di Leuca (SML) Coral Province were analyzed by a video and acoustic survey during the National Italian Project Apulian Plateau Bank Ecosystem Study (APLABES). Site MS04 (Atlantis Mound) is characterized by a sub-conical mound, 500 m wide and 25 m high, located at a water depth of about 650 m. Site MS06 (Yellow Chain) comprises several elongated reliefs (NNW-SSE-oriented), up to 25 m high and 500 m in maximum lateral extent, located at a depth of between 490 and 540 m. At both sites, two main mesohabitats (mound and intermound) containing several coral-bearing and -barren macrohabitats were observed in recorded videos and detected in side-scan sonographs. The coral-rich macrohabitats, characterized by densely packed colonies of the scleractinians Madrepora oculata and, secondarily, Lophelia pertusa ( M/ L), are typically restricted to the mound areas. The mud-dominated ones, almost devoid of M/L colonies, are more common within the intermound mesohabitat. However, on the most extensive mounds, both macrohabitat typologies exist. They are heterogeneously distributed on the mound surface, often showing a clear differentiation along two opposite flanks of the same topographic feature. M/ L-rich macrohabitats are preferentially located on top and along the mound northeastern flank, showing a typical step-like distribution, probably reflecting the arrangement of hard substrate outcrops. Along this flank, fan-shaped Madrepora colonies and sponges are often oriented NNW-SSE, implying, together with other evidence, a primary southwestern current flow. The hard-bottom macrohabitats of the southwestern mound flank are generally restricted to sparse exposed, subvertical to overhanging scarps as well as to heterometric boulders located at the scarp base. Their fauna is mainly characterized by small-sized organisms (such as sponges and solitary scleractinians) although m-sized boulders may locally host very large antipatharian