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Sample records for aao ref misc

  1. Multi-Index Stochastic Collocation (MISC) for random elliptic PDEs

    KAUST Repository

    Haji Ali, Abdul Lateef

    2016-01-06

    In this work we introduce the Multi-Index Stochastic Collocation method (MISC) for computing statistics of the solution of a PDE with random data. MISC is a combination technique based on mixed differences of spatial approximations and quadratures over the space of random data. We propose an optimization procedure to select the most effective mixed differences to include in the MISC estimator: such optimization is a crucial step and allows us to build a method that, provided with sufficient solution regularity, is potentially more effective than other multi-level collocation methods already available in literature. We then provide a complexity analysis that assumes decay rates of product type for such mixed differences, showing that in the optimal case the convergence rate of MISC is only dictated by the convergence of the deterministic solver applied to a one dimensional problem. We show the effectiveness of MISC with some computational tests, comparing it with other related methods available in the literature, such as the Multi-Index and Multilevel Monte Carlo, Multilevel Stochastic Collocation, Quasi Optimal Stochastic Collocation and Sparse Composite Collocation methods.

  2. Luminescence parameters of InP/ZnS@AAO nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Savchenko, S. S.; Vokhmintsev, A. S.; Weinstein, I. A., E-mail: i.a.weinstein@urfu.ru [Ural Federal University, NANOTECH Centre, Mira str., 19, Yekaterinburg, Russia, 620002 (Russian Federation)

    2016-03-29

    Nanostructured membranes of anodic aluminum oxide (AAO) with InP/ZnS semiconductor nanocrystals deposited in pores were synthesized by electrochemical technique, physical deposition and post processing in an ultrasonic bath. Photoluminescence spectra of the samples were studied. Fluorescent properties of the quantum dots are found to be retained after the deposition. The color range is illustrated that can be covered using membranes annealed at temperatures < 900°C and by varying the concentration of the deposited InP/ZnS nanocrystals. Chromaticity coordinates and correlated color temperature for the fabricated white InP/ZnS@AAO phosphor are (0.21, 0.26) and 4115 K, respectively.

  3. Role of operon aaoSo-mutT in antioxidant defense in Streptococcus oligofermentans.

    Science.gov (United States)

    Zhou, Peng; Liu, Lei; Tong, Huichun; Dong, Xiuzhu

    2012-01-01

    Previously, we have found that an insertional inactivation of aao(So), a gene encoding L-amino acid oxidase (LAAO), causes marked repression of the growth of Streptococcus oligofermentans. Here, we found that aao(So) and mutT, a homolog of pyrophosphohydrolase gene of Escherichia coli, constituted an operon. Deletion of either gene did not impair the growth of S. oligofermentans, but double deletion of both aao(So) and mutT was lethal. Quantitative PCR showed that the transcript abundance of mutT was reduced for 13-fold in the aao(So) insertional mutant, indicating that gene polarity derived from the inactivation of aao(So) attenuated the expression of mutT. Enzymatic assays were conducted to determine the biochemical functions of LAAO and MutT of S. oligofermentans. The results indicated that LAAO functioned as an aminoacetone oxidase [47.75 nmol H(2)O(2) (min · mg protein)(-1)]; and MutT showed the pyrophosphohydrolase activity, which removed mutagens such as 8-oxo-dGTP. Like paraquat, aao(So) mutations increased the expression of SOD, and addition of aminoacetone (final concentration, 5 mM) decreased the mutant's growth by 11%, indicating that the aao(So) mutants are under ROS stress. HPLC did reveal elevated levels of cytoplasmic aminoacetone in both the deletion and insertional gene mutants of aao(So). Electron spin resonance spectroscopy showed increased hydroxyl radicals in both types of aao(So) mutant. This demonstrated that inactivation of aao(So) caused the elevation of the prooxidant aminoacetone, resulting the cellular ROS stress. Our study indicates that the presence of both LAAO and MutT can prevent endogenous metabolites-generated ROS and mutagens. In this way, we were able to determine the role of the aao(So)-mutT operon in antioxidant defense in S. oligofermentans.

  4. Role of operon aaoSo-mutT in antioxidant defense in Streptococcus oligofermentans.

    Directory of Open Access Journals (Sweden)

    Peng Zhou

    Full Text Available Previously, we have found that an insertional inactivation of aao(So, a gene encoding L-amino acid oxidase (LAAO, causes marked repression of the growth of Streptococcus oligofermentans. Here, we found that aao(So and mutT, a homolog of pyrophosphohydrolase gene of Escherichia coli, constituted an operon. Deletion of either gene did not impair the growth of S. oligofermentans, but double deletion of both aao(So and mutT was lethal. Quantitative PCR showed that the transcript abundance of mutT was reduced for 13-fold in the aao(So insertional mutant, indicating that gene polarity derived from the inactivation of aao(So attenuated the expression of mutT. Enzymatic assays were conducted to determine the biochemical functions of LAAO and MutT of S. oligofermentans. The results indicated that LAAO functioned as an aminoacetone oxidase [47.75 nmol H(2O(2 (min · mg protein(-1]; and MutT showed the pyrophosphohydrolase activity, which removed mutagens such as 8-oxo-dGTP. Like paraquat, aao(So mutations increased the expression of SOD, and addition of aminoacetone (final concentration, 5 mM decreased the mutant's growth by 11%, indicating that the aao(So mutants are under ROS stress. HPLC did reveal elevated levels of cytoplasmic aminoacetone in both the deletion and insertional gene mutants of aao(So. Electron spin resonance spectroscopy showed increased hydroxyl radicals in both types of aao(So mutant. This demonstrated that inactivation of aao(So caused the elevation of the prooxidant aminoacetone, resulting the cellular ROS stress. Our study indicates that the presence of both LAAO and MutT can prevent endogenous metabolites-generated ROS and mutagens. In this way, we were able to determine the role of the aao(So-mutT operon in antioxidant defense in S. oligofermentans.

  5. Four-year-BS-position-paper.pdf | misc docs | academy | Indian ...

    Indian Academy of Sciences (India)

    Home; academy; misc docs; Four-year-BS-position-paper.pdf. 404! error. The page your are looking for can not be found! Please check the link or use the navigation bar at the top. YouTube; Twitter; Facebook; Blog. Academy News. IAS Logo. 29th Mid-year meeting. Posted on 19 January 2018. The 29th Mid-year meeting of ...

  6. A Brief Note on the Magnetowetting of Magnetic Nanofluids on AAO Surfaces

    Directory of Open Access Journals (Sweden)

    Yu-Chin Chien

    2018-02-01

    Full Text Available In magnetowetting, the material properties of liquid, surface morphology of solid, and applied external field are three major factors used to determine the wettability of a liquid droplet on a surface. For wetting measurements, an irregular or uneven surface could result in a significant experimental uncertainty. The periodic array with a hexagonal symmetry structure is an advantage of the anodic aluminum oxide (AAO structure. This study presents the results of the wetting properties of magnetic nanofluid sessile droplets on surfaces of various AAO pore sizes under an applied external magnetic field. Stable, water-based magnetite nanofluids are prepared by combining the chemical co-precipitation with the sol-gel technique, and AAO surfaces are then generated by anodizing the aluminum sheet in the beginning. The influence of pore size and magnetic field gradient on the magnetowetting of magnetic nanofluids on AAO surfaces is then investigated by an optical test system. Experimental results show that increasing the processing voltage of AAO templates could result in enhanced non-wettability behavior; that is, the increase in AAO pore size could lead to the increase in contact angle. The contact angle could be reduced by the applied magnetic field gradient. In general, the magnetic field has a more significant effect at smaller AAO pore sizes.

  7. The Mid-Infrared Imager/Spectrometer/Coronagraph Instrument (MISC) for the Origins Space Telescope

    Science.gov (United States)

    Roellig, Thomas; Sakon, Itsuki; Ennico, Kimberly; MISC Instrument Study Team, Origins Space Telescope Study Team

    2018-01-01

    The Origins Space Telescope (OST) is one of four potential flagship missions that have been funded by NASA for study for consideration in the upcoming Astrophysics Decadal Review expected in 2020. The OST telescope will be up to 9.3 meters in diameter, cooled to ~4K, and the mission will be optimized for efficient mid and far-infrared astronomical observations. An initial suite of five focal plane instruments are being baselined for this observatory. The Mid-infrared Imager Spectrometer Coronagraph (MISC) instrument will observe at the shortest wavelengths of any of these instruments, ranging from 5 to 38 microns, and consists of three separate optical modules providing imaging, spectroscopy, and coronagraph capabilities. The imaging camera covers a 3 arcmin x 3 arcmin field with filters and grisms from 6-38 microns. The spectrometers have spectral resolving powers R~1,000 from 9-38 microns (with a goal of 5-38 microns) and R~25,000 for 12-18 and 25-36 microns. The coronagraph covers 6-38 microns. There is a special densified pupil spectrometer channel that provides R~100-300 exoplanet transit and emission spectroscopy from 6-26 microns with very high spectro-photometric stability. As the shortest wavelength focal plane imager the MISC instrument will also be used for focal plane guiding as needed for the other OST science instruments. The science that MISC enables on OST includes: studying episodic accretion in protostellar envelopes, tracing the rise in metallacity and dust over cosmic time (when combined with far-infrared measurements), measuring dust in galactic outflows, assessing feedback from supernovae and AGN on the multi-phase ISM in galaxies, characterizing the AGN and starburst power in normal and massive galaxies, detecting exoplanet atmospheric biosignatures, and direct imaging of Jovian planets orbiting older stars at separations of 5-20 AU.

  8. Effects of MISC Intervention on Cognition, Autonomy, and Behavioral Functioning of Adult Consumers with Severe Intellectual Disability

    Science.gov (United States)

    Lifshitz, Hefziba; Klein, Pnina S.; Cohen, Sara Fridel

    2010-01-01

    This study examined the effects of a yearlong Mediational Intervention for Sensitizing Caregivers (MISC; Klein, 1992) on: (a) the quality of interactions between rehabilitation day center paraprofessional staff (n=10) and their adult consumers (n=19) with severe intellectual disability (ID) and (b) the consumers' cognition, autonomy, and…

  9. Depolarized haze of nano-porous AAO film via porosity and aspect control

    Science.gov (United States)

    Tseng, Chun-Wei; Lin, Yung-Hsiang; Cheng, Chih-Hsien; Lin, Gong-Ru

    2018-01-01

    Multiple scattering induced haze and depolarization effects of nano-porous AAO films controlled by detuning the porosity and aspect ratio of the nano holes are investigated. The nano-porous AAO film with its porosity increasing from 12.6% to 19.3% enhances the scattering of the incident laser beam with its maximal scattering angle enlarged from 5° to 8° under TM-mode incidence and from 6° to 10° under TE-mode incidence. Because of multiple scattering within the porous holes of the AAO, the depolarization on the reflected beam by transferring its electric field from horizontal to the vertical such that the polarization ratio is degraded with a randomized haze. The porosity of AAO surface broadens from 12.6% to 19.3% when increasing the bias voltage from 40 to 60 V during the second-step of the electro-chemical anodization process, which essentially adjusts the polarization ratio under TM-mode and TE-mode incidences raise from 0.31 to 0.35 and from 0.32 to 0.48, respectively. The depolarized haze of the nano-porous AAO film is correlated with its porosity and aspect ratio controlled by the pore size and etched depth of the AAO. Under TM-mode incidence, the simulated polarization ratio increases from 0.35 to 0.38, which correlates well with experimental results. In contrast, the experiment result slightly deviates from the theoretical prediction as the TE-mode field interacts more surface area than the TM-mode field does. Such a nano-porous AAO exhibits tunable depolarized haze via the control porosity and aspect ratio, which is particularly suitable to serve as the catalytic buffer for synthesizing the hydrophobic and hazed solar energy converters.

  10. Simulation of Photon energy Spectra Using MISC, SOURCES, MCNP and GADRAS

    Energy Technology Data Exchange (ETDEWEB)

    Tucker, Lucas P. [Los Alamos National Laboratory; Shores, Erik F. [Los Alamos National Laboratory; Myers, Steven C. [Los Alamos National Laboratory; Felsher, Paul D. [Los Alamos National Laboratory; Garner, Scott E. [Los Alamos National Laboratory; Solomon, Clell J. Jr. [Los Alamos National Laboratory

    2012-08-14

    The detector response functions included in the Gamma Detector Response and Analysis Software (GADRAS) are a valuable resource for simulating radioactive source emission spectra. Application of these response functions to the results of three-dimensional transport calculations is a useful modeling capability. Using a 26.2 kg shell of depleted uranium (DU) as a simple test problem, this work illustrates a method for manipulating current tally results from MCNP into the GAM file format necessary for a practical link to GADRAS detector response functions. MISC (MCNP Intrinsic Source Constructor) and SOURCES 4C were used to develop photon and neutron source terms for subsequent MCNP transport, and the resultant spectrum is shown to be in good agreement with that from GADRAS. A 1 kg DU sphere was also modeled with the method described here and showed similarly encouraging results.

  11. Simulation of Photon energy Spectra Using MISC, SOURCES, MCNP and GADRAS

    International Nuclear Information System (INIS)

    Tucker, Lucas P.; Shores, Erik F.; Myers, Steven C.; Felsher, Paul D.; Garner, Scott E.; Solomon, Clell J. Jr.

    2012-01-01

    The detector response functions included in the Gamma Detector Response and Analysis Software (GADRAS) are a valuable resource for simulating radioactive source emission spectra. Application of these response functions to the results of three-dimensional transport calculations is a useful modeling capability. Using a 26.2 kg shell of depleted uranium (DU) as a simple test problem, this work illustrates a method for manipulating current tally results from MCNP into the GAM file format necessary for a practical link to GADRAS detector response functions. MISC (MCNP Intrinsic Source Constructor) and SOURCES 4C were used to develop photon and neutron source terms for subsequent MCNP transport, and the resultant spectrum is shown to be in good agreement with that from GADRAS. A 1 kg DU sphere was also modeled with the method described here and showed similarly encouraging results.

  12. Is A/A/O process effective in toxicity removal? Case study with coking wastewater.

    Science.gov (United States)

    Shi, Liu; Wang, Dong; Cao, Di; Na, Chunhong; Quan, Xie; Zhang, Ying

    2017-08-01

    The anaerobic-anoxic-oxic (A/A/O) process is the commonly used biological wastewater treatment process, especially for the coking wastewater. However, limit is known about its ability in bio-toxicity removal from wastewater. In this study, we evaluated the performance of A/A/O process in bio-toxicity removal from the coking wastewater, using two test species (i.e. crustacean (Daphnia magna) and zebra fish (Danio rerio)) in respect of acute toxicity, oxidative damage and genotoxicity. Our results showed that the acute toxicity of raw influent was reduced gradually along with A/A/O process and the effluent presented no acute toxicity to Daphnia magna (D. magna) and zebra fish. The reactive oxygen species (ROS) level in D. magna and zebra fish was promoted by the effluent from each tank of A/A/O process, showing that coking wastewater induced oxidative damage. Herein, the oxidative damage to D. magna was mitigated in the oxic tank, while the toxicity to zebra fish was reduced in the anoxic tank. The comet assays showed that genotoxicity to zebra fish was removed stepwise by A/A/O process, although the final effluent still presented genotoxicity to zebra fish. Our results indicated that the A/A/O process was efficient in acute toxicity removal, but not so effective in the removal of other toxicity (e.g. oxidative damage and genotoxicity). Considering the potential risks of wastewater discharge, further advanced toxicity mitigation technology should be applied in the conventional biological treatment process, and the toxicity index should be introduced in the regulation system of wastewater discharge. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Fabrication of indium sulfide nanofibers via a hydrothermal method assisted by AAO template

    International Nuclear Information System (INIS)

    Zhu Xiaoyi; Ma Junfeng; Wang Yonggang; Tao Jiantao; Zhou Jun; Zhao Zhongqiang; Xie Lijin; Tian Hua

    2006-01-01

    β-In 2 S 3 nanofibers were successfully synthesized via a hydrothermal method with AAO membrane as a template at 150 deg. C for 15 h. XRD patterns indicated the perfect crystallization of β-In 2 S 3 . SEM images showed that the β-In 2 S 3 nanofibers grew up from the channel ends of the AAO template. TEM images confirmed that the nanofibers had a high aspect ratio of ca. 40-50 and diameters of about 10 nm. The room temperature photoluminescence (PL) spectrum of the β-In 2 S 3 nanofibers indicated its potential applications in light-emission devices

  14. A NAP-AAO3 regulatory module promotes chlorophyll degradation via ABA biosynthesis in Arabidopsis leaves.

    Science.gov (United States)

    Yang, Jiading; Worley, Eric; Udvardi, Michael

    2014-12-01

    Chlorophyll degradation is an important part of leaf senescence, but the underlying regulatory mechanisms are largely unknown. Excised leaves of an Arabidopsis thaliana NAC-LIKE, ACTIVATED BY AP3/PI (NAP) transcription factor mutant (nap) exhibited lower transcript levels of known chlorophyll degradation genes, STAY-GREEN1 (SGR1), NON-YELLOW COLORING1 (NYC1), PHEOPHYTINASE (PPH), and PHEIDE a OXYGENASE (PaO), and higher chlorophyll retention than the wild type during dark-induced senescence. Transcriptome coexpression analysis revealed that abscisic acid (ABA) metabolism/signaling genes were disproportionately represented among those positively correlated with NAP expression. ABA levels were abnormally low in nap leaves during extended darkness. The ABA biosynthetic genes 9-CIS-EPOXYCAROTENOID DIOXYGENASE2, ABA DEFICIENT3, and ABSCISIC ALDEHYDE OXIDASE3 (AAO3) exhibited abnormally low transcript levels in dark-treated nap leaves. NAP transactivated the promoter of AAO3 in mesophyll cell protoplasts, and electrophoretic mobility shift assays showed that NAP can bind directly to a segment (-196 to -162 relative to the ATG start codon) of the AAO3 promoter. Exogenous application of ABA increased the transcript levels of SGR1, NYC1, PPH, and PaO and suppressed the stay-green phenotype of nap leaves during extended darkness. Overexpression of AAO3 in nap leaves also suppressed the stay-green phenotype under extended darkness. Collectively, the results show that NAP promotes chlorophyll degradation by enhancing transcription of AAO3, which leads to increased levels of the senescence-inducing hormone ABA. © 2014 American Society of Plant Biologists. All rights reserved.

  15. Fabrication of vertically aligned Pd nanowire array in AAO template by electrodeposition using neutral electrolyte

    Directory of Open Access Journals (Sweden)

    Yüzer Hayrettin

    2010-01-01

    Full Text Available Abstract A vertically aligned Pd nanowire array was successfully fabricated on an Au/Ti substrate using an anodic aluminum oxide (AAO template by a direct voltage electrodeposition method at room temperature using diluted neutral electrolyte. The fabrication of Pd nanowires was controlled by analyzing the current–time transient during electrodeposition using potentiostat. The AAO template and the Pd nanowires were characterized by scanning electron microscopy (SEM, energy-dispersive X-ray (EDX methods and X-Ray diffraction (XRD. It was observed that the Pd nanowire array was standing freely on an Au-coated Ti substrate after removing the AAO template in a relatively large area of about 5 cm2, approximately 50 nm in diameter and 2.5 μm in length with a high aspect ratio. The nucleation rate and the number of atoms in the critical nucleus were determined from the analysis of current transients. Pd nuclei density was calculated as 3.55 × 108 cm−2. Usage of diluted neutral electrolyte enables slower growing of Pd nanowires owing to increase in the electrodeposition potential and thus obtained Pd nanowires have higher crystallinity with lower dislocations. In fact, this high crystallinity of Pd nanowires provides them positive effect for sensor performances especially.

  16. Effects of heat treatment on optical absorption properties of Ni-P/AAO nano-array composite structure

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yi-Fan; Wang, Feng-Hua; Guo, Dong-Lai; Huang, Sheng-You; Zou, Xian-Wu [Wuhan University, Department of Physics, Wuhan (China); Sang, Jian-Ping [Wuhan University, Department of Physics, Wuhan (China); Jianghan University, Department of Physics, Wuhan (China)

    2009-11-15

    Ni-P/AAO nano-array composite structure assemblies with Ni and P grown in the pores of anodic aluminum oxide (AAO) membranes were prepared by electroless deposition. The results of SEM, TEM and SAED show that as-deposited Ni-P nanowires have an amorphous structure and a few nanocrystallites form after annealing. The optical absorption spectra reveal that, as the annealing temperature increases, the absorption band edge of the Ni-P/AAO composite structure is obviously blue shifted, which is attributed to a decrease of the internal pressure after heat treatment. Meanwhile, the annealed Ni-P/AAO nano-array composite structure exhibits the absorption behavior of a direct band gap semiconductor. Details of this behavior are discussed together with the implications for potential device applications. (orig.)

  17. Reconciling the clinical practice guidelines on Bell's palsy from the AAO-HNSF and the AAN.

    Science.gov (United States)

    Schwartz, Seth R; Jones, Stephanie L; Getchius, Thomas S D; Gronseth, Gary S

    2014-05-01

    Bell's palsy, named after the Scottish anatomist, Sir Charles Bell, is the most common acute mononeuropathy, or disorder affecting a single nerve, and is the most common diagnosis associated with facial nerve weakness/paralysis. In the past 2 years, both the American Academy of Neurology (AAN) and the American Academy of Otolaryngology-Head and Neck Surgery Foundation (AAO-HNSF) have published clinical practice guidelines aimed to improve the quality of care and outcomes for patients diagnosed with Bell's palsy. This commentary aims to address the similarities and differences in the scope and final recommendations made by each guideline development group.

  18. DC electrodeposition of NiGa alloy nanowires in AAO template

    Energy Technology Data Exchange (ETDEWEB)

    Maleki, K. [Nanomaterials Group, Department of Materials Engineering, Tarbiat Modares University, Iran, P.O. Box: 14115-143, Tehran (Iran, Islamic Republic of); Sanjabi, S., E-mail: sanjabi@modares.ac.ir [Nanomaterials Group, Department of Materials Engineering, Tarbiat Modares University, Iran, P.O. Box: 14115-143, Tehran (Iran, Islamic Republic of); Alemipour, Z. [Department of Physics, University of Kurdistan, Sanandaj (Iran, Islamic Republic of)

    2015-12-01

    NiGa alloy nanowires were electrodeposited from an acidic sulfate bath into nanoporous anodized alumina oxide (AAO). This template was fabricated by two-step anodizing. The effects of bath composition and current density were explored on the Ga content of electrodeposited nanowires. The Ga content in the deposits was increased by increasing both Ga in the bath composition and electrodepositing current density. The NiGa alloy nanowires were synthesized for Ga content up to 2–4% without significant improving the magnetic properties. Above this threshold Ga clusters were formed and decreased the magnetic properties of the nanowires. For Ga content of the alloy above 30%, the wires were too short and incomplete. X-ray diffraction patterns reveal that the significant increase of Ga content in the nanowires, changes the FCC crystal structure of Ni to an amorphous phase. It also causes a sizeable increase in the Ga cluster size; these both lead to a significant reduction in the coercivity and the magnetization respectively. - Highlights: • NiGa alloy nanowires were electrodeposited from acidic sulphate baths into nanoporous anodized alumina oxide (AAO) template. • The Ga content was increased by increasing the Ga in the bath composition and electrodeposition current density. • The magnetic parameters such as coercivity and magnetization were not changed for the alloy nanowire with Ga content less than 4%.

  19. Syntheses of Nd2O3 nanowires through sol-gel process assisted with porous anodic aluminum oxide (AAO) template

    International Nuclear Information System (INIS)

    Qu Xiaofei; Dai Jinhui; Tian Jintao; Huang Xiang; Liu Zhongfang; Shen Zhenlei; Wang Peipei

    2009-01-01

    The syntheses of Nd 2 O 3 nanowires were performed through sol-gel process assisted with porous anodic aluminum oxide (AAO) as a template. The morphology and the phase composition of the prepared nanowires were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), and energy disperse spectroscopy (EDS). The results showed that the Nd 2 O 3 nanowires could be successfully synthesized by using this method. The nanowires had successfully grown into the nanochannels of the AAO template. The prepared nanowires were quite uniform. Both the XRD and EDS examinations revealed that the obtained nanowires were not others but Nd 2 O 3

  20. Rank hypocrisies the insult of the REF

    CERN Document Server

    Sayer, Derek

    2015-01-01

    "The REF is right out of Havel's and Kundera's Eastern Europe: a state-administered exercise to rank academic research like hotel chains dependent on the active collaboration of the UK professoriate. In crystalline text steeped in cold rage, Sayer takes aim at the REF's central claim, that it is a legitimate process of expert peer review. He critiques university and national-level REF processes against actual practices of scholarly review as found in academic journals, university presses, and North American tenure procedures. His analysis is damning. If the REF fails as scholarly review, how can academics and universities continue to participate? And how can government use its rankings as a basis for public policy?" - Tarak Barkawi, Reader in the Department of International Relations, London School of Economics "Many academics across the world have come to see the REF as an arrogant attempt to raise national research standards that has resulted in a variety of self-inflicted wounds to UK higher education. Der...

  1. HeREF-2003: Helium Refrigeration Techniques

    CERN Multimedia

    2003-01-01

    CERN Technical Training 2003: Learning for the LHC ! Theory, Technology, Maintenance and Control of Helium Refrigerators HeREF-2003 is a course in the framework of the 2002 Technical Training Programme, that will provide a complete introduction to Helium refrigeration, with a practical approach to theory, technology, maintenance and control of Helium refrigeration installations. Theoretical aspects and equations will be limited to a minimum. HeREF-2003 targets an audience of technicians and operators of Helium refrigeration plants at CERN, as well as physicists and engineers needing an overview of current Helium refrigeration techniques. HeREF-2003 will address, among other, issues related to component technology, installation maintenance, process control and Helium purity. A commented visit to a couple of CERN Helium refrigeration or liquefaction plants will also take place. Duration: 7 half days (4 mornings and 3 afternoons), 6-10 October, 2003 Cost per participant: 500.- CHF Language: Bilingual English...

  2. HeREF-2003 : Helium Refrigeration Techniques

    CERN Multimedia

    2003-01-01

    CERN Technical Training 2003: Learning for the LHC ! Theory, Technology, Maintenance and Control of Helium Refrigerators HeREF-2003 is a course in the framework of the 2002 Technical Training Programme, that will provide a complete introduction to Helium refrigeration, with a practical approach to theory, technology, maintenance and control of Helium refrigeration installations. Theoretical aspects and equations will be limited to a minimum. HeREF-2003 targets an audience of technicians and operators of Helium refrigeration plants at CERN, as well as physicists and engineers needing an overview of current Helium refrigeration techniques. HeREF-2003 will address, among other, issues related to component technology, installation maintenance, process control and Helium purity. A commented visit to a couple of CERN Helium refrigeration or liquefaction plants will also take place. • Duration: 7 half days (4 mornings and 3 afternoons), 6-10 October, 2003 • Cost per participant: 500.- CHF ...

  3. The Hong Kong/AAO/Strasbourg Hα (HASH) Planetary Nebula Database

    Science.gov (United States)

    Bojičić, Ivan S.; Parker, Quentin A.; Frew, David J.

    2017-10-01

    The Hong Kong/AAO/Strasbourg Hα (HASH) planetary nebula database is an online research platform providing free and easy access to the largest and most comprehensive catalogue of known Galactic PNe and a repository of observational data (imaging and spectroscopy) for these and related astronomical objects. The main motivation for creating this system is resolving some of long standing problems in the field e.g. problems with mimics and dubious and/or misidentifications, errors in observational data and consolidation of the widely scattered data-sets. This facility allows researchers quick and easy access to the archived and new observational data and creating and sharing of non-redundant PN samples and catalogues.

  4. Effect of electrolyte temperature on the thickness of anodic aluminium oxide (AAO layer

    Directory of Open Access Journals (Sweden)

    P. Michal

    2016-07-01

    Full Text Available Effect of electrolyte temperature on the thickness of resulting oxide layer has been studied. Unlike previous published studies this article was aimed to monitor the relationship between electrolyte temperature and resulting AAO layer thickness in interaction with other input factors affecting during anodizing process under special process condition, i.e. lower concentration of sulphuric acid, oxalic acid, boric acid and sodium chloride. According to Design of Experiments (DOE 80 individual test runs of experiment were carried out. Using statistical analysis and artificial intelligence for evaluation, the computational model predicting the thickness of oxide layer in the range from 5 / μm to 15 / μm with tolerance ± 0,5 / μm was developed.

  5. A NAP-AAO3 Regulatory Module Promotes Chlorophyll Degradation via ABA Biosynthesis in Arabidopsis Leaves[W][OPEN

    Science.gov (United States)

    Yang, Jiading; Worley, Eric

    2014-01-01

    Chlorophyll degradation is an important part of leaf senescence, but the underlying regulatory mechanisms are largely unknown. Excised leaves of an Arabidopsis thaliana NAC-LIKE, ACTIVATED BY AP3/PI (NAP) transcription factor mutant (nap) exhibited lower transcript levels of known chlorophyll degradation genes, STAY-GREEN1 (SGR1), NON-YELLOW COLORING1 (NYC1), PHEOPHYTINASE (PPH), and PHEIDE a OXYGENASE (PaO), and higher chlorophyll retention than the wild type during dark-induced senescence. Transcriptome coexpression analysis revealed that abscisic acid (ABA) metabolism/signaling genes were disproportionately represented among those positively correlated with NAP expression. ABA levels were abnormally low in nap leaves during extended darkness. The ABA biosynthetic genes 9-CIS-EPOXYCAROTENOID DIOXYGENASE2, ABA DEFICIENT3, and ABSCISIC ALDEHYDE OXIDASE3 (AAO3) exhibited abnormally low transcript levels in dark-treated nap leaves. NAP transactivated the promoter of AAO3 in mesophyll cell protoplasts, and electrophoretic mobility shift assays showed that NAP can bind directly to a segment (−196 to −162 relative to the ATG start codon) of the AAO3 promoter. Exogenous application of ABA increased the transcript levels of SGR1, NYC1, PPH, and PaO and suppressed the stay-green phenotype of nap leaves during extended darkness. Overexpression of AAO3 in nap leaves also suppressed the stay-green phenotype under extended darkness. Collectively, the results show that NAP promotes chlorophyll degradation by enhancing transcription of AAO3, which leads to increased levels of the senescence-inducing hormone ABA. PMID:25516602

  6. Podium disclosures at the 2012 AAOS meeting: an exercise in going through the motions.

    Science.gov (United States)

    Sassoon, Adam A; Trousdale, Robert T

    2013-04-17

    Slide-based disclosure of potential conflicts of interest prior to presentations is practiced at most orthopaedic meetings to help audiences critically evaluate the data presented. These slides are often supplemented with a printed disclosure in program guides and occasionally on Internet sites. The fidelity and usefulness of this format have not been investigated. We report the practice of disclosure of potential conflicts of interest during the 2012 American Academy of Orthopaedic Surgeons (AAOS) Annual Meeting to determine if the process is accomplishing its primary goal. Orthopaedic residents and fellow volunteers completed questionnaires related to the disclosures presented at symposia and instructional course lectures they attended at the 2012 AAOS Annual Meeting. The attendees were instructed to record the duration of time for which a disclosure slide remained visible to the audience. An attempt to count the words appearing on the disclosure slide, or photograph the disclosure slide so that a subsequent word count could be obtained, was also performed. One hundred and thirty-nine disclosures were observed across a range of subspecialties including adult reconstruction, hand and wrist, pediatrics, shoulder and elbow, sports medicine, trauma, and oncology. Of these, 125 (90%) included the required disclosure slide and underwent additional analysis. Ninety-five slides had a number of words that were countable, with an average of 19.6 words per slide; thirty slides were not presented long enough to permit an accurate word count or photograph. The average time that disclosure slides were viewable was 3.1 seconds. Only 52% of slides noted whether the author disclosures were related to the data presented; 59% of presenters failed to mention this fact verbally. Only 45% of studies with multiple authors included coauthor disclosures on the slide. Institutional disclosures were absent from slides and discussion in 85% of presentations. Slides disclosing potential

  7. Role of AAO template filling process parameters in controlling the structure of one-dimensional polymer nanoparticles.

    Science.gov (United States)

    Pasquali, M; Liang, J; Shivkumar, S

    2011-09-16

    Solution template wetting is a common technique used to fabricate elongated polymer nanostructures; however, the parameters controlling the resulting morphology remain unclear. The purpose of this investigation was to elucidate the effects of process variables on the types of nanostructures obtained and to understand the physical mechanisms associated with structure development. 1 wt% polystyrene-THF solutions were infiltrated into commercial and homemade anodized aluminum oxide (AAO) templates. The wetting interaction between the AAO template and the polymer solution was examined through contact angle measurements. In general, for moderate dipping times (<18 h), the morphology of the nanopolymer was rod-like at low molecular weights, while tubes were observed at high molecular weight, even at this low concentration. Nanorods were obtained for all molecular weights for extended dipping times. The data suggest that phase separated layers may grow sequentially from the pore walls and yield nanotubes if the growth is interrupted or produce nanorods for unhindered deposition over long periods.

  8. A Clinical Practice Update on the Latest AAOS/ADA Guideline (December 2012) on Prevention of Orthopaedic Implant Infection in Dental Patients

    OpenAIRE

    Hamedani, Sh

    2013-01-01

    The American Academy of Orthopaedic Surgeons (AAOS) and the American Dental Association (ADA), along with 10 other academic associations and societies recently (December 2012) published their mutual clinical practice guideline “Prevention of Orthopaedic Implant Infection in Patients Undergoing Dental Procedures.” This evidence-based guideline ,detailed in 325 pages, has three recommendations and substitutes the previous AAOS guideline. The new published clinical guideline is a protocol to pre...

  9. Nano integrated lithium polymer electrolytes based on anodic aluminum oxide (AAO) templates

    Science.gov (United States)

    Bokalawela, Roshan S. P.

    Since their discovery in the 1970s, polymer electrolytes have been actively studied because they have properties important for many device applications. However, even after 40 years, the detailed mechanisms of conductivity in these electrolytes are still not completely understood. Moreover, the conductivity in polymer electrolytes is one of the limiting factors of these devices so that different methods to enhance conductivity are actively being explored. One proposed method of enhancing the conductivity is to confine the polymer electrolyte in the nanoscale, but the study of material properties at the nanoscale is challenging in this area. In this work, we confine poly(ethylene oxide) lithium triflate (PEO:LiTf)(X:1)X=10,30 polymer electrolytes in carefully fabricated nanometer-diameter anodized aluminum oxide (AAO) pore structures. We demonstrate two orders of magnitude higher conductivity in the confined structures versus that of bulk films. Using x-ray characterization we show that this increased conductivity is associated with ordered PEO polymer chains aligned in the template pore direction. The activation energy of the AAO-confined polymer electrolyte is found to be smaller than that of the unconfined melt and about half that of the unconfined solid. This result indicates that not only is the room-temperature confined polymer ordered, but that this order persists at temperatures where the nano-confined polymer electrolyte is expected to be a liquid. The geometric bulk resistances of the electrolytes were obtained by AC-impedance spectra, from which the ionic conductivities were calculated. The Arrhenius plots of temperature dependent ionic conductivities showed that the usual melting temperature of the PEO phase in confined PEO:LiTf(X:1) X=10,30 is suppressed and a single activation energy was evident throughout the temperature range 25--90 °C. Wide-angle x-ray scattering (WAXS) patterns show that the polymer chains in both the pure PEO and PEO:LiTf(10

  10. Deslocamento miscível de um efluente de indústria de explosivo em colunas de solo

    Directory of Open Access Journals (Sweden)

    William Vilar Garcia

    2012-01-01

    Full Text Available Este estudo teve como objetivo avaliar alguns impactos decorrentes do deslocamento miscível de efluente de nitração de uma indústria de explosivos aplicado em colunas de um Latossolo Amarelo, horizonte B (LA-B, submetido aos tratamentos: adição de carbonatos (BASE, ácidos (ACID, fosfato (FOSF, carbonatos e fosfato (BASE-FOSF e ácidos e fosfatos (ACID-FOSF. A recuperação de nitrogênio em relação ao total aplicado varia entre 10,1 (ACID e 65,5% (BASE. Há correlação significativa entre as curvas de transposição de N obtidas experimentalmente e as simuladas pelo aplicativo STANMOD para a maioria das colunas (p<0,001. A exceção ocorreu para ACID-FOSF (p=0,202. Não há correlação entre carga eletrostática líquida (CEL e as variáveis de ajuste do modelo: fator de retardamento (FR, coeficiente de dispersão-difusão (D e taxa de decaimento de primeira ordem (µ. A adição de fosfato (FOSF favorece a movimentação do nitrogênio, pois diminui FR (2,35±0,05 e µ (0,498±0,050 h-1 e aumenta D (41,8±5,5 cm² h-1 em relação ao observado na coluna LA-B (2,51±0,03; 1,697±0,084 h-1 e 2,8±1,3 cm² h-1 respectivamente. A adição de carbonatos e/ou fosfatos (BASE, BASE/FOSF e FOSF resultou nos maiores valores máximos de demanda química de oxigênio (DQO MÁX. A pequena quantidade de DNA extraída das células bacterianas nos solos sugere que, possivelmente, os processos que governam a adsorção e movimentação de N sejam de natureza não biológica ou que a elevada DQO do líquido percolado prejudica os microrganismos do solo.

  11. ToxRefDB - Release user-friendly web-based tool for mining ToxRefDB

    Science.gov (United States)

    The updated URL link is for a table of NCCT ToxCast public datasets. The next to last row of the table has the link for the US EPA ToxCast ToxRefDB Data Release October 2014. ToxRefDB provides detailed chemical toxicity data in a publically accessible searchable format. ToxRefD...

  12. CrossRef text and data mining services

    Directory of Open Access Journals (Sweden)

    Rachael Lammey

    2015-02-01

    Full Text Available CrossRef is an association of scholarly publishers that develops shared infrastructure to support more effective scholarly communications. It is a registration agency for the digital object identifier (DOI, and has built additional services for CrossRef members around the DOI and the bibliographic metadata that publishers deposit in order to register DOIs for their publications. Among these services are CrossCheck, powered by iThenticate, which helps publishers screen for plagiarism in submitted manuscripts and FundRef, which gives publishers standard way to report funding sources for published scholarly research. To add to these services, Cross-Ref launched CrossRef text and data mining services in May 2014. This article will explain the thinking behind CrossRef launching this new service, what it offers to publishers and researchers alike, how publishers can participate in it, and the uptake of the service so far.

  13. CDDIS_MISC_information

    Data.gov (United States)

    National Aeronautics and Space Administration — Miscellaneous documentation, information, and ancillary data to be used with GNSS, laser ranging, VLBI and DORIS data and analyzed products available through the...

  14. The North Slope of Alaska and Adjacent Arctic Ocean (NSA/AAO) cart site begins operation: Collaboration with SHEBA and FIRE

    Energy Technology Data Exchange (ETDEWEB)

    Zak, D. B.; Church, H.; Ivey, M.; Yellowhorse, L.; Zirzow, J.; Widener, K. B.; Rhodes, P.; Turney, C.; Koontz, A.; Stamnes, K.; Storvold, R.; Eide, H. A.; Utley, P.; Eagan, R.; Cook, D.; Hart, D.; Wesely, M.

    2000-04-04

    Since the 1997 Atmospheric Radiation Measurement (ARM) Science Team Meeting, the North Slope of Alaska and Adjacent Arctic Ocean (NSA/AAO) Cloud and Radiation Testbed (CART) site has come into being. Much has happened even since the 1998 Science Team Meeting at which this paper was presented. To maximize its usefulness, this paper has been updated to include developments through July 1998.

  15. Preparing Impact Submissions for REF 2014: An Evaluation. Research Brief

    Science.gov (United States)

    Manville, Catriona; Jones, Molly Morgan; Frearson, Michael; Castle-Clarke, Sophie; Henham, Marie-Louise; Gunashekar, Salil; Grant, Jonathan

    2015-01-01

    The Research Excellence Framework (REF) 2014 is a nationwide initiative designed to assess the quality of research in UK higher education institutions (HEIs). For the first time, REF 2014 introduced the wider impact of research, alongside the quality of research and the vitality of the research environment, into the assessment of research…

  16. Genomic organization of the REF gene in Hevea brasiliensis

    International Nuclear Information System (INIS)

    Attanayaka, D.P.S.T.G.; Karunanayake, E.H.; Lawrence, M.J.; Franklin, F.C.H.; Kekwick, R.G.O.

    1995-01-01

    The genomic organization of the rubber elongation factor (REF) gene in the Hevea genome was investigated by nucelotide sequence analysis and genomic Southern blots. The nucleotide sequence of a genomic clone of the REF gene was obtained. A genomic library of Hevea brasiliensis was constructed and screened with a REF cDNA clone. Ten putative positive clones were detected, five of which were purified by secondary screening. A total of 1099 nucleotides was determined from the insert contained in pGREF1 and found to encode 127 amino acids, including the carboxyl terminus of the REF protein. Nucleotide sequences that encode the rest of the amino terminal amino acids were then obtained using a polymerase chain reaction (PCR) product derived from the same genomic fragment. The nucleotide sequence of the genomic clone revealed the presence of two introns within the coding of the gene. The location of the putative intron/exon splicing sites of both the introns falls between the two codons. The coding region of the REF genomic clone showed 85% nucleotide homology with the REF cDNA sequence, and the deduced amino acid sequence showed 91% homology. The difference in nucleotide sequence between the cDNA and the genomic clones showed the occurrence of polymorphic forms of the REF gene in the Hevea genome. Genomic Southern blot analysis of different Hevea genotypes with the REF cDNA probe revealed the presence of restriction fragment length polymorphism (RFLP). Preliminary studies indicated that this polymorphism could be due to the presence of a multi-allelic REF gene locus. The RFLP pattern obtained using this DNA probe also showed that fingerprinting of the commercial rubber clones is possible. 1 ref., 2 figs

  17. The basics of CrossRef extensible markup language

    Directory of Open Access Journals (Sweden)

    Rachael Lammey

    2014-08-01

    Full Text Available CrossRef is an association of scholarly publishers that develops shared infrastructure to support more effective scholarly communications. Launched in 2000, CrossRef’s citation-linking network today covers over 68 million journal articles and other content items (books chapters, data, theses, and technical reports from thousands of scholarly and professional publishers around the globe. CrossRef has over 4,000 member publishers who join as members in order to avail of a number of CrossRef services, reference linking via the Digital Object Identifier (DOI being the core service. To deposit CrossRef DOIs, publishers and editors need to become familiar with the basics of extensible markup language (XML. This article will give an introduction to CrossRef XML and what publishers need to do in order to start to deposit DOIs with CrossRef and thus ensure their publications are discoverable and can be linked to consistently in an online environment.

  18. Changes of bacterial diversity and tetracycline resistance in sludge from AAO systems upon exposure to tetracycline pressure.

    Science.gov (United States)

    Huang, Manhong; Qi, Fangfang; Wang, Jue; Xu, Qi; Lin, Li

    2015-11-15

    Two lab-scale anaerobic-anoxic-oxic (AAO) systems were used to investigate the changes in tetracycline (TC) resistance and bacterial diversity upon exposure to TC pressure. High-throughput sequencing was used to detect diversity changes in microorganisms at the level of class in sludge from different bioreactors with and without TC. Real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) was used to detect the abundances of eight tetracycline resistance genes (TRGs), tetA, tetB, tetC, tetE, tetM, tetO, tetS and tetX. The results showed that the diversities of the microbial communities of anoxic, anaerobic and aerobic sludge all increased with the addition of TC. TC substantially changed the structure of the microbial community regardless of oxygen conditions. Bacteroidetes and Proteobacteria were the dominant species in the three kinds of sludge and were substantially enriched with TC pressure. In sludge with TC added, almost all target TRGs proliferated more than those in sludge without TC except tetX, which decreased in anaerobic sludge with TC addition. The concentration of efflux pump genes, tet(A-C, E), was the highest among the three groups of TRGs in the different kinds of sludge. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Enhanced water vapour flow in silica microchannels and interdiffusive water vapour flow through anodic aluminium oxide (AAO) membranes

    Science.gov (United States)

    Lei, Wenwen; McKenzie, David R.

    2015-12-01

    Enhanced liquid water flows through carbon nanotubes reinvigorated the study of moisture permeation through membranes and micro- and nano-channels. The study of water vapour through micro-and nano-channels has been neglected even though water vapour is as important as liquid water for industry, especially for encapsulation of electronic devices. Here we measure moisture flow rates in silica microchannels and interdiffusive water vapour flows in anodic aluminium oxide (AAO) membrane channels for the first time. We construct theory for the flow rates of the dominant modes of water transport through four previously defined standard configurations and benchmark it against our new measurements. The findings show that measurements of leak behaviour made using other molecules, such as helium, are not reliable. Single phase water vapour flow is overestimated by a helium measurement, while Washburn or capillary flow is underestimated or for all channels when boundary slip applies, to an extent that depends on the slip length for the liquid phase flows.

  20. The Influence of the Antarctic Oscillation (AAO on Cold Waves and Occurrence of Frosts in the State of Santa Catarina, Brazil

    Directory of Open Access Journals (Sweden)

    Maikon Passos A. Alves

    2017-03-01

    Full Text Available This paper examines the relationship between the Antarctic Oscillation (AAO, cold waves and occurrence of frosts in the state of Santa Catarina, Brazil, during the winter quarter. Research on this topic can assist different spheres of society, such as public health and agriculture, since cold waves can influence and/or aggravate health problems and frosts can inflict economic losses especially in the agricultural sector. For the purpose of this paper, cold wave is considered as the event in which the daily average surface air temperature was at least two standard deviations below the average value of the series on the day and for two consecutive days or more. The data on the average air temperature and frost occurrences are provided by the Company of Agricultural Research and Rural Extension of Santa Catarina/Center for Environmental Information and Hydrometeorology (EPAGRI/CIRAM. The AAO was subjected to statistical analysis using significance tests for the averages (Student’s t-test and variances (F-test with a significance level of α = 5%. The results show that cold waves are unevenly distributed in the agroecological zones of Santa Catarina. It is found that the AAO is associated with the occurrence of frosts (in the agroecological zones represented by the municipalities of Itajaí and São José in the state of Santa Catarina.

  1. A Clinical Practice Update on the Latest AAOS/ADA Guideline (December 2012) on Prevention of Orthopaedic Implant Infection in Dental Patients.

    Science.gov (United States)

    Hamedani, Sh

    2013-03-01

    The American Academy of Orthopaedic Surgeons (AAOS) and the American Dental Association (ADA), along with 10 other academic associations and societies recently (December 2012) published their mutual clinical practice guideline "Prevention of Orthopaedic Implant Infection in Patients Undergoing Dental Procedures." This evidence-based guideline ,detailed in 325 pages, has three recommendations and substitutes the previous AAOS guideline. The new published clinical guideline is a protocol to prevent patients undertaking dental procedures from orthopaedic implant infection. The guideline is developed on the basis of a collaborative systematic review to provide practical advice for training clinicians, dentists and any qualified physicians who need to consider prevention of orthopaedic implant (prosthesis) infection in their patients. This systematic review found no explicit evidence of cause-and-effect relationship between dental procedures and periprosthetic joint infection (PJI). This LTTE wishes to present a vivid summary of AAOS/ADA clinical practice guideline as a clinical update and an academic implementation to inform and assist Iranian competent clinicians and dentists in the course of their treatment decisions, to enrich the value and quality of health care on the latest international basis.

  2. Changes of bacterial diversity and tetracycline resistance in sludge from AAO systems upon exposure to tetracycline pressure

    International Nuclear Information System (INIS)

    Huang, Manhong; Qi, Fangfang; Wang, Jue; Xu, Qi; Lin, Li

    2015-01-01

    Highlights: • High-throughput sequencing was used to compare sludge bacteria with and without TC. • Bacterial diversity increased with TC addition despite of various oxygen conditions. • Total TRGs proliferated with TC addition in three kinds of sludge. • The concentration of efflux pump genes was the highest in the three groups of TRGs. - Abstract: Two lab-scale anaerobic-anoxic-oxic (AAO) systems were used to investigate the changes in tetracycline (TC) resistance and bacterial diversity upon exposure to TC pressure. High-throughput sequencing was used to detect diversity changes in microorganisms at the level of class in sludge from different bioreactors with and without TC. Real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) was used to detect the abundances of eight tetracycline resistance genes (TRGs), tetA, tetB, tetC, tetE, tetM, tetO, tetS and tetX. The results showed that the diversities of the microbial communities of anoxic, anaerobic and aerobic sludge all increased with the addition of TC. TC substantially changed the structure of the microbial community regardless of oxygen conditions. Bacteroidetes and Proteobacteria were the dominant species in the three kinds of sludge and were substantially enriched with TC pressure. In sludge with TC added, almost all target TRGs proliferated more than those in sludge without TC except tetX, which decreased in anaerobic sludge with TC addition. The concentration of efflux pump genes, tet(A–C, E), was the highest among the three groups of TRGs in the different kinds of sludge

  3. Changes of bacterial diversity and tetracycline resistance in sludge from AAO systems upon exposure to tetracycline pressure

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Manhong, E-mail: egghmh@163.com; Qi, Fangfang; Wang, Jue; Xu, Qi; Lin, Li

    2015-11-15

    Highlights: • High-throughput sequencing was used to compare sludge bacteria with and without TC. • Bacterial diversity increased with TC addition despite of various oxygen conditions. • Total TRGs proliferated with TC addition in three kinds of sludge. • The concentration of efflux pump genes was the highest in the three groups of TRGs. - Abstract: Two lab-scale anaerobic-anoxic-oxic (AAO) systems were used to investigate the changes in tetracycline (TC) resistance and bacterial diversity upon exposure to TC pressure. High-throughput sequencing was used to detect diversity changes in microorganisms at the level of class in sludge from different bioreactors with and without TC. Real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) was used to detect the abundances of eight tetracycline resistance genes (TRGs), tetA, tetB, tetC, tetE, tetM, tetO, tetS and tetX. The results showed that the diversities of the microbial communities of anoxic, anaerobic and aerobic sludge all increased with the addition of TC. TC substantially changed the structure of the microbial community regardless of oxygen conditions. Bacteroidetes and Proteobacteria were the dominant species in the three kinds of sludge and were substantially enriched with TC pressure. In sludge with TC added, almost all target TRGs proliferated more than those in sludge without TC except tetX, which decreased in anaerobic sludge with TC addition. The concentration of efflux pump genes, tet(A–C, E), was the highest among the three groups of TRGs in the different kinds of sludge.

  4. Studies of neutron irradiation effects at IPNS-REF

    International Nuclear Information System (INIS)

    Kirk, M.A.

    1983-09-01

    Neutron irradiation effects studies at the Radiation Effects Facility (REF) at the Intense Pulsed Neutron Source (IPNS) located at Argonne National Laboratory (ANL) are reviewed. A brief history of the development of this user facility is followed by an overview of the scientific program. Experiments unique to a spallation neutron source are covered in more detail. Future direction of research at this facility is suggested

  5. Perfil da REF dos anos 1999-2012

    Directory of Open Access Journals (Sweden)

    Lucila Scavone

    2013-11-01

    Full Text Available http://dx.doi.org/10.1590/S0104-026X2013000200010 O artigo resulta de pesquisa mais ampla sobre a produção acadêmica de gênero efeminista em revistas científicas deste campo, com metodologia peculiar. Trata dos eixostemáticos da Revista Estudos Feministas/REF de 1999-2012 por meio de levantamento de todos osartigos publicados neste período. Analisa a coerência de seu conteúdo com a política editorialproposta, bem como as tendências e características de suas publicações.

  6. Cross-cultural adaptation and validation of the Spanish version of the American Academy of Orthopaedic Surgeons-Foot and Ankle Module (AAOS-FAMsp).

    Science.gov (United States)

    González-Sánchez, Manuel; Velasco-Ramos, Esther; Ruiz-Muñoz, Maria; Cuesta-Vargas, Antonio I

    2016-07-06

    The current study performed a cross-cultural adaptation to Spanish and examined the internal and external validation of the AAOS-FAM questionnaire. A direct translation (English to Spanish) and a reverse translation (Spanish to English) were performed by two independent professional native translators. Cronbach's α coefficients were calculated to analyse the internal consistency of the measure. The factor structure and construct validity were analysed after extraction by maximum likelihood (EML); extraction was necessary if the following three requirements were met: accounting for ≥10 % of variance, Eigenvalue >1.0 and a scree plot inflexion point. The standard error of measurement and minimal detectable change 90 (MDC90) were calculated. Criterion validity was calculated by analysing the correlation between the American Academy of Orthopaedic Surgeons-Foot and Ankle Module (Spanish version) (AAOS-FAMsp) and Spanish versions of the questionnaires FFI and FHSQ. Regarding internal consistency, Cronbach's α was 0.877, and in the test-retest analysis, the ICC ranged between 0.899 and 0.942. Error measures were calculated by MDC90 and SEM, which showed values of 3.444 and 1.476 %, respectively. The analysis demonstrated a goodness of fit chi-squared value of 803.166 (p validity, the correlation value with FFIsp was r = 0.837 (p Spanish-speaking individuals into both research and clinical practice.

  7. Data Flow for the TERRA-REF project

    Science.gov (United States)

    Kooper, R.; Burnette, M.; Maloney, J.; LeBauer, D.

    2017-12-01

    The Transportation Energy Resources from Renewable Agriculture Phenotyping Reference Platform (TERRA-REF) program aims to identify crop traits that are best suited to producing high-energy sustainable biofuels and match those plant characteristics to their genes to speed the plant breeding process. One tool used to achieve this goal is a high-throughput phenotyping robot outfitted with sensors and cameras to monitor the growth of 1.25 acres of sorghum. Data types range from hyperspectral imaging to 3D reconstructions and thermal profiles, all at 1mm resolution. This system produces thousands of daily measurements with high spatiotemporal resolution. The team at NCSA processes, annotates, organizes and stores the massive amounts of data produced by this system - up to 5 TB per day. Data from the sensors is streamed to a local gantry-cache server. The standardized sensor raw data stream is automatically and securely delivered to NCSA using Globus Connect service. Once files have been successfully received by the Globus endpoint, the files are removed from the gantry-cache server. As each dataset arrives or is created the Clowder system automatically triggers different software tools to analyze each file, extract information, and convert files to a common format. Other tools can be triggered to run after all required data is uploaded. For example, a stitched image of the entire field is created after all images of the field become available. Some of these tools were developed by external collaborators based on predictive models and algorithms, others were developed as part of other projects and could be leveraged by the TERRA project. Data will be stored for the lifetime of the project and is estimated to reach 10 PB over 3 years. The Clowder system, BETY and other systems will allow users to easily find data by browsing or searching the extracted information.

  8. A high-performance and low cost SERS substrate of plasmonic nanopillars on plastic film fabricated by nanoimprint lithography with AAO template

    Directory of Open Access Journals (Sweden)

    Long Liu

    2017-06-01

    Full Text Available As a powerful spectroscopy technique, surface-enhanced Raman scattering (SERS can provide non-destructive and sensitive characterization down to a single molecular level. Aiming to the main challenges of high-performance SERS-active substrates for their real-world applications involving the ultra-sensitive and reproducible signals detection and signal uniformity with large-area, herein, a facile and reliable strategy based on combination of thermal imprinting polycarbonate (PC film with porous anodic aluminum oxide (AAO mold and E-beam evaporation of gold is provided to fabricate a high-quality SERS-active substrate consisting of ultra-dense hot-spots with large-area uniformity. Two kinds of sub-10 nm gaps were obtained, including the nanogaps between the neighboring gold coated PC-nanopillars and those between gold on the top of the nanopillars and that on the base, which actually build up a three-dimensional (3D hot-spot network for high-performance SERS detection. The effect of structural parameters on SERS enhancement was investigated numerically and experimentally, and by optimizing the structural parameters, a remarkable average SERS enhancement factor up to of 1.4×108 is achieved and it shows an excellent reproducibility with a relative standard deviation of 18%, which allows for enhanced practicability in the application of quantitative biochemical detection.

  9. Test Review: Delis, D. (2012) "Delis Rating of Executive Function (D-REF)." Bloomington, Minnesota: Pearson

    Science.gov (United States)

    Warnick, Brittany; Drake, Morgan; Vidrine, Stephanie

    2015-01-01

    The Delis Rating of Executive Function (D-REF) is a set of rating scales designed to assess executive functions and their constituent sub-processes in children and adolescents between the ages of 5 and 18. More specifically, the D-REF is a supplemental assessment of children and adolescents demonstrating behavioral or cognitive difficulties often…

  10. The HuRef Browser: a web resource for individual human genomics.

    Science.gov (United States)

    Axelrod, Nelson; Lin, Yuan; Ng, Pauline C; Stockwell, Timothy B; Crabtree, Jonathan; Huang, Jiaqi; Kirkness, Ewen; Strausberg, Robert L; Frazier, Marvin E; Venter, J Craig; Kravitz, Saul; Levy, Samuel

    2009-01-01

    The HuRef Genome Browser is a web application for the navigation and analysis of the previously published genome of a human individual, termed HuRef. The browser provides a comparative view between the NCBI human reference sequence and the HuRef assembly, and it enables the navigation of the HuRef genome in the context of HuRef, NCBI and Ensembl annotations. Single nucleotide polymorphisms, indels, inversions, structural and copy-number variations are shown in the context of existing functional annotations on either genome in the comparative view. Demonstrated here are some potential uses of the browser to enable a better understanding of individual human genetic variation. The browser provides full access to the underlying reads with sequence and quality information, the genome assembly and the evidence supporting the identification of DNA polymorphisms. The HuRef Browser is a unique and versatile tool for browsing genome assemblies and studying individual human sequence variation in a diploid context. The browser is available online at http://huref.jcvi.org.

  11. CERN Technical Training 2002: Learning for the LHC ! HeREF-2002 : Helium Refrigeration Techniques

    CERN Multimedia

    Davide Vitè

    2002-01-01

    Theory, Technology, Maintenance and Control of Helium Refrigerators HeREF-2002 is a new course, in the framework of the 2002 Technical Training Programme, that will provide a complete introduction to Helium refrigeration, with a practical approach to theory, technology, maintenance and control of Helium refrigeration installations. Theoretical aspects and equations will be limited to a minimum. HeREF-2002 targets an audience of technicians and operators of Helium refrigeration plants at CERN, as well as physicists and engineers needing an overview of current Helium refrigeration techniques. HeREF-2002 will address, among other, issues related to component technology, installation maintenance, process control and Helium purity. A commented visit to a couple of CERN Helium refrigeration or liquefaction plants will also take place. Duration: 7 half days (5 mornings and 2 afternoons), 21-25 October 2002. Estimated cost: 300.- CHF Language: Bilingual English-French. The course support will be in English, the...

  12. Fazer a REF é fazer política: memórias de uma metamorfose editorial Making REF is making politics: memories of an editorial metamorphosis

    Directory of Open Access Journals (Sweden)

    Luzinete Simões Minella

    2008-04-01

    Full Text Available Este artigo pretende refletir sobre o novo modelo editorial inaugurado na Revista Estudos Feministas em 2002, ou seja, três anos após a sua instalação na Universidade Federal de Santa Catarina (UFSC. Ao elaborar as memórias dessa metamorfose, nos primeiros itens, refiro-me às transições do formato da editoria da REF, às razões e aos critérios da sua nova estruturação, bem como aos significados da expansão da equipe diante da situação de algumas publicações feministas nacionais e internacionais. No último item elaboro um breve balanço das vantagens e dos desafios implicados nessa nova política editorial.This article focuses on the new editorial model launched in Revista Estudos Feministas in 2002, that is, three years after its installation in Universidade Federal de Santa Catarina (UFSC. While firstly detailing the memories of such metamorphosis, the text refers to the transitions of REF's editorship format, to the purposes and criteria of the new structure, as well as the meanings of the team expansion in relation to some national and international feminist publications. Eventually the article briefly discusses the advantages and challenges implicated in this new editorial policy.

  13. Highly pathogenic avian influenza virus nucleoprotein interacts with TREX complex adaptor protein Aly/REF.

    Directory of Open Access Journals (Sweden)

    Vinod R M T Balasubramaniam

    Full Text Available We constructed a novel chicken (Gallus gallus lung cDNA library fused inside yeast acting domain vector (pGADT7. Using yeast two-hybrid screening with highly pathogenic avian influenza (HPAI nucleoprotein (NP from the strain (A/chicken/Malaysia/5858/2004(H5N1 as bait, and the Gallus gallus lung cDNA library as prey, a novel interaction between the Gallus gallus cellular RNA export adaptor protein Aly/REF and the viral NP was identified. This interaction was confirmed and validated with mammalian two hybrid studies and co-immunoprecipitation assay. Cellular localization studies using confocal microscopy showed that NP and Aly/REF co-localize primarily in the nucleus. Further investigations by mammalian two hybrid studies into the binding of NP of other subtypes of influenza virus such as the swine A/New Jersey/1976/H1N1 and pandemic A/Malaysia/854/2009(H1N1 to human Aly/REF, also showed that the NP of these viruses interacts with human Aly/REF. Our findings are also supported by docking studies which showed tight and favorable binding between H5N1 NP and human Aly/REF, using crystal structures from Protein Data Bank. siRNA knockdown of Aly/REF had little effect on the export of HPAI NP and other viral RNA as it showed no significant reduction in virus titer. However, UAP56, another component of the TREX complex, which recruits Aly/REF to mRNA was found to interact even better with H5N1 NP through molecular docking studies. Both these proteins also co-localizes in the nucleus at early infection similar to Aly/REF. Intriguingly, knockdown of UAP56 in A549 infected cells shows significant reduction in viral titer (close to 10 fold reduction. Conclusively, our study have opened new avenues for research of other cellular RNA export adaptors crucial in aiding viral RNA export such as the SRSF3, 9G8 and ASF/SF2 that may play role in influenza virus RNA nucleocytoplasmic transport.

  14. Peer2ref: a peer-reviewer finding web tool that uses author disambiguation

    Directory of Open Access Journals (Sweden)

    Andrade-Navarro Miguel A

    2012-09-01

    Full Text Available Abstract Background Reviewer and editor selection for peer review is getting harder for authors and publishers due to the specialization onto narrower areas of research carried by the progressive growth of the body of knowledge. Examination of the literature facilitates finding appropriate reviewers but is time consuming and complicated by author name ambiguities. Results We have developed a method called peer2ref to support authors and editors in selecting suitable reviewers for scientific manuscripts. Peer2ref works from a text input, usually the abstract of the manuscript, from which important concepts are extracted as keywords using a fuzzy binary relations approach. The keywords are searched on indexed profiles of words constructed from the bibliography attributed to authors in MEDLINE. The names of these scientists have been previously disambiguated by coauthors identified across the whole MEDLINE. The methods have been implemented in a web server that automatically suggests experts for peer-review among scientists that have authored manuscripts published during the last decade in more than 3,800 journals indexed in MEDLINE. Conclusion peer2ref web server is publicly available at http://www.ogic.ca/projects/peer2ref/.

  15. Rubber Elongation Factor (REF), a Major Allergen Component in Hevea brasiliensis Latex Has Amyloid Properties

    Science.gov (United States)

    Berthelot, Karine; Lecomte, Sophie; Estevez, Yannick; Coulary-Salin, Bénédicte; Bentaleb, Ahmed; Cullin, Christophe; Deffieux, Alain; Peruch, Frédéric

    2012-01-01

    REF (Hevb1) and SRPP (Hevb3) are two major components of Hevea brasiliensis latex, well known for their allergenic properties. They are obviously taking part in the biosynthesis of natural rubber, but their exact function is still unclear. They could be involved in defense/stress mechanisms after tapping or directly acting on the isoprenoid biosynthetic pathway. The structure of these two proteins is still not described. In this work, it was discovered that REF has amyloid properties, contrary to SRPP. We investigated their structure by CD, TEM, ATR-FTIR and WAXS and neatly showed the presence of β-sheet organized aggregates for REF, whereas SRPP mainly fold as a helical protein. Both proteins are highly hydrophobic but differ in their interaction with lipid monolayers used to mimic the monomembrane surrounding the rubber particles. Ellipsometry experiments showed that REF seems to penetrate deeply into the monolayer and SRPP only binds to the lipid surface. These results could therefore clarify the role of these two paralogous proteins in latex production, either in the coagulation of natural rubber or in stress-related responses. To our knowledge, this is the first report of an amyloid formed from a plant protein. This suggests also the presence of functional amyloid in the plant kingdom. PMID:23133547

  16. Ref-1/APE1 as a Transcriptional Regulator and Novel Therapeutic Target in Pediatric T-cell Leukemia.

    Science.gov (United States)

    Ding, Jixin; Fishel, Melissa L; Reed, April M; McAdams, Erin; Czader, Magdalena B; Cardoso, Angelo A; Kelley, Mark R

    2017-07-01

    The increasing characterization of childhood acute lymphoblastic leukemia (ALL) has led to the identification of multiple molecular targets but has yet to translate into more effective targeted therapies, particularly for high-risk, relapsed T-cell ALL. Searching for master regulators controlling multiple signaling pathways in T-ALL, we investigated the multifunctional protein redox factor-1 (Ref-1/APE1), which acts as a signaling "node" by exerting redox regulatory control of transcription factors important in leukemia. Leukemia patients' transcriptome databases showed increased expression in T-ALL of Ref-1 and other genes of the Ref-1/SET interactome. Validation studies demonstrated that Ref-1 is expressed in high-risk leukemia T cells, including in patient biopsies. Ref-1 redox function is active in leukemia T cells, regulating the Ref-1 target NF-κB, and inhibited by the redox-selective Ref-1 inhibitor E3330. Ref-1 expression is not regulated by Notch signaling, but is upregulated by glucocorticoid treatment. E3330 disrupted Ref-1 redox activity in functional studies and resulted in marked inhibition of leukemia cell viability, including T-ALL lines representing different genotypes and risk groups. Potent leukemia cell inhibition was seen in primary cells from ALL patients, relapsed and glucocorticoid-resistant T-ALL cells, and cells from a murine model of Notch-induced leukemia. Ref-1 redox inhibition triggered leukemia cell apoptosis and downregulation of survival genes regulated by Ref-1 targets. For the first time, this work identifies Ref-1 as a novel molecular effector in T-ALL and demonstrates that Ref-1 redox inhibition results in potent inhibition of leukemia T cells, including relapsed T-ALL. These data also support E3330 as a specific Ref-1 small-molecule inhibitor for leukemia. Mol Cancer Ther; 16(7); 1401-11. ©2017 AACR . ©2017 American Association for Cancer Research.

  17. Ref2RIS: Importing Word-Processed Bibliographies into Bibliographic Management Software

    OpenAIRE

    Deborah Fitchett

    2012-01-01

    Many who would benefit the most from timesaving bibliographic managers hesitate to adopt the technology due to the difficulties in importing legacy bibliographies developed over years. Existing shortcuts rely on manual reformatting or on re-searching online databases for the records - often almost as laborious as retyping the references. Ref2RIS was developed to automate the task of converting a bibliography in specific citation styles from common word processing document formats into the wid...

  18. The FachRef-Assistant: Personalised, subject specific, and transparent stock management

    OpenAIRE

    Eike T. Spielberg; Frank Lützenkirchen

    2017-01-01

    We present in this paper a personalized web application for the weeding of printed resources: the FachRef-Assistant. It offers an extensive range of tools for evidence based stock management, based on the thorough analysis of usage statistics. Special attention is paid to the criteria individualization, transparency of the parameters used, and generic functions. Currently, it is designed to work with the Aleph-System from ExLibris, but efforts were spent to keep the application as generic as ...

  19. DNA Repair and Cancer Therapy: Targeting APE1/Ref-1 Using Dietary Agents

    Directory of Open Access Journals (Sweden)

    Julian J. Raffoul

    2012-01-01

    Full Text Available Epidemiological studies have demonstrated the cancer protective effects of dietary agents and other natural compounds isolated from fruits, soybeans, and vegetables on neoplasia. Studies have also revealed the potential for these natural products to be combined with chemotherapy or radiotherapy for the more effective treatment of cancer. In this paper we discuss the potential for targeting the DNA base excision repair enzyme APE1/Ref-1 using dietary agents such as soy isoflavones, resveratrol, curcumin, and the vitamins ascorbate and α-tocopherol. We also discuss the potential role of soy isoflavones in sensitizing cancer cells to the effects of radiotherapy. A comprehensive review of the dual nature of APE1/Ref-1 in DNA repair and redox activation of cellular transcription factors, NF-κB and HIF-1α, is also discussed. Further research efforts dedicated to delineating the role of APE1/Ref-1 DNA repair versus redox activity in sensitizing cancer cells to conventional treatment are warranted.

  20. WhiteRef: A New Tower-Based Hyperspectral System for Continuous Reflectance Measurements

    Directory of Open Access Journals (Sweden)

    Karolina Sakowska

    2015-01-01

    Full Text Available Proximal sensing is fundamental to monitor the spatial and seasonal dynamics of ecosystems and can be considered as a crucial validation tool to upscale in situ observations to the satellite level. Linking hyperspectral remote sensing with carbon fluxes and biophysical parameters is critical to allow the exploitation of spatial and temporal extensive information for validating model simulations at different scales. In this study, we present the WhiteRef, a new hyperspectral system designed as a direct result of the needs identified during the EUROSPEC ES0903 Cost Action, and developed by Fondazione Edmund Mach and the Institute of Biometeorology, CNR, Italy. The system is based on the ASD FieldSpec Pro spectroradiometer and was designed to acquire continuous radiometric measurements at the Eddy Covariance (EC towers and to fill a gap in the scientific community: in fact, no system for continuous spectral measurements in the Short Wave Infrared was tested before at the EC sites. The paper illustrates the functioning of the WhiteRef and describes its main advantages and disadvantages. The WhiteRef system, being based on a robust and high quality commercially available instrument, has a clear potential for unattended continuous measurements aiming at the validation of satellites’ vegetation products.

  1. TERRA REF: Advancing phenomics with high resolution, open access sensor and genomics data

    Science.gov (United States)

    LeBauer, D.; Kooper, R.; Burnette, M.; Willis, C.

    2017-12-01

    Automated plant measurement has the potential to improve understanding of genetic and environmental controls on plant traits (phenotypes). The application of sensors and software in the automation of high throughput phenotyping reflects a fundamental shift from labor intensive hand measurements to drone, tractor, and robot mounted sensing platforms. These tools are expected to speed the rate of crop improvement by enabling plant breeders to more accurately select plants with improved yields, resource use efficiency, and stress tolerance. However, there are many challenges facing high throughput phenomics: sensors and platforms are expensive, currently there are few standard methods of data collection and storage, and the analysis of large data sets requires high performance computers and automated, reproducible computing pipelines. To overcome these obstacles and advance the science of high throughput phenomics, the TERRA Phenotyping Reference Platform (TERRA-REF) team is developing an open-access database of high resolution sensor data. TERRA REF is an integrated field and greenhouse phenotyping system that includes: a reference field scanner with fifteen sensors that can generate terrabytes of data each day at mm resolution; UAV, tractor, and fixed field sensing platforms; and an automated controlled-environment scanner. These platforms will enable investigation of diverse sensing modalities, and the investigation of traits under controlled and field environments. It is the goal of TERRA REF to lower the barrier to entry for academic and industry researchers by providing high-resolution data, open source software, and online computing resources. Our project is unique in that all data will be made fully public in November 2018, and is already available to early adopters through the beta-user program. We will describe the datasets and how to use them as well as the databases and computing pipeline and how these can be reused and remixed in other phenomics pipelines

  2. Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network.

    Directory of Open Access Journals (Sweden)

    Tommi Aho

    2010-05-01

    Full Text Available Molecular interaction networks establish all cell biological processes. The networks are under intensive research that is facilitated by new high-throughput measurement techniques for the detection, quantification, and characterization of molecules and their physical interactions. For the common model organism yeast Saccharomyces cerevisiae, public databases store a significant part of the accumulated information and, on the way to better understanding of the cellular processes, there is a need to integrate this information into a consistent reconstruction of the molecular interaction network. This work presents and validates RefRec, the most comprehensive molecular interaction network reconstruction currently available for yeast. The reconstruction integrates protein synthesis pathways, a metabolic network, and a protein-protein interaction network from major biological databases. The core of the reconstruction is based on a reference object approach in which genes, transcripts, and proteins are identified using their primary sequences. This enables their unambiguous identification and non-redundant integration. The obtained total number of different molecular species and their connecting interactions is approximately 67,000. In order to demonstrate the capacity of RefRec for functional predictions, it was used for simulating the gene knockout damage propagation in the molecular interaction network in approximately 590,000 experimentally validated mutant strains. Based on the simulation results, a statistical classifier was subsequently able to correctly predict the viability of most of the strains. The results also showed that the usage of different types of molecular species in the reconstruction is important for accurate phenotype prediction. In general, the findings demonstrate the benefits of global reconstructions of molecular interaction networks. With all the molecular species and their physical interactions explicitly modeled, our

  3. Clinical neurorehabilitation - implications of the Reorganization of Elementary Functions (REF) model

    DEFF Research Database (Denmark)

    Rytter, Hana Malá; Mogensen, Jesper

    The REF (Reorganization of Elementary Functions) model suggests mechanisms of posttraumatic reorganization, and resolves the contradiction between localization and functional recovery. In the process of developing this model, we have reconceptualised the term ‘function’ and introduced a concept...... as ‘function’. After brain injury, the EFs of the affected structure are irreversibly lost. However, during neurorehabilitation, the remaining EFs are reorganized into novel ASs. Creation and utilization of these novel ASs constitutes the basis for functional recovery. The degree to which recovery appears...

  4. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names

    Directory of Open Access Journals (Sweden)

    Jens H. Kuhn

    2014-09-01

    Full Text Available Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s RefSeq is a non-redundant, curated database for reference (or type nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ (////-], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.

  5. The FachRef-Assistant: Personalised, subject specific, and transparent stock management

    Directory of Open Access Journals (Sweden)

    Eike T. Spielberg

    2017-07-01

    Full Text Available We present in this paper a personalized web application for the weeding of printed resources: the FachRef-Assistant. It offers an extensive range of tools for evidence based stock management, based on the thorough analysis of usage statistics. Special attention is paid to the criteria individualization, transparency of the parameters used, and generic functions. Currently, it is designed to work with the Aleph-System from ExLibris, but efforts were spent to keep the application as generic as possible. For example, all procedures specific to the local library system have been collected in one Java package. The inclusion of library specific properties such as collections and systematics has been designed to be highly generic as well by mapping the individual entries onto an in-memory database. Hence simple adaption of the package and the mappings would render the FachRef-Assistant compatible to other library systems. The personalization of the application allows for the inclusion of subject specific usage properties as well as of variations between different collections within one subject area. The parameter sets used to analyse the stock and to prepare weeding and purchase proposal lists are included in the output XML-files to facilitate a high degree of transparency, objectivity and reproducibility.

  6. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names

    Science.gov (United States)

    Kuhn, Jens H.; Andersen, Kristian G.; Bào, Yīmíng; Bavari, Sina; Becker, Stephan; Bennett, Richard S.; Bergman, Nicholas H.; Blinkova, Olga; Bradfute, Steven; Brister, J. Rodney; Bukreyev, Alexander; Chandran, Kartik; Chepurnov, Alexander A.; Davey, Robert A.; Dietzgen, Ralf G.; Doggett, Norman A.; Dolnik, Olga; Dye, John M.; Enterlein, Sven; Fenimore, Paul W.; Formenty, Pierre; Freiberg, Alexander N.; Garry, Robert F.; Garza, Nicole L.; Gire, Stephen K.; Gonzalez, Jean-Paul; Griffiths, Anthony; Happi, Christian T.; Hensley, Lisa E.; Herbert, Andrew S.; Hevey, Michael C.; Hoenen, Thomas; Honko, Anna N.; Ignatyev, Georgy M.; Jahrling, Peter B.; Johnson, Joshua C.; Johnson, Karl M.; Kindrachuk, Jason; Klenk, Hans-Dieter; Kobinger, Gary; Kochel, Tadeusz J.; Lackemeyer, Matthew G.; Lackner, Daniel F.; Leroy, Eric M.; Lever, Mark S.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Omilabu, Sunday A.; Palacios, Gustavo; Panchal, Rekha G.; Park, Daniel J.; Patterson, Jean L.; Paweska, Janusz T.; Peters, Clarence J.; Pettitt, James; Pitt, Louise; Radoshitzky, Sheli R.; Ryabchikova, Elena I.; Saphire, Erica Ollmann; Sabeti, Pardis C.; Sealfon, Rachel; Shestopalov, Aleksandr M.; Smither, Sophie J.; Sullivan, Nancy J.; Swanepoel, Robert; Takada, Ayato; Towner, Jonathan S.; van der Groen, Guido; Volchkov, Viktor E.; Volchkova, Valentina A.; Wahl-Jensen, Victoria; Warren, Travis K.; Warfield, Kelly L.; Weidmann, Manfred; Nichol, Stuart T.

    2014-01-01

    Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [virus name> ()////-], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences. PMID:25256396

  7. ToxRefDB 2.0: Improvements in Capturing Qualitative and Quantitative Data from in vivo Toxicity Studies (SOT)

    Science.gov (United States)

    The Toxicity Reference Database (ToxRefDB) is a publicly accessible resource that contains 40+ years of in vivo dose-response toxicological studies. ToxRefDB provides curated in vivo toxicity data for systematic evaluation of a continuously expanding catalog of chemicals, and co...

  8. Ref2RIS: Importing Word-Processed Bibliographies into Bibliographic Management Software

    Directory of Open Access Journals (Sweden)

    Deborah Fitchett

    2012-02-01

    Full Text Available Many who would benefit the most from timesaving bibliographic managers hesitate to adopt the technology due to the difficulties in importing legacy bibliographies developed over years. Existing shortcuts rely on manual reformatting or on re-searching online databases for the records - often almost as laborious as retyping the references. Ref2RIS was developed to automate the task of converting a bibliography in specific citation styles from common word processing document formats into the widely used RIS format. It uses the Unix stream editor sed and the conversion options of Apple's textutil. It can be invoked as a series of simple shell commands on any Linux terminal, or more simply as a drag-and-drop Applescript application on MacOS 10.4 or higher.

  9. Identification of a novel potential antitumor activity of gossypol as an APE1/Ref-1 inhibitor

    Directory of Open Access Journals (Sweden)

    Qian CY

    2014-05-01

    Full Text Available Chengyuan Qian, Mengxia Li, Jiangdong Sui, Tao Ren, Zheng Li, Liang Zhang, Liwei Zhou, Yi Cheng, Dong WangCancer Center, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing, People's Republic of ChinaAbstract: The human apurinic/apyrimidinic endonuclease 1/redox enhancing factor-1 (APE1/Ref-1, an essential multifunctional protein involved in the repair of oxidative deoxyribonucleic acid (DNA damage and transcriptional regulation, is often overexpressed in tumor tissues and cancer cells. Moreover, APE1/Ref-1 (APE1 overexpression has been linked to chemoresistance in human tumors. Thus, inhibiting APE1 function in cancer cells is considered a promising strategy to overcome resistance to therapeutic agents. Gossypol is a Bcl-2 homology 3 (BH3-mimetic agent and is able to bind to the BH3 domain of B-cell lymphoma 2 (Bcl-2 family members. Other studies demonstrated that Bcl-2 directly interacted with APE1 via its BH domains. Using apurinic/apyrimidinic (AP endonuclease assays, we found that gossypol inhibits the repair activity of APE1. Electrophoretic mobility shift assays and dual luciferase assays showed that gossypol could also inhibit the redox function of APE1. Using dual polarization interferometry technology, we show that gossypol can directly interact with APE1. Furthermore, addition of gossypol, in conjunction with APE1 overexpression, leads to cancer cell death. The addition of gossypol also enhances the cell killing effect of the laboratory alkylating agent methyl methanesulfonate and the clinical agent cisplatin (DDP. Administration of gossypol significantly inhibited the growth of xenografts. Furthermore, the combined treatment of gossypol and DDP resulted in a statistically higher antitumor activity compared with DDP alone in vivo. In conclusion, we have demonstrated that gossypol effectively inhibits the repair and redox activity of APE1 through a direct interaction.Keywords: cancer

  10. REF4 and RFR1, subunits of the transcriptional coregulatory complex mediator, are required for phenylpropanoid homeostasis in Arabidopsis.

    Science.gov (United States)

    Bonawitz, Nicholas D; Soltau, Whitney L; Blatchley, Michael R; Powers, Brendan L; Hurlock, Anna K; Seals, Leslie A; Weng, Jing-Ke; Stout, Jake; Chapple, Clint

    2012-02-17

    The plant phenylpropanoid pathway produces an array of metabolites that impact human health and the utility of feed and fiber crops. We previously characterized several Arabidopsis thaliana mutants with dominant mutations in REDUCED EPIDERMAL FLUORESCENCE 4 (REF4) that cause dwarfing and decreased accumulation of phenylpropanoids. In contrast, ref4 null plants are of normal stature and have no apparent defect in phenylpropanoid biosynthesis. Here we show that disruption of both REF4 and its paralog, REF4-RELATED 1 (RFR1), results in enhanced expression of multiple phenylpropanoid biosynthetic genes, as well as increased accumulation of numerous downstream products. We also show that the dominant ref4-3 mutant protein interferes with the ability of the PAP1/MYB75 transcription factor to induce the expression of PAL1 and drive anthocyanin accumulation. Consistent with our experimental results, both REF4 and RFR1 have been shown to physically associate with the conserved transcriptional coregulatory complex, Mediator, which transduces information from cis-acting DNA elements to RNA polymerase II at the core promoter. Taken together, our data provide critical genetic support for a functional role of REF4 and RFR1 in the Mediator complex, and for Mediator in the maintenance of phenylpropanoid homeostasis. Finally, we show that wild-type RFR1 substantially mitigates the phenotype of the dominant ref4-3 mutant, suggesting that REF4 and RFR1 may compete with one another for common binding partners or for occupancy in Mediator. Determining the functions of diverse Mediator subunits is essential to understand eukaryotic gene regulation, and to facilitate rational manipulation of plant metabolic pathways to better suit human needs.

  11. Initial clinical experience with implantation of left ventricular lead guided by Overlay Ref for the treatment of congestive heart failure.

    Science.gov (United States)

    Zhang, Bu-Chun; Tang, Kai; Xu, Ya-Wei

    2011-01-01

    Cardiac resynchronization therapy (CRT) improves clinical outcome in selected patients with advanced congestive heart failure. The Overlay Ref technique may facilitate the procedure for implanting left ventricular (LV) pacing leads to deliver CRT. To assess the feasibility of deploying a LV pacing lead into a coronary sinus side branch guided by Overlay Ref. Data from 88 consecutive patients who met the CRT implantation criteria in our hospital between 28 November 2007 and 30 December 2009 were randomly assigned to two groups. Forty-four patients underwent CRT device implantation using Overlay Ref to guide target vein selection and advance a specifically designed pacing lead into the target vein (Overlay Ref group); 44 patients were conventionally implanted (control group). LV lead implantation was successful in all patients. Mean CRT total procedure times (skin-to-skin) were: Overlay Ref group, 80.7 ± 18.0 min; control group, 98.5 ± 32.2 min; p = 0.029. Mean placement of LV pacing lead into target vein times were: Overlay Ref group, 16.2 ± 7.7 min; control group, 36.4 ± 23.4 min; p=0.004. Mean total fluoroscopy times were: Overlay Ref group, 13.6 ± 4.3 min; control group, 23.8 ± 15.7 min; p=0.007. Mean LV lead fluoroscopy times were: Overlay Ref group, 5.7 ± 2.9 min; control group, 14.4 ± 4.6 min; p=0.003. No major complications occurred. Overlay Ref facilitates location of and entry into the coronary sinus, and shortens the duration of LV pacing lead implantation into the target vein. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

  12. A cultura musical erudita na universidade: refúgio, resistência e expectativas

    Directory of Open Access Journals (Sweden)

    José Eduardo Martins

    1993-08-01

    Full Text Available O ensino musical do Brasil Colônia à atualidade. A decadência dos conservatórios. A música na Universidade: graduação e pós-graduação; publicações; gravações. A performance musical e a pesquisa, dentro e fora da Universidade. Progressões da cultura musical erudita: aritmética (decrescente e geométrica (ascendente. Governo (voto, iniciativa privada (lucro, mídia (massa receptiva: inter-relacionamento pragmático resultando o desmonte da cultura musical erudita. Impasse da crítica musical. Eventos internacionais no Brasil e a malversação de verbas. Festivais de música: comparações. Músico brasileiro: sobreviver na concessão ou resistir na qualidade? Despreparo cultural do homem público, do empresário e do agente cultural. A Universidade como refúgio da cultura musical erudita.The musical training from Colonial Brazil to the present. The fall of the conservatory. The University: under graduate musical studies and graduate studies; publications; recordings. The musical performance research within and out of the University. Arithmetic progression (descending of the erudite musical culture and geometric progression (ascending of the mass musical culture. Government (vote, private iniciative (profit, media (mass reception : pragmatic interrelations, resulting in the dismanting of the erudite musical culture. Check of musical critique. International events in Brazil and misuse of funds. Musical festivals: comparisons. Brazilian musicians: surviving by catering to the market or insisting on quality? Cultural dispreparation of the politician: Business man and musical manager. The University as refuge of the erudite musical culture.

  13. HSCT Ref-H Transonic Flap Data Base: Wind-Tunnel Test and Comparison with Theory

    Science.gov (United States)

    Vijgen, Paul M.

    1999-01-01

    In cooperation with personnel from the Boeing ANP Laboratory and NASA Langley, a performance test was conducted using the Reference-H 1.675% model ("NASA Modular Model") without nacelles at the NASA Langley 16-Ft Transonic Tunnel. The main objective of the test was to determine the drag reduction achievable with leading-edge and trailing-edge flaps deflected along the outboard wing span at transonic Mach numbers (M = 0.9 to 1.2) for purpose of preliminary design and for comparison with computational predictions. The obtained drag data with flap deflections for Mach numbers of 1.07 to 1.20 are unique for the Reference H wing. Four leading-edge and two trailing-edge flap deflection angles were tested at a mean-wing chord-Reynolds number of about 5.7 million. An outboard-wing leading-edge flap deflection of 81 provides a 4.5 percent drag reduction at M = 1.2 A = 0.2), and much larger values at lower Mach numbers with larger flap deflections. The present results for the baseline (no flaps deflected) compare reasonably well with previous Boeing and NASA Ref-H tunnel tests, including high-Reynolds number NTF results. Viscous CFD simulations using the OVERFLOW thin-layer N.S. method properly predict the observed trend in drag reduction at M = 1.2 as function of leading-edge flap deflection. Modified linear theory properly predicts the flap effects on drag at subsonic conditions (Aero2S code), and properly predicts the absolute drag for the 40 and 80 leading-edge deflection at M = 1.2 (A389 code).

  14. Rubber particle proteins REF1 and SRPP1 interact differently with native lipids extracted from Hevea brasiliensis latex.

    Science.gov (United States)

    Wadeesirisak, Kanthida; Castano, Sabine; Berthelot, Karine; Vaysse, Laurent; Bonfils, Frédéric; Peruch, Frédéric; Rattanaporn, Kittipong; Liengprayoon, Siriluck; Lecomte, Sophie; Bottier, Céline

    2017-02-01

    Rubber particle membranes from the Hevea latex contain predominantly two proteins, REF1 and SRPP1 involved in poly(cis-1,4-isoprene) synthesis or rubber quality. The repartition of both proteins on the small or large rubber particles seems to differ, but their role in the irreversible coagulation of the rubber particle is still unknown. In this study we highlighted the different modes of interactions of both recombinant proteins with different classes of lipids extracted from Hevea brasiliensis latex, and defined as phospholipids (PL), glycolipids (GL) and neutral lipids (NL). We combined two biophysical methods, polarization modulated-infrared reflection adsorption spectroscopy (PM-IRRAS) and ellipsometry to elucidate their interactions with monolayers of each class of lipids. REF1 and SRPP1 interactions with native lipids are clearly different; SRPP1 interacts mostly in surface with PL, GL or NL, without modification of its structure. In contrast REF1 inserts deeply in the lipid monolayers with all lipid classes. With NL, REF1 is even able to switch from α-helice conformation to β-sheet structure, as in its aggregated form (amyloid form). Interaction between REF1 and NL may therefore have a specific role in the irreversible coagulation of rubber particles. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Selling "Impact": Peer Reviewer Projections of What Is Needed and What Counts in REF Impact Case Studies. A Retrospective Analysis

    Science.gov (United States)

    Watermeyer, Richard; Hedgecoe, Adam

    2016-01-01

    The intensification of an audit culture in higher education is made no more apparent than with the growing prevalence of performance-based research funding systems like the UK's Research Excellence Framework (REF) and the introduction of new measures of assessment like "impact" or more specifically, the economic and societal impacts of…

  16. The Experimental Regional Ensemble Forecast System (ExREF): Its Use in NWS Forecast Operations and Preliminary Verification

    Science.gov (United States)

    Reynolds, David; Rasch, William; Kozlowski, Daniel; Burks, Jason; Zavodsky, Bradley; Bernardet, Ligia; Jankov, Isidora; Albers, Steve

    2014-01-01

    The Experimental Regional Ensemble Forecast (ExREF) system is a tool for the development and testing of new Numerical Weather Prediction (NWP) methodologies. ExREF is run in near-realtime by the Global Systems Division (GSD) of the NOAA Earth System Research Laboratory (ESRL) and its products are made available through a website, an ftp site, and via the Unidata Local Data Manager (LDM). The ExREF domain covers most of North America and has 9-km horizontal grid spacing. The ensemble has eight members, all employing WRF-ARW. The ensemble uses a variety of initial conditions from LAPS and the Global Forecasting System (GFS) and multiple boundary conditions from the GFS ensemble. Additionally, a diversity of physical parameterizations is used to increase ensemble spread and to account for the uncertainty in forecasting extreme precipitation events. ExREF has been a component of the Hydrometeorology Testbed (HMT) NWP suite in the 2012-2013 and 2013-2014 winters. A smaller domain covering just the West Coast was created to minimize band-width consumption for the NWS. This smaller domain has and is being distributed to the National Weather Service (NWS) Weather Forecast Office and California Nevada River Forecast Center in Sacramento, California, where it is ingested into the Advanced Weather Interactive Processing System (AWIPS I and II) to provide guidance on the forecasting of extreme precipitation events. This paper will review the cooperative effort employed by NOAA ESRL, NASA SPoRT (Short-term Prediction Research and Transition Center), and the NWS to facilitate the ingest and display of ExREF data utilizing the AWIPS I and II D2D and GFE (Graphical Software Editor) software. Within GFE is a very useful verification software package called BoiVer that allows the NWS to utilize the River Forecast Center's 4 km gridded QPE to compare with all operational NWP models 6-hr QPF along with the ExREF mean 6-hr QPF so the forecasters can build confidence in the use of the

  17. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis.

    Science.gov (United States)

    Lindahl, Erik; Azuara, Cyril; Koehl, Patrice; Delarue, Marc

    2006-07-01

    Normal mode analysis (NMA) is an efficient way to study collective motions in biomolecules that bypasses the computational costs and many limitations associated with full dynamics simulations. The NOMAD-Ref web server presented here provides tools for online calculation of the normal modes of large molecules (up to 100,000 atoms) maintaining a full all-atom representation of their structures, as well as access to a number of programs that utilize these collective motions for deformation and refinement of biomolecular structures. Applications include the generation of sets of decoys with correct stereochemistry but arbitrary large amplitude movements, the quantification of the overlap between alternative conformations of a molecule, refinement of structures against experimental data, such as X-ray diffraction structure factors or Cryo-EM maps and optimization of docked complexes by modeling receptor/ligand flexibility through normal mode motions. The server can be accessed at the URL http://lorentz.immstr.pasteur.fr/nomad-ref.php.

  18. Comparative Proteomics of Rubber Latex Revealed Multiple Protein Species of REF/SRPP Family Respond Diversely to Ethylene Stimulation among Different Rubber Tree Clones.

    Science.gov (United States)

    Tong, Zheng; Wang, Dan; Sun, Yong; Yang, Qian; Meng, Xueru; Wang, Limin; Feng, Weiqiang; Li, Ling; Wurtele, Eve Syrkin; Wang, Xuchu

    2017-05-02

    Rubber elongation factor (REF) and small rubber particle protein (SRPP) are two key factors for natural rubber biosynthesis. To further understand the roles of these proteins in rubber formation, six different genes for latex abundant REF or SRPP proteins, including REF 138,175,258 and SRPP 117,204,243 , were characterized from Hevea brasiliensis Reyan (RY) 7-33-97. Sequence analysis showed that REFs have a variable and long N-terminal, whereas SRPPs have a variable and long C-terminal beyond the REF domain, and REF 258 has a β subunit of ATPase in its N-terminal. Through two-dimensional electrophoresis (2-DE), each REF/SRPP protein was separated into multiple protein spots on 2-DE gels, indicating they have multiple protein species. The abundance of REF/SRPP proteins was compared between ethylene and control treatments or among rubber tree clones with different levels of latex productivity by analyzing 2-DE gels. The total abundance of each REF/SRPP protein decreased or changed a little upon ethylene stimulation, whereas the abundance of multiple protein species of the same REF/SRPP changed diversely. Among the three rubber tree clones, the abundance of the protein species also differed significantly. Especially, two protein species of REF 175 or REF 258 were ethylene-responsive only in the high latex productivity clone RY 8-79 instead of in RY 7-33-97 and PR 107. Some individual protein species were positively related to ethylene stimulation and latex productivity. These results suggested that the specific protein species could be more important than others for rubber production and post-translational modifications might play important roles in rubber biosynthesis.

  19. Comparative Proteomics of Rubber Latex Revealed Multiple Protein Species of REF/SRPP Family Respond Diversely to Ethylene Stimulation among Different Rubber Tree Clones

    Directory of Open Access Journals (Sweden)

    Zheng Tong

    2017-05-01

    Full Text Available Rubber elongation factor (REF and small rubber particle protein (SRPP are two key factors for natural rubber biosynthesis. To further understand the roles of these proteins in rubber formation, six different genes for latex abundant REF or SRPP proteins, including REF138,175,258 and SRPP117,204,243, were characterized from Hevea brasiliensis Reyan (RY 7-33-97. Sequence analysis showed that REFs have a variable and long N-terminal, whereas SRPPs have a variable and long C-terminal beyond the REF domain, and REF258 has a β subunit of ATPase in its N-terminal. Through two-dimensional electrophoresis (2-DE, each REF/SRPP protein was separated into multiple protein spots on 2-DE gels, indicating they have multiple protein species. The abundance of REF/SRPP proteins was compared between ethylene and control treatments or among rubber tree clones with different levels of latex productivity by analyzing 2-DE gels. The total abundance of each REF/SRPP protein decreased or changed a little upon ethylene stimulation, whereas the abundance of multiple protein species of the same REF/SRPP changed diversely. Among the three rubber tree clones, the abundance of the protein species also differed significantly. Especially, two protein species of REF175 or REF258 were ethylene-responsive only in the high latex productivity clone RY 8-79 instead of in RY 7-33-97 and PR 107. Some individual protein species were positively related to ethylene stimulation and latex productivity. These results suggested that the specific protein species could be more important than others for rubber production and post-translational modifications might play important roles in rubber biosynthesis.

  20. Creating Directed Double-strand Breaks with the Ref Protein: A Novel Rec A-Dependent Nuclease from Bacteriophage P1

    Energy Technology Data Exchange (ETDEWEB)

    Gruenig, Marielle C.; Lu, Duo; Won, Sang Joon; Dulberger, Charles L.; Manlick, Angela J.; Keck, James L.; Cox, Michael M. (UW)

    2012-03-16

    The bacteriophage P1-encoded Ref protein enhances RecA-dependent recombination in vivo by an unknown mechanism. We demonstrate that Ref is a new type of enzyme; that is, a RecA-dependent nuclease. Ref binds to ss- and dsDNA but does not cleave any DNA substrate until RecA protein and ATP are added to form RecA nucleoprotein filaments. Ref cleaves only where RecA protein is bound. RecA functions as a co-nuclease in the Ref/RecA system. Ref nuclease activity can be limited to the targeted strands of short RecA-containing D-loops. The result is a uniquely programmable endonuclease activity, producing targeted double-strand breaks at any chosen DNA sequence in an oligonucleotide-directed fashion. We present evidence indicating that cleavage occurs in the RecA filament groove. The structure of the Ref protein has been determined to 1.4 {angstrom} resolution. The core structure, consisting of residues 77-186, consists of a central 2-stranded {beta}-hairpin that is sandwiched between several {alpha}-helical and extended loop elements. The N-terminal 76 amino acid residues are disordered; this flexible region is required for optimal activity. The overall structure of Ref, including several putative active site histidine residues, defines a new subclass of HNH-family nucleases. We propose that enhancement of recombination by Ref reflects the introduction of directed, recombinogenic double-strand breaks.

  1. The ERESE Project: Interfacing with the ERDA Digital Archive and ERR Reference Database in EarthRef.org

    Science.gov (United States)

    Koppers, A. A.; Staudigel, H.; Mills, H.; Keller, M.; Wallace, A.; Bachman, N.; Helly, J.; Helly, M.; Miller, S. P.; Massell Symons, C.

    2004-12-01

    To bridge the gap between Earth science teachers, librarians, scientists and data archive managers, we have started the ERESE project that will create, archive and make available "Enduring Resources in Earth Science Education" through information technology (IT) portals. In the first phase of this National Science Digital Library (NSDL) project, we are focusing on the development of these ERESE resources for middle and high school teachers to be used in lesson plans with "plate tectonics" and "magnetics" as their main theme. In this presentation, we will show how these new ERESE resources are being generated, how they can be uploaded via online web wizards, how they are archived, how we make them available via the EarthRef.org Digital Archive (ERDA) and Reference Database (ERR), and how they relate to the SIOExplorer database containing data objects for all seagoing cruises carried out by the Scripps Institution of Oceanography. The EarthRef.org web resource uses the vision of a "general description" of the Earth as a geological system to provide an IT infrastructure for the Earth sciences. This emphasizes the marriage of the "scientific process" (and its results) with an educational cyber-infrastructure for teaching Earth sciences, on any level, from middle school to college and graduate levels. Eight different databases reside under EarthRef.org from which ERDA holds any digital object that has been uploaded by other scientists, teachers and students for free, while the ERR holds more than 80,000 publications. For more than 1,500 of these publications, this latter database makes available for downloading JPG/PDF images of the abstracts, data tables, methods and appendices, together with their digitized contents in Microsoft Word and Excel format. Both holdings are being used to store the ERESE objects that are being generated by a group of undergraduate students majoring in Environmental Systems (ESYS) program at the UCSD with an emphasis on the Earth Sciences

  2. An analysis of the titles of papers submitted to the UK REF in 2014: authors, disciplines, and stylistic details.

    Science.gov (United States)

    Hudson, John

    In 2014 over 52,000 academics submitted >155,500 journal articles in 36 different disciplines for assessment in the UK's four-year Research Evaluation Framework (the REF). In this paper the characteristics of the titles of these papers are assessed. Although these varied considerably between the disciplines, the main findings were that: (i) the lengths of the titles increased with the number of authors in almost all disciplines, (ii) the use of colons and question marks tended to decline with increasing author numbers-although there were a few disciplines, such as economics, where the reverse was evident, (iii) papers published later on in the 4-year period tended to have more authors than those published earlier, and (iv), in some disciplines, the numbers of subsequent citations to papers were higher when the titles were shorter and when they employed colons but lower when they used question marks.

  3. Genistein alleviates radiation-induced pneumonitis by depressing Ape1/Ref-1 expression to down-regulate inflammatory cytokines.

    Science.gov (United States)

    Liu, Guo-Dong; Xia, Lei; Zhu, Jian-Wu; Ou, Shan; Li, Meng-Xia; He, Yong; Luo, Wei; Li, Juan; Zhou, Qian; Yang, Xue-Qin; Shan, Jin-Lu; Wang, Ge; Wang, Dong; Yang, Zhen-Zhou

    2014-07-01

    The aim of the study was to investigate the role of genistein in alleviating radiation-induced pneumonitis(RIP) through down-regulating levels of the inflammatory cytokines by inhibiting the expression of apurinic/apyrimidinic endonuclease 1/redox factor-1 (Ape1/Ref-1). Fifty female C57BL/6J mice (8 weeks old) were randomly divided into a control group, a pure irradiation (IR) group and a genistein + IR group. At the four time points after IR, hematoxylin, and Masson’s trichrome stainings were used to examine the pathological changes and collagen fiber deposition. Flow cytometry was used to detect reactive oxygen system (ROS) changes, EMSA was used to estimate the nuclear factor kappa B (NF-κB) transcriptional activities and an ELISA assay was used to measure the levels of TGF-β1, IL-1β, TNF-α, and IL-6 in the serum and bronchoalveolar lavage fluid (BALF) 2 weeks after IR.The pathological detection results showed acute inflammatory/fibrinoid exudation of the thoracic tissue after IR,which was significantly alleviated with genistein. The IR inducedan APE1 protein expression increase and NF-jB was effectively suppressed by genistein (P < 0.05). The induction of the inflammatory cytokines TGF-β1, IL-1β,TNF-α, and IL-6 by IR were in turn inhibited in the serum and BALF of the genistein-pretreated mice (P < 0.05). In addition, the ROS production was significantly boosted in the A549 cells after IR, which could be down-regulated by the pretreatment of genistein. The results demonstrate that genistein alleviates RIP by attenuating the inflammatory response in the initiation of RIP. A possible target of genistein is the Ape1/ref-1, which regulates key inflammatory cytokines by activating the NF-κB.

  4. Development of a system for receiving, crushing and screening recycled fuel (REF) material; Kierraetyspolttoaineen vastaanotto-, murskaus- ja seulontajaerjestelmaen kehittaeminen

    Energy Technology Data Exchange (ETDEWEB)

    Nurmi, A. [VTT Energy, Jyvaeskylae (Finland)

    1997-12-01

    The goal of this project is to develop a system to which source sorted combustible industrial, office and municipal waste material can be taken and where it is then processed in such way that it can be burnt in modern fluidized bed and circulating bed boilers. The project started in the end of year 1995. The main stages of the project are: (1) Study and analysis of existing technology and equipment, (2) Development of system components, (3) Development of the system, (4) Building a pilot/demonstration plant, (5) Tests and results analysis and (6) Decisions on further actions. In the year 1996 the main stage was development of system components; especially crushing. Results of running slow-speed big crushers were collected, analysed and the main development details determined. Additionally, particle size distribution from different crushing methods were analyzed using also primary and secondary crushing. Development of a heavy-duty 2-rotor ECO-Crusher and a crushing screen was started. Regarding to the development of the REF-system, different alternatives have been analyzed and possible demonstration places have been searched. The first multi-crushing line will be demonstrated in Sweden. (orig.)

  5. [Effects on survival of shRNA mediated APE/Ref1 gene silencing in rat spiral ganglion cells in oxidative stress].

    Science.gov (United States)

    Jiang, Zhendong; Zhong, Cheng; Li, Taijun; Xiang, Zhaolan; Zhang, Xueyuan

    2014-02-01

    To investigate the effects of reducing APE/Ref1 expression in the cultures of rat spiral ganglion cells with oxidative damage induced by H(2)O(2). Primary cultured rat spiral ganglion cells were infected with small interfering RNA to APE/Ref1 (Ape1siRNA) for 72 h, followed by treating with H(2)O(2) (0, 10, 25, 50, 100 and 300 µmol/L) for 1 h , and then cultured in normal medium for 24 h. Western blot were used to detect the level of APE/Ref1 protein and phosphorylation of histone protein H2AX in the infected cells. The caspase3 activation was tested by spectrophotometric method . The cell viability was determined by MTT and the apoptosis of spiral ganglion cells was determined by terminal-deoxynucleotidyl transferase mediated nick and labeling (TUNEL). Western blot showed that infection with Ape1siRNA resulted in APE/Ref1 reduced expression in the spiral ganglion cells. Exposing spiral ganglion cultures with reduced expression of APE/Ref1 to H(2)O(2) (50, 100, 300 µmol/L) for 1 h resulted in increasing in the phosphorylation of histone protein H2AX. The reduction in APE/Ref1 significantly reduced cell viability in cultures 24 h after 1 h expression to 50-300 µmol/L H(2)O(2). The apoptosis of cells and caspase 3 activity was detected significantly improved. The induced of APE/Ref1 results in significantly decrease in spiral ganglion cells viability in oxidative stress. The repairing function of APE/Ref1 is necessary for optimal levels of neuronal rat spiral ganglion cells survival.

  6. Initial experience with circumferential pulmonary vein isolation guided by Overlay Ref and CartoMerge in the treatment of paroxysmal atrial fibrillation.

    Science.gov (United States)

    Tang, Kai; Zhao, Dong-dong; Zhang, Jing-ying; Chen, Yan-qing; Xu, Ya-wei

    2010-05-20

    CartoMerge has been widely used in guiding circumferential pulmonary vein isolation (CPVI) for the treatment of paroxysmal atrial fibrillation (PAF). However, the procedure of landmarks selection varies among operators according to their experience. Techniques have to be established to standardize this procedure. We propose that Overlay Ref could facilitate this procedure. This paper aimed to report our initial experience with CPVI guided by Overlay Ref and CartoMerge for the treatment of PAF. Fifty-nine patients with PAF were enrolled in this study. Using Overlay Ref technique, a reference image (inverted) was faded into the live fluoroscopic image. Landmarks of CartoMerge were selected from anatomic points of the top of superior pulmonary veins (PVs) and the bottom of inferior PVs guided by Overlay Ref image. Overlay Ref images were also used to guide the ablation procedure combining with CartoMerge. All patients were successfully mapped by CartoMerge guided by Overlay Ref. The distance between the mapping points and the CT surfaces was (1.42 +/- 0.67) mm for the patients as a whole. This led to a successful rate of 96% for isolation of pulmonary veins. Duration of ablation procedure was (92 +/- 17) minutes. And the total duration of procedure was (139 +/- 32) minutes. CartoMerge could also be performed just with 3 paries to 4 paries selected landmarks guided by Overlay Ref without a full anatomic model constructed by Carto. Then, the total duration of procedure could be shortened to (115 +/- 38) minutes. Overlay Ref technique can facilitate the catheter ablation of PAF and can help to standardize the procedure of landmarks selection.

  7. The Open Science Peer Review Oath [v1; ref status: indexed, http://f1000r.es/4ou

    Directory of Open Access Journals (Sweden)

    Jelena Aleksic

    2014-11-01

    Full Text Available One of the foundations of the scientific method is to be able to reproduce experiments and corroborate the results of research that has been done before. However, with the increasing complexities of new technologies and techniques, coupled with the specialisation of experiments, reproducing research findings has become a growing challenge. Clearly, scientific methods must be conveyed succinctly, and with clarity and rigour, in order for research to be reproducible. Here, we propose steps to help increase the transparency of the scientific method and the reproducibility of research results: specifically, we introduce a peer-review oath and accompanying manifesto. These have been designed to offer guidelines to enable reviewers (with the minimum friction or bias to follow and apply open science principles, and support the ideas of transparency, reproducibility and ultimately greater societal impact. Introducing the oath and manifesto at the stage of peer review will help to check that the research being published includes everything that other researchers would need to successfully repeat the work. Peer review is the lynchpin of the publishing system: encouraging the community to consciously (and conscientiously uphold these principles should help to improve published papers, increase confidence in the reproducibility of the work and, ultimately, provide strategic benefits to authors and their institutions. Future incarnations of the various national Research Excellence Frameworks (REFs will evolve away from simple citations towards measurable societal value and impact. The proposed manifesto aspires to facilitate this goal by making transparency, reproducibility and citizen-scientist engagement (with the knowledge-creation and dissemination processes the default parameters for performing sound research.

  8. Nuclear depletion of apurinic/apyrimidinic endonuclease 1 (Ape1/Ref-1) is an indicator of energy disruption in neurons.

    Science.gov (United States)

    Singh, Shilpee; Englander, Ella W

    2012-11-01

    Apurinic/apyrimidinic endonuclease 1 (Ape1/Ref-1) is a multifunctional protein critical for cellular survival. Its involvement in adaptive survival responses includes key roles in redox sensing, transcriptional regulation, and repair of DNA damage via the base excision repair (BER) pathway. Ape1 is abundant in most cell types and central in integrating the first BER step catalyzed by different DNA glycosylases. BER is the main process for removal of oxidative DNA lesions in postmitotic brain cells, and after ischemic brain injury preservation of Ape1 coincides with neuronal survival, while its loss has been associated with neuronal death. Here, we report that in cultured primary neurons, diminution of cellular ATP by either oligomycin or H(2)O(2) is accompanied by depletion of nuclear Ape1, while other BER proteins are unaffected and retain their nuclear localization under these conditions. Importantly, while H(2)O(2) induces γH2AX phosphorylation, indicative of chromatin rearrangements in response to DNA damage, oligomycin does not. Furthermore, despite comparable diminution of ATP content, H(2)O(2) and oligomycin differentially affect critical parameters of mitochondrial respiration that ultimately determine cellular ATP content. Taken together, our findings demonstrate that in neurons, nuclear compartmentalization of Ape1 depends on ATP and loss of nuclear Ape1 reflects disruption of neuronal energy homeostasis. Energy crisis is a hallmark of stroke and other ischemic/hypoxic brain injuries. In vivo studies have shown that Ape1 deficit precedes neuronal loss in injured brain regions. Thus, our findings bring to light the possibility that energy failure-induced Ape1 depletion triggers neuronal death in ischemic brain injuries. Copyright © 2012 Elsevier Inc. All rights reserved.

  9. Deslocamento miscível de cátions básicos provenientes da água residuária de mandioca em colunas de solo Miscible displacement of basic cations from cassava processing wastewater in soil columns

    Directory of Open Access Journals (Sweden)

    Ralini F. de Melo

    2006-06-01

    Full Text Available Objetivou-se, com este estudo, determinar os fatores de retardamento e os coeficientes de dispersão-difusão dos íons potássio, sódio, cálcio e magnésio, presentes na água residuária de fecularias ou manipueira, e simular as concentrações residentes em colunas de solos de 160 cm, pelo período de 5 h. Os ensaios foram realizados em laboratório utilizando-se colunas de percolação preenchidas com amostras de Neossolo Quartzarênico órtico espódico (RQo, Latossolo Amarelo distrófico típico (LAd e Latossolo Vermelho Amarelo distrófico típico (LVAd. A concentração dos íons no efluente foram analisados empregando-se a metodologia de deslocamento de fluidos miscíveis. Os valores mais elevados dos fatores de retardamento ocorreram no LVAd, indicando maior retenção dos íons potássio, sódio, cálcio e magnésio nesse solo. Os valores dos coeficientes dispersivos-difusivos decresceram no sentido do RQo para o LVAd, sendo que o maior valor ocorreu no RQo para o íon potássio, e o menor no LVAd, para o íon cálcio. A simulação para um período de aplicação da manipueira de 5 h, mostrou pequeno avanço dos íons na coluna do LVAd, em comparação com RQo e LAd alertando, assim, para os perigos de contaminação de águas subterrâneas ao se aplicar a manipueira nesses solos.This study aimed to determine the retardation factors and the diffusion-dispersion coefficients of the potassium, sodium, calcium and magnesium ions found in the cassava wastewater, as well as to simulate the resident concentrations in soil columns with 160 cm over a five-hours period. The trials were accomplished under laboratory conditions, by using percolation columns fulfilled with materials from the spodic ortic Quartzarenic Neosol (RQo, typical distrophic Yellow Latosol (LAd and typical distrophic Yellow Red Latosol (LVAd. The data of the ion concentrations in effluent were analyzed, by using the miscible fluid displacement methodology. The highest

  10. dbtdstoapolicy.pdf | misc docs | academy | Indian Academy of ...

    Indian Academy of Sciences (India)

    REGISTRATIONS CLOSED. Announcement of selected candidates will commence towards the end of February. Focus Area Science Technology Summer Fellowship (FAST-SF). REGISTRATIONS CLOSED. Announcement of selected candidates will commence towards the end of February. Associates – 2017. Posted on ...

  11. [The expression of p53, MDM2 and Ref1 gene in cultured retina neurons of SD rats treated with vitamin B1 and/or elevated pressure].

    Science.gov (United States)

    Yang, Zhikuan; Ge, Jian; Yin, Wei; Shen, Huangxuan; Liu, Haiquan; Guo, Yan

    2004-12-01

    To investigate the expression of p53, MDM2 and Ref1 gene in cultured retina neurons of SD rats treated with Vitamin B1 and (or) elevated pressure. The retinal neuron of postnatal SD rats were cultured in vivo, the elevated pressure was produced after 7 days, and the total RNA was extracted after another 2 days, expression of p53, MDM2 and Ref1 gene were analyzed with RT-PCR. The expression level of p53 and MDM2 gene were increased in elevated pressure group, normal with Ref1 gene expression. But the expression of p53 and MDM2 gene were decreased significantly in elevated pressure group treated with vitamine B1 compare to the elevated group. Apoptosis seem to be a mechanism of cell death in retinal neurons of SD rats with elevated pressure.Vitamine B1 have protect effects against elevated pressure.

  12. [Diagnostic criteria for Menière's disease. Consensus document of the Bárány Society, the Japan Society for Equilibrium Research, the European Academy of Otology and Neurotology (EAONO), the American Academy of Otolaryngology-Head and Neck Surgery (AAO-HNS) and the Korean Balance Society].

    Science.gov (United States)

    Lopez-Escamez, José A; Carey, John; Chung, Won-Ho; Goebel, Joel A; Magnusson, Måns; Mandalà, Marco; Newman-Toker, David E; Strupp, Michael; Suzuki, Mamoru; Trabalzini, Franco; Bisdorff, Alexandre

    2016-01-01

    This paper presents diagnostic criteria for Menière's disease jointly formulated by the Classification Committee of the Bárány Society, The Japan Society for Equilibrium Research, the European Academy of Otology and Neurotology (EAONO), the Equilibrium Committee of the American Academy of Otolaryngology-Head and Neck Surgery (AAO-HNS) and the Korean Balance Society. The classification includes 2 categories: definite Menière's disease and probable Menière's disease. The diagnosis of definite Menière's disease is based on clinical criteria and requires the observation of an episodic vertigo syndrome associated with low-to medium-frequency sensorineural hearing loss and fluctuating aural symptoms (hearing, tinnitus and/or fullness) in the affected ear. Duration of vertigo episodes is limited to a period between 20 min and 12h. Probable Menière's disease is a broader concept defined by episodic vestibular symptoms (vertigo or dizziness) associated with fluctuating aural symptoms occurring in a period from 20 min to 24h. Copyright © 2015 Elsevier España, S.L.U. and Sociedad Española de Otorrinolaringología y Patología Cérvico-Facial. All rights reserved.

  13. The effect of altered dosage of a mutant allele of Teosinte branched 1 (tb1-ref) on the root system of modern maize.

    Science.gov (United States)

    Gaudin, Amelie C M; McClymont, Sarah A; Soliman, Sameh S M; Raizada, Manish N

    2014-02-14

    There was ancient human selection on the wild progenitor of modern maize, Balsas teosinte, for decreased shoot branching (tillering), in order to allow more nutrients to be diverted to grain. Mechanistically, the decline in shoot tillering has been associated with selection for increased expression of the major domestication gene Teosinte Branched 1 (Tb1) in shoot primordia. Therefore, TB1 has been defined as a repressor of shoot branching. It is known that plants respond to changes in shoot size by compensatory changes in root growth and architecture. However, it has not been reported whether altered TB1 expression affects any plant traits below ground. Previously, changes in dosage of a well-studied mutant allele of Tb1 in modern maize, called tb1-ref, from one to two copies, was shown to increase tillering. As a result, plants with two copies of the tb1-ref allele have a larger shoot biomass than heterozygotes. Here we used aeroponics to phenotype the effects of tb1-ref copy number on maize roots at macro-, meso- and micro scales of development. An increase in the tb1-ref copy number from one to two copies resulted in: (1) an increase in crown root number due to the cumulative initiation of crown roots from successive tillers; (2) higher density of first and second order lateral roots; and (3) reduced average lateral root length. The resulting increase in root system biomass in homozygous tb1-ref mutants balanced the increase in shoot biomass caused by enhanced tillering. These changes caused homozygous tb1-ref mutants of modern maize to more closely resemble its ancestor Balsas teosinte below ground. We conclude that a decrease in TB1 function in maize results in a larger root system, due to an increase in the number of crown roots and lateral roots. Given that decreased TB1 expression results in a more highly branched and larger shoot, the impact of TB1 below ground may be direct or indirect. We discuss the potential implications of these findings for whole

  14. Comparison of the Accuracy of Bibliographical References Generated for Medical Citation Styles by EndNote, Mendeley, RefWorks and Zotero

    OpenAIRE

    Kratochvíl, Jiří

    2017-01-01

    Bibliographical references to online and printed articles, books, contributions to edited books and web resources generated by EndNote, Mendeley, RefWorks and Zotero were compared with manually written references according to the citation instructions in 15 biomedical journals and the NLM citation style. The fewest mistakes were detected in references generated by Zotero for 11 journals and the NLM style, while the second fewest number of mistakes was found in Mendeley. The largest number of ...

  15. CERN Technical Training 2002: Learning for the LHC! HeREF-2002 : Techniques de la Réfrigération Hélium - French version only

    CERN Multimedia

    Davide Vitè

    2002-01-01

    Théorie, Technologie, Entretien et Contrôle des Réfrigérateurs Hélium HeREF-2002 est un nouveau cours dans le cadre du programme de l'Enseignement Technique 2002, qui offre une présentation complète de la réfrigération hélium, avec une approche pratique de la théorie, la technologie, l'entretien et le contrôle des installations de réfrigération hélium. Les aspects théoriques et les équations seront réduits au maximum. HeREF-2002 concerne une assistance de techniciens et d'opérateurs d'installations de réfrigération hélium au CERN, autant que de physiciens et d'ingénieurs ayant besoin d'une bonne notion des techniques classiques de réfrigération hélium. HeREF-2002 s'intéresse, entre autres, à la technologie de...

  16. Active Sites of Reduced Epidermal Fluorescence1 (REF1 Isoforms Contain Amino Acid Substitutions That Are Different between Monocots and Dicots.

    Directory of Open Access Journals (Sweden)

    Tagnon D Missihoun

    Full Text Available Plant aldehyde dehydrogenases (ALDHs play important roles in cell wall biosynthesis, growth, development, and tolerance to biotic and abiotic stresses. The Reduced Epidermal Fluorescence1 is encoded by the subfamily 2C of ALDHs and was shown to oxidise coniferaldehyde and sinapaldehyde to ferulic acid and sinapic acid in the phenylpropanoid pathway, respectively. This knowledge has been gained from works in the dicotyledon model species Arabidopsis thaliana then used to functionally annotate ALDH2C isoforms in other species, based on the orthology principle. However, the extent to which the ALDH isoforms differ between monocotyledons and dicotyledons has rarely been accessed side-by-side. In this study, we used a phylogenetic approach to address this question. We have analysed the ALDH genes in Brachypodium distachyon, alongside those of other sequenced monocotyledon and dicotyledon species to examine traits supporting either a convergent or divergent evolution of the ALDH2C/REF1-type proteins. We found that B. distachyon, like other grasses, contains more ALDH2C/REF1 isoforms than A. thaliana and other dicotyledon species. Some amino acid residues in ALDH2C/REF1 isoforms were found as being conserved in dicotyledons but substituted by non-equivalent residues in monocotyledons. One example of those substitutions concerns a conserved phenylalanine and a conserved tyrosine in monocotyledons and dicotyledons, respectively. Protein structure modelling suggests that the presence of tyrosine would widen the substrate-binding pocket in the dicotyledons, and thereby influence substrate specificity. We discussed the importance of these findings as new hints to investigate why ferulic acid contents and cell wall digestibility differ between the dicotyledon and monocotyledon species.

  17. CrossRef Neutrino factories

    CERN Document Server

    Wildner, Elena

    2016-01-01

    Neutrinos are produced by many processes in our universe. These elusive particles reach the earth having a certain energy permitting them to react with nuclei in detectors that are specifically designed to probe their properties. However, to get higher intensities and higher energy neutrinos for better statistics and better physics reach, the use of accelerators is necessary to advance in the field of neutrino research. To produce neutrinos with an accelerator, one needs to send a high power beam onto a target to get particles or isotopes that produce neutrinos with the required properties, by decay. The parent particles have to be collected and prepared for injection into an accelerating structure. Accelerator-based experiments can tune the energy of the produced neutrinos by boosting and controlling the energy of the parent particle. The produced neutrinos will travel the distance between the source and the detector, generally through earth; the distance the neutrino travels through earth, the energy of the...

  18. US trends in refractive surgery: 2003 ISRS/AAO survey.

    Science.gov (United States)

    Duffey, Richard J; Leaming, David

    2005-01-01

    To determine the latest trends in refractive surgery in the United States. All U.S. members of the International Society of Refractive Surgery of the American Academy of Ophthalmology were mailed the 2003 refractive surgery survey dealing with volumes, types, preferences of refractive surgery performed, and use of new emerging technology. Questions regarding radial keratotomy (RK), astigmatic keratotomy (AK), limbal relaxing incisions (LRI), photorefractive keratectomy (PRK), laser in situ keratomileusis (LASIK), laser subepithelial keratomileusis (LASEK), intracorneal ring segments (ICRS), laser thermokeratoplasty (LTK), conductive keratoplasty (CK), phakic intraocular lenses (PIOL), clear lens extractions (CLE), and scleral expansion (SE) procedures were examined in the survey. Use of lasers, microkeratomes, pupillometry instruments, postoperative medications, wavefront analyzers, topographers, etc were examined. In 2003, LASIK continued to dominate for refractive errors between -8.00 to +3 diopters. Surgeons are waiting on the PIOL for high myopes and are performing CLE for high hyperopes. Photorefractive keratectomy, LASIK, LASEK, CLE, PIOL, and CK appeared to have bright futures; whereas, RK, ICR, LTK and SE were on the decline. Bilateral LASIK at the same surgical session is offered by 98% of surgeons. VISX lasers are used 2:1 over all other lasers in the United States. Zeiss-Humphrey still dominates topographers at 37%. The Bausch & Lomb Hansatome (48%) leads microkeratomes. Surgeons are charging, on average, 300-500 dollars more per eye for custom ablations and these ablations have already been accepted and integrated into refractive practices. Comanaging of refractive surgery patients is significantly down from previous years. Fourth-generation fluoroquinolones overtook the postoperative antibiotic prescriptions, with prednisolone and fluoromethalone dominating as anti-inflammatories. Trends and changes as refractive surgery grows in the mainstream of ophthalmology in the United States continue to be elucidated by this professional organization survey.

  19. Ref Tek Ultra-low Power Seismic Recorder With Low-cost High Speed Internet Telemetry U An Advanced Real-time Seismological Data Acquisition System

    Science.gov (United States)

    Passmore, P.; Zimakov, L.; Rozhkov, M.

    The 3rd Generation Seismic Recorder, Model 130-01, has been designed to be easier to use - more compact, lighter in weight, lower power, and requires less maintenance than other recorders. Not only is the hardware optimized for field deployments, soft- ware tools as well have been specially developed to support both field and base station operation. The 130's case is a clamshell design, inherently waterproof, with easy access to all user features on the top of the unit. The 130 has 6 input/output connectors, an LCD display, and a removable lid on top of the case. There are two Channel input connectors on a 6-channel unit (only one on a 3-channel unit), a Terminal connector for setup and control, a Net connector combining Ethernet and Serial PPP for network access, a 12 VDC Power connector, and a GPS receiver connector. The LCD display allows the user to monitor the status of various sub systems within the 130 without having a terminal device attached. For storing large amounts of data the IBM MicrodriveTM is offered. User setup, control and status monitoring is done either with a Personal Digital Assistant (PDA) (Palm OS compatible) using our Palm Field Controller (PFC) software or from a PC/workstation using our REF TEK Network Controller (RNC) GUI interface. StarBand VSAT is the premier two-way, always-on, high-speed satellite Internet ser- vice. StarBand means high-speed Internet without the constraints and congestion of land-based cable or telephone networks. StarBand uses a single satellite dish antenna for receiving and for sending dataUno telephone connection is needed. The hardware ° cost is much less than standard VSAT equipment with double or single hop transmis- sion. REF TEK protocol (RTP) provides end-to-end error-correcting data transmission and command/control. StarBandSs low cost VSAT provides two-way, always-on, high speed satellite Internet data availability. REF TEK and StarBand create the most ad- vanced real-time seismological data acquisition

  20. Direitos humanos e refúgio: uma análise sobre o momento pós-determinação do status de refugiado

    Directory of Open Access Journals (Sweden)

    Thais Silva Menezes

    2013-01-01

    Full Text Available A literatura sobre refugiados tem explorado a vinculação entre refúgio e direitos humanos nos países de acolhida - aspecto fundamental do regime internacional dos refugiados - em uma perspectiva predominantemente descritiva. Ressaltando a necessidade de abordagens analíticas sobre a temática, este trabalho analisa como o Alto Comissariado das Nações Unidas para os Refugiados (ACNUR tem se manifestado no que concerne aos direitos humanos dos refugiados nos países de acolhida, apontando a influência da política internacional nesse contexto. Entende-se que, uma vez compreendido o regime em sua relação com os direitos humanos, estes devem representar o parâmetro para se analisar a forma como ocorre a concretização da proteção internacional.

  1. One-step synthesis of small-sized and water-soluble NaREF4 upconversion nanoparticles for in vitro cell imaging and drug delivery.

    Science.gov (United States)

    Yang, Dongmei; Dai, Yunlu; Ma, Pingan; Kang, Xiaojiao; Cheng, Ziyong; Li, Chunxia; Lin, Jun

    2013-02-18

    Small (2-28 nm) NaREF(4) (rare earth (RE)=Nd-Lu, Y) nanoparticles (NPs) were prepared by an oil/water two-phase approach. Meanwhile, hydrophilic NPs can be obtained through a successful phase-transition process by introducing the amphiphilic surfactant sodium dodecylsulfate (SDS) into the same reaction system. Hollow-structured NaREF(4) (RE=Y, Yb, Lu) NPs can be fabricated in situ by electron-beam lithography on solid NPs. The MTT assay indicates that these hydrophilic NPs with hollow structures exhibit good biocompatibility. The as-prepared hollow-structured NPs can be used as anti-cancer drug carriers for drug storage/release investigations. Doxorubicin hydrochloride (DOX) was taken as model drug. The release of DOX from hollow α-NaLuF(4):20% Yb(3+), 2% Er(3+) exhibits a pH-sensitive release patterns. Confocal microscopy observations indicate that the NPs can be taken up by HeLa cells and show obvious anti-cancer efficacy. Furthermore, α-NaLuF(4):20% Yb(3+), 2% Er(3+) NPs show bright-red emission under IR excitation, making both the excitation and emission light fall within the "optical window" of biological tissues. The application of α-NaLuF(4):20% Yb(3+), 2% Er(3+) in the luminescence imaging of cells was also investigated, which shows a bright-red emission without background noise. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Nucleotide receptors stimulation by extracellular ATP controls Hsp90 expression through APE1/Ref-1 in thyroid cancer cells: a novel tumorigenic pathway.

    Science.gov (United States)

    Pines, Alex; Bivi, Nicoletta; Vascotto, Carlo; Romanello, Milena; D'Ambrosio, Chiara; Scaloni, Andrea; Damante, Giuseppe; Morisi, Roberta; Filetti, Sebastiano; Ferretti, Elisabetta; Quadrifoglio, Franco; Tell, Gianluca

    2006-10-01

    Nucleotide receptors signaling affects cell proliferation, with possible implications on tumorigenic processes. However, molecular targets and action mechanisms of the extracellular nucleotides are still poorly elucidated. We have previously shown in ARO cells that APE1/Ref-1, a transcriptional coactivator responsible for the maintenance of the cellular proliferative rate, is functionally controlled by P2-mediated signaling. Here, we demonstrate that extracellular ATP has a mitogenic effect on ARO cells, increasing ERK phosphorylation, AP1 activation, and cyclin D1 expression. Using the ATP/ADPase apyrase and the P2 receptor antagonist suramin, we show that the extracellular ATP, physiologically released by ARO cells, exerts mitogenic effects. A differential proteomic approach was used to identify molecular events associated with the ATP-induced cell proliferation. Among other proteins, Hsp90 was found upregulated upon ATP stimulation. Pretreatment with suramin completely blocked the ATP-induced Hsp90 activation, confirming the involvement of cell-surface P2 nucleotide receptors in the ATP-mediated activation of ARO cells. Treatment of proliferating ARO cells with suramin and apyrase significantly reduced the intracellular levels of Hsp90, suggesting an autocrine/paracrine mechanism of control on Hsp90 expression by extracellular ATP. The influence of Hsp90 on ATP-induced cell proliferation was also demonstrated by its specific inhibition with 17-AAG. The molecular pathway by which ATP stimulates cell proliferation was further investigated by siRNA strategies showing that Hsp90 is a target of APE1/Ref-1 functional activation. Stimulation of ARO cells with specific nucleotide receptors agonists evidenced a major involvement of P2Y1 and P2Y2 receptors in controlling the Hsp90 activation. Accordingly, these two receptors resulted significantly upregulated in sample biopsies from different thyroid tumors. Copyright 2006 Wiley-Liss, Inc.

  3. Desenvolvimento de larvas de Steindachneridion sp. em diferentes condições de refúgio e luminosidade Development of larvae of Steindachneridion sp. under different conditions of refuge and luminosity

    Directory of Open Access Journals (Sweden)

    Aldi Feiden

    2006-01-01

    Full Text Available Avaliou-se a influência da luminosidade e do uso de refúgios no desenvolvimento inicial de larvas de surubim do Iguaçu (Steindachneridion sp. Garavello (Siluriforme: Pimelodidae. Utilizaram-se 1.000 larvas com peso e comprimento inicial de 62,2 mg e 18,02 mm, respectivamente, distribuídas em 20 aquários de 35 L, durante 22 dias. Os tratamentos consistiram dos ambientes: escuro sem refúgio, claro com refúgio artificial, escuro com refúgio artificial, claro com refúgio natural e claro sem refúgio, com quatro repetições cada, distribuídos em delineamento inteiramente casualizado. As larvas receberam a mesma alimentação em todos os tratamentos. As melhores taxas de sobrevivência foram verificadas nos ambientes: escuro sem refúgio, claro com refúgio natural e claro sem refúgio, com 84, 76 e 70%, respectivamente. O melhor desenvolvimento das larvas ocorreu em ambiente escuro e sem refúgio. O tratamento escuro com refúgio artificial apresentou diferenças significativas em relação à sobrevivência e ao peso final dos outros tratamentos, com grande heterogeneidade quanto ao peso. Ambientes escuros e sem refúgios são os mais adequados para o desenvolvimento inicial de larvas de surubim do Iguaçu.The influence of luminosity and of the use of refuges on the initial development of Steindachneridion sp. Garavello (Siluriforme: Pimelodidae larvae was evaluated. A thousand larvae 18.02 mm high and 62.2 mg weight were used in an entirely randomized design, with five treatments and four replicates, in 35 L-aquarium during 22 days. The treatments consisted on the following environments: darkness without refuges, clear with artificial refuge, darkness with artificial refuge, clear with natural refuge and clear without refuge. All larvae received the same feeding during the experiment. The best survival rates were found for darkness without refuges, clear with artificial refuge and clear without refuge, with 84, 76 and 70%, respectively

  4. Beneficiários ou reféns? o patrimonialismo na perspectiva dos cidadãos de Poço Fundo, Minas Gerais

    Directory of Open Access Journals (Sweden)

    Renato Ferreira de Oliveira

    Full Text Available Há uma diversidade de elementos na cultura política dos pequenos municípios brasileiros agindo em anteposição ao processo democrático, à solidariedade social e para a desconstrução do espírito de comunidade cívica. Nesse cenário, merece destaque a ação do clientelismo, do patrimonialismo e do personalismo. Com objetivo de discutir a dominação e a vigência desses elementos em rotinas públicas e relações sociais, este artigo apresenta o caso de Poço Fundo, município de pequeno porte localizado no Sul de Minas Gerais. Três situações foram destacadas para demonstrar como tais práticas, além de toleradas, são convertidas em estratégia individual diante da ineficiência e da insensibilidade pública, esclarecendo como os políticos capitalizam para si e para seus partidos os favores prestados e como a natureza cíclica dos privilégios constrange ações coletivas, capazes de oferecer resistência ao "loteamento" político da cidade. A precariedade dos serviços públicos identificada nos depoimentos, embora pareça causa da cultura do favor é, antes de tudo, produto desta. Desse modo, ficou evidenciado que a população poçofundense não se tornou beneficiária dessas práticas, mas sim, refém do sistema político.

  5. Response to Dr Stevens' letter ref. Visitisen et al: "Short-term effects of night shift work on breast cancer risk: a cohort study of payroll data".

    Science.gov (United States)

    Kolstad, Henrik A; Garde, Anne Helene; Hansen, Åse Marie; Frydenberg, Morten; Christiansen, Peer; Vistisen, Helene Tilma; Bonde, Jens Peter E

    2017-01-01

    selection bias, but we observed similar risk estimates as for the total study population. Taken together, we find that our study provides rather robust evidence of no short-term breast cancer risk following recent night shift work. It must, however, be stressed that data did not allow assessment of a possible long-term risk. Reference 1. Stevens R. Letter ref. Vitisen et al: "Short-term effects of night shift work on breast cancer risk: a cohort study of payroll data". Scand J Work Environ Health. 2017;43(1):95. http://dx.doi.org/10.5271/sjweh.3607 2. Vistisen HT, Garde AH, Frydenberg M, Christiansen P, Hansen AM, Hansen J, Bonde JP, Kolstad HA. Short-term effects of night shift work on breast cancer risk: A cohort study of payroll data. Scand J Work Environ Health. 2017;43(1):59-67. http://dx.doi.org/10.5271/sjweh.3603. 3. Ijaz S, Verbeek J, Seidler A, Lindbohm ML, Ojajarvi A, Orsini N, Costa G, Neuvonen K. Night-shift work and breast cancer--a systematic review and meta-analysis. Scand J Work Environ Health. 2013 Sep 1;39(5):431-47. http://dx.doi.org/10.5271/sjweh.3371.

  6. Refúgios artificiais coloridos e o desempenho e sobrevivência de alevinos de Leporinus macrocephalus (Garavello & Britsky, 1988 Artificial colour haven evaluation, aveting and survival of Leporinus macrocephalus (Garavello & Britsky, 1988 fryes

    Directory of Open Access Journals (Sweden)

    Luciana Segura de Andrade

    2006-02-01

    Full Text Available O presente experimento foi realizado no Laboratório de Aqüicultura da Universidade Estadual de Maringá com o objetivo de avaliar o desempenho e a sobrevivência de alevinos de Leporinus macrocephalus alojados em aquários de vidro com capacidade para 12L, com ou sem refúgios artificiais de diferentes colorações. Foram utilizados 240 alevinos com peso inicial de 0,20 ± 0,06g por um período de 28 dias. Os animais foram distribuídos em um delineamento inteiramente casualizado com seis tratamentos (sem refúgio e com refúgios de cor verde, vermelha, azul, marrom e branca e quatro repetições. As variáveis analisadas foram peso, comprimento total, sobrevivência, fator de condição e uniformidade do lote. Ao fim do experimento, verificou-se que as variáveis peso, comprimento e fator de condição não diferiram entre os tratamentos com e sem refúgio. Houve maior índice de sobrevivência com a não utilização de refúgio e com refúgios de cor vermelha e verde (P Weight, length and survival of Leporinus macrocephalus fryes, grown in differently colored artificial havens, were evaluated at the Aquaculture Lab of the Universidade Estadual de Maringá. The experiment was done during 28 days with 240 piavuçu (Leporinus macrocephalus fryes with initial weight of 0.20±0.06g. The animals were distributed in a entirely randomized design with six treatments (without and green, red, blue, brown and white havens and four repetitions in 12L-glass aquaria. Final weight, total length, condition factor and uniformity were the analized variables. At the end of the experimental period, weight, lenght and condition factor were not affected by the treatment without or with haven color. Higher survival was observed in the treatments without haven and those with red and green havens (P<0.05 than in those with blue haven. The use of white haven provided more uniform lots (P<0.05 than brown and green havens. It is recomended the use of white or red

  7. Empirical Evaluation of a Model of Team Collaboration Using Selected Transcripts from September 11, 2001

    Science.gov (United States)

    2009-06-01

    working a tanker. TIE TIE TIE 703 Sergeant McCain: There is a bomb on board Boston - TKS TIE TIE 704 Male Speaker: Fuck . MISC MISC MISC 705...Yeah, I’m all right. I’m all right. I’m all right. MISC US MISC Send them to Bermuda. MISC US MISC Fuck them. MISC US MISC I... fuck . MISC US MISC Yeah, we’re working it. TIE TIE TIE 143 1113 Sergeant McCain: We’re working it. TIE TIE TIE 1114 Male Speaker: Here’s

  8. CrossRef and DOIs: New Developments

    Directory of Open Access Journals (Sweden)

    Ed Pentz

    2003-12-01

    Full Text Available Profound changes to scholarly communications have been taking place since the advent of the World Wide Web and changes are continuing. Publishers and librarians are facing a new generation of students, researchers and scientists. The Pew Internet and American Life Project The Internet goes to College (Jones, 2002found that 73% of students use the Internet more than the library for information searching. The Survey also revealed a danger for publishers of scholarly journals - that of losing readers. To quote from the survey: “Many students are likely to use information found on search engines and various Web sites as research material ... and faculty often report concerns about the number of URLs included in research paper bibliographies and the decrease in citations from traditional scholarly sources.” In order to counter these trends, publishers and librarians must work together to make it easy for users to access authoritative scholarly sources online. This can be difficult to do since users' expectations of online journals have increased dramatically over the last 8 years and continue to increase. For most users these days content must be online and it must be linked. If it's not linked, it doesn't exist. Linking on the web works very well in conjunction with traditional references in journals. The practice of citing other articles has been around since the first journals appeared in the 17th century and it's a crucial part of the scientific process. So naturally, with online journals there is immense value in users being able to go to a cited item with one or two clicks. Another important trend is the development of the article economy - journal issues are becoming less important. Most publishers now post articles online, “ahead of print”, without volume, issue and page number, and for many journals the e-article is the article “of record”. Because of this trend and the need for reference links, uniquely identifying each article, creating standardized metadata and creating a system to link references are of critical importance for publishers.

  9. ToxCast/ToxRefDB

    Data.gov (United States)

    U.S. Environmental Protection Agency — ToxCast is used as a cost-effective approach for efficiently prioritizing the toxicity testing of thousands of chemicals. It uses data from state-of-the-art high...

  10. Saksa politsei testib imerelva / ref. Aadu Hiietamm

    Index Scriptorium Estoniae

    2004-01-01

    Saksa politseinikud testivad relva (Air Taser), mis ei tapa, kuuli asemel tabab ohvrit elektrilöök. Seni pole Saksamaa politseijuhid elektripüstoli ametlikuks kasutusele võtuks veel luba andnud, USA-s on relv aga kasutusel

  11. sci edu-insa ias.pdf | misc docs | academy | Indian Academy of ...

    Indian Academy of Sciences (India)

    SPEAKER: Prof. Krishnaswamy Ravi-Chandar. VENUE: Faculty Hall, Indian Institute of Science. 23 February 2018 ǀ 1500. Event poster · Introducing: Summer Schools. Posted on 21 December 2017. ASTROPHYSICS: An Observational View of the Universe. Math Art and Design: MAD about Math, Math Education and ...

  12. Four-year-BS-position-paper.pdf | misc docs | academy | Indian ...

    Indian Academy of Sciences (India)

    error. The page your are looking for can not be found! Please check the link or use the navigation bar at the top. YouTube; Twitter; Facebook; Blog. Academy News. IAS Logo. Theory Of Evolution. Posted on 23 January 2018. Joint Statement by the Three Science Academies of India on the teaching of the theory of evolution

  13. Telementoring: use of augmented reality in orthopaedic education: AAOS exhibit selection.

    Science.gov (United States)

    Ponce, Brent A; Jennings, Jonathan K; Clay, Terry B; May, Mathew B; Huisingh, Carrie; Sheppard, Evan D

    2014-05-21

    Virtual interactive presence (VIP) is a new technology that allows an individual to deliver real-time virtual assistance to another geographically remote individual via a standard Internet connection. The objectives of this pilot study were to evaluate the efficiency and performance of a VIP system implemented in an operating room setting, determine the potential utility of the system for guidance of surgical procedures, and assess the safety of the system. Following institutional review board approval, fifteen patients underwent arthroscopic shoulder procedures. Two VIP stations were used, one in the operating room and the other in an adjoining dictation room. The attending surgeon proctored operating resident surgeons from the dictation room until his physical presence was required in the operating room. Following each procedure, the attending surgeon, resident surgeons, and three surgical staff members completed a Likert-scale questionnaire regarding the educational utility, efficiency of use, and safety of the system. The operative time was also compared with historical data. Both attending and resident surgeons assigned a favorable rating to the utility of the VIP to highlight anatomy and provide feedback to the resident (p > 0.05 for the difference). Both groups agreed that the system was easy to use and that safety was not compromised (p > 0.05). The majority of resident and attending surgeon responses indicated no perceptible lag between motions (95% and 100%, respectively; p > 0.99) and no interference of the VIP system with the surgical procedure (85% and 100%, respectively; p = 0.24). The mean operative times with and without VIP use did not differ significantly for rotator cuff repair (p = 0.90) or for treatment of instability (p = 0.57). This pilot study revealed that the VIP technology was efficient, safe, and effective as a teaching tool. The attending and resident surgeons agreed that training was enhanced, and this occurred without increasing operative times. Furthermore, the attending surgeon believed that this technology improved teaching effectiveness. These results are promising, and further objective quantification is warranted.

  14. An Evaluation of Industry Relationships Among Contributors to AAOS Clinical Practice Guidelines and Appropriate Use Criteria.

    Science.gov (United States)

    Checketts, Jake X; Cook, Courtney; Vassar, Matt

    2018-01-17

    A long-standing relationship between orthopaedic surgeons and industry has made financial conflicts of interest a concerning issue. Research supports that financial conflicts of interest can influence both medical research and clinical practice. Financial conflicts of interest may also influence clinical practice guideline recommendations and their corresponding appropriate use criteria. Because of the influential nature of these guidelines, it is imperative that care be taken to minimize bias during guideline development. We retrieved clinical practice guidelines and their corresponding appropriate use criteria from the American Academy of Orthopaedic Surgery that were published or revised between 2013 and 2016. We extracted industry payments received by physicians using the Centers for Medicare & Medicaid Services Open Payments database. We then evaluated the value and types of these payments. We also used these data to determine whether disclosure statements were accurate and whether guideline development was in adherence with the Institute of Medicine's (IOM's) standards. Of the 106 physicians that were evaluated, 85 (80%) received at least 1 industry payment, 56 (53%) accepted >$1,000, and 35 (33%) accepted >$10,000. Financial payments amounted to a mean of $93,512 per physician. Total reimbursement for the 85 clinical practice guideline and appropriate use criteria contributors was $9,912,309. We found that disclosure statements disagreed with the Open Payments data and that the IOM standards were not completely enforced. Clinical practice guideline and appropriate use criteria contributors received substantial payments from industry, many disclosure statements were inaccurate, and the IOM standards were not completely met. Clinical practice guidelines and appropriate use criteria are critical for practicing evidence-based medicine. If financial conflicts of interest are present during their development, it is possible that patient care may be compromised.

  15. The new MQ/AAO/Strasbourg multi-wavelength and spectroscopic PNe database: MASPN

    Science.gov (United States)

    Parker, Quentin Andrew; Bojicic, Ivan; Frew, David; Acker, Agnes; Ochsenbein, Francois; MASPN Database Team

    2015-01-01

    We are in a new golden age of PN discovery. This is thanks in particular to high sensitivity, wide-field, narrow-band surveys of the Galactic plane undertaken on the UKST in Australia and the Isaac Newton telescope on La Palma. Together these telescopes and their H-alpha surveys have provided very significant Planetary Nebulae (PNe) discoveries that have more than doubled the totals accrued by all telescopes over the previous 250 years. However, these PNe are not simply more of the same found in previous catalogues. Most new PNe are more obscured, evolved and of lower surface brightness than previous compilations while others are faint but compact and more distant. This has required an extensive and time-consuming programme of spectroscopic confirmation on a variety of 2m and 4m telescopes that is now largely complete. The scope of any future large-scale PNe studies, particularly those of a statistical nature or undertaken to understand true PNe diversity and evolution should now reflect this fresh PN population landscape of the combined sample of ~3500 Galactic PNe now available. Such studies should be coloured and nuanced by these recent major discoveries and the massive, high sensitivity, high resolution, multi-wavelength imaging surveys now available across much of the electromagnetic spectrum.Following this motivation we provide, for the first time, an accessible, reliable, on-line "one-stop" SQL database for essential, up-to date information for all known Galactic PN. We have attempted to: i) Reliably remove the many PN mimics/false ID's that have biased previous compilations and subsequent studies; ii) Provide accurate, updated positions, sizes, morphologies, radial velocities, fluxes, multi-wavelength imagery and spectroscopy; iii) Link to CDS/Vizier and hence provide archival history for each object; iv) Provide an interface to sift, select, browse, collate, investigate, download and visualise the complete currently known Galactic PNe diaspora and v) provide the community with the most complete and reliable data with which to undertake new science.

  16. Pelvic Fixation in Adult and Pediatric Spine Surgery: Historical Perspective, Indications, and Techniques: AAOS Exhibit Selection.

    Science.gov (United States)

    Jain, Amit; Hassanzadeh, Hamid; Strike, Sophia A; Menga, Emmanuel N; Sponseller, Paul D; Kebaish, Khaled M

    2015-09-16

    Achieving solid osseous fusion across the lumbosacral junction has historically been, and continues to be, a challenge in spine surgery. Robust pelvic fixation plays an integral role in achieving this goal. The goals of this review are to describe the history of and indications for spinopelvic fixation, examine conventional spinopelvic fixation techniques, and review the newer S2-alar-iliac technique and its outcomes in adult and pediatric patients with spinal deformity. Since the introduction of Harrington rods in the 1960s, spinal instrumentation has evolved substantially. Indications for spinopelvic fixation as a means to achieve lumbosacral arthrodesis include a long arthrodesis (five or more vertebral levels) or use of three-column osteotomies in the lower thoracic or lumbar spine, surgical treatment of high-grade spondylolisthesis, and correction of lumbar deformity and pelvic obliquity. A variety of techniques have been described over the years, including Galveston iliac rods, Jackson intrasacral rods, the Kostuik transiliac bar, iliac screws, and S2-alar-iliac screws. Modern iliac screws and S2-alar-iliac screws are associated with relatively low rates of pseudarthrosis. S2-alar-iliac screws have the advantages of less implant prominence and inline placement with proximal spinal anchors. Collectively, these techniques provide powerful methods for obtaining control of the pelvis in facilitating lumbosacral arthrodesis. Copyright © 2015 by The Journal of Bone and Joint Surgery, Incorporated.

  17. Taiwanese Grade-Five Students Reading a Chinese Science Text of Mixed Sub-Genres: A Misce Analysis Study

    Science.gov (United States)

    Hung, Yueh-Nu

    2015-01-01

    This study aimed to understand Taiwanese grade-five students' reading of a science text with mixed sub-genres based on their oral reading miscues. Twenty students participated in the study. Each of the one-on-one interviews started with a reader profile interview followed by oral reading of a Chinese science text and retelling. Miscue data were…

  18. Carbon Monitoring System Flux for Shipping, Aviation, and Chemical Sources L4 V1 (CMSFluxMISC) at GES DISC

    Data.gov (United States)

    National Aeronautics and Space Administration — This dataset provides the Carbon Flux for Shipping, Aviation, and Chemical Sources. The NASA Carbon Monitoring System (CMS) is designed to make significant...

  19. WAft GRAVES REf.ISTERS., MONIJMENTS., HEADSTONES AND f ...

    African Journals Online (AJOL)

    Introduction. The study of warfare, military matters and battles has a great romantic appeal and in recent years has attracted a great deal of public interest. Evidence of this is seen in the growth of military museums or the military sections of museums, the large number of books on military matters which are published and the.

  20. CrossRef The CERN Axion Solar Telescope

    CERN Document Server

    Hasinoff, M D; Arik, E; Autiero, D; Avignone, F; Barth, K; Bingol, E; Brauninger, H; Brodzinski, R; Carmona, J; Chesi, E; Cebrian, S; Cetin, S; Collar, J; Creswick, R; Dafni, T; De Oliveira, R; Dedoussis, S; Delbart, A; Di Lella, L; Eleftheriadis, C; Fanourakis, G; Farach, H; Fischer, H; Formenti, F; Geralis, T; Giomataris, I; Gninenko, S; Goloubev, N; Hartmann, R; Hoffmann, D; Irastorza, I G; Jacoby, J; Kang, D; Konigsmann, K; Kotthaus, R; Krcmar, M; Kuster, M; Lakic, B; Liolios, A; LJubicic, A; Lutz, G; Luzon, G; Miley, H; Morales, A; Morales, J; Mutterer, M; Nikolaidis, A; Ortiz, A; Papaevangelou, T; Placci, A; Raffelt, G; Riege, H; Sarsa, M; Savvidis, I; Schopper, R; Semertzidis, I; Spano, C; Villar, J; Vullierme, B; Walckiers, L; Zachariadou, K; Zioutas, K

    2003-01-01

    The CAST experiment at CERN is using a decommissioned LHC prototype magnet to search for solar axions through their Primakoff conversion into x-ray photons. The magnet (B = 9.0 Tesla, L = 10 m) can track the sun each day for a total exposure time of ~180 minutes (sunrise + sunset). We expect to reach a sensitivity in axion-photon coupling, gaγγ ≲ 5 × 10-11 GeV-1 for ma ≲ 10-2 eV after ˜1 year's running time. By filling the beam tube with 4He or 3He gas we should be able to extend the sensitive axion mass region into the eV mass range.

  1. CrossRef Neutrino factory proton driver and target design

    CERN Document Server

    Garoby, Roland; Thomason, John; Davenne, Tristan; Caretta, Ottone; Back, John J

    2016-01-01

    Neutrinos are very elusive particles belonging to the lepton family. They exist in different types corresponding to the different charged leptons, namely electrons, muons and taus. Contrary to electrons, neutrinos hardly interact with matter which makes them very difficult to detect and study. To the best of today’s knowledge, neutrinos have hardly any mass and they can change from one type to another (so-called “neutrino oscillation”). Most physicists think that this oscillation occurs because neutrinos have mass. A Neutrino Factory [1] is a special facility producing a large amount of neutrinos every year (typically 10$^{21}$ neutrinos/year). Its main purpose is to study the change of type of neutrinos between the place where they are generated and a remote location. In a Neutrino Factory, neutrinos result from the decay of muons, unstable particles with a mean lifetime of 2.2 $\\mu$s in their rest frame. Sharp beams of high energy neutrinos are obtained at the end of the long straight sections of a mu...

  2. Sõda vangidega : iraaklaste piinajad astusid kohtu ette / ref. Virgo Kruve

    Index Scriptorium Estoniae

    2004-01-01

    USA sõjatribunal mõistis Abu Ghraibi vanglas Iraagi vange ahistanud sõjaväelase Jeremy Sivitsi aastaks vangi. Teistest kohtualustest. Väljavõtteid USA Senatile tutvustatud salaraportist, mis keskendus Abu Ghraibi vanglale ja sõjaväepolitsei tegevusele

  3. Making REF is Making Politics: Memories of an Editorial Metamorphosis

    Directory of Open Access Journals (Sweden)

    Luzinete Simões Minella

    2008-01-01

    Full Text Available This article focuses on the new editorial model launched in Revista Estudos Feministas in 2002, that is, three years after its installation in Universidade Federal de Santa Catarina (UFSC. While firstly detailing the memories of such metamorphosis, the text refers to the transitions of REF’s editorship format, to the purposes and criteria of the new structure, as well as the meanings of the team expansion in relation to some national and international feminist publications. Eventually the article briefly discusses the advantages and challenges implicated in this new editorial policy.

  4. Sõrmuste isand. Sünopsis / ref. Erkki Luuk

    Index Scriptorium Estoniae

    2003-01-01

    J.R.R. Tolkieni "Sõrmuste isanda" järgi loodud Peter Jacksoni kaks filmi - "Sõrmuste isand : Sõrmuste vennaskond" ("The Lord of the Rings : The Fellowship of the Ring") ja "Kaks kantsi" ("The Lord of the Rings : The Two Towers"). Ekraniseeringute lühitutvustus ning operaatori Andrew Lesnie ja režissööri raskustest teose ekraniseerimisel

  5. Venus Express uurib Maa kurja kaksikut / ref. Triin Thalheim

    Index Scriptorium Estoniae

    2005-01-01

    9. novembril startis Baikonuri kosmodroomilt Veenusele Euroopa Kosmoseagentuuri sond Venus Express, mis peaks planeedi atmosfääri sisenema aprillis. Teadlaste sõnul peab sondi saadetav info aitama mõista naaberplaneedi kliimat ja atmosfääri ning tooma selgust, kas Maa võib kunagi Veenuse sarnaseks muutuda. Lisaks joonis: Venus Express

  6. NCBI nr-aa BLAST: CBRC-TTRU-01-0641 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0641 ref|NP_782112.1| membrane spanning protein [Clostridium tetani E8...8] gb|AAO36049.1| membrane spanning protein [Clostridium tetani E88] NP_782112.1 0.013 25% ...

  7. NCBI nr-aa BLAST: CBRC-TTRU-01-0750 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0750 ref|NP_782112.1| membrane spanning protein [Clostridium tetani E8...8] gb|AAO36049.1| membrane spanning protein [Clostridium tetani E88] NP_782112.1 0.020 21% ...

  8. NCBI nr-aa BLAST: CBRC-TTRU-01-0941 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0941 ref|NP_782112.1| membrane spanning protein [Clostridium tetani E8...8] gb|AAO36049.1| membrane spanning protein [Clostridium tetani E88] NP_782112.1 0.030 26% ...

  9. NCBI nr-aa BLAST: CBRC-TTRU-01-0333 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0333 ref|NP_782112.1| membrane spanning protein [Clostridium tetani E8...8] gb|AAO36049.1| membrane spanning protein [Clostridium tetani E88] NP_782112.1 0.022 24% ...

  10. NCBI nr-aa BLAST: CBRC-TTRU-01-0482 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0482 ref|NP_782112.1| membrane spanning protein [Clostridium tetani E8...8] gb|AAO36049.1| membrane spanning protein [Clostridium tetani E88] NP_782112.1 0.013 27% ...

  11. ORF Alignment: NC_004578 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004578 gi|28870083 >1vm9A 1 108 6 116 3e-17 ... ref|NP_792702.1| vanillate O-demet...hylase, oxygenase subunit [Pseudomonas syringae ... pv. tomato str. DC3000] gb|AAO56397.1| vanillate

  12. ORF Alignment: NC_004461 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004461 gi|27467672 >1pwgA 4 344 72 389 1e-36 ... ref|NP_764309.1| autolysis and me...thicillin resistant-related protein [Staphylococcus ... epidermidis ATCC 12228] gb|AAO04351.1| autolysis

  13. ORF Alignment: NC_003071 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003071 gi|18398317 >1e0gA 4 45 339 382 4e-05 ... ref|NP_814147.1| endolysin, putat...ive [Enterococcus faecalis V583] gb|AAO80218.1| ... endolysin, putative [Enterococcus faecalis V583

  14. ORF Alignment: NC_004668 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004668 gi|29376513 >1e0gA 4 45 319 362 2e-04 ... ref|NP_815667.1| endolysin [Enter...ococcus faecalis V583] gb|AAO81737.1| endolysin ... [Enterococcus faecalis V583] ... Length = 4

  15. ORF Alignment: NC_004668 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004668 gi|29374994 >1e0gA 4 45 339 382 4e-05 ... ref|NP_814147.1| endolysin, putat...ive [Enterococcus faecalis V583] gb|AAO80218.1| ... endolysin, putative [Enterococcus faecalis V583

  16. ORF Alignment: NC_004668 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004668 gi|29377273 >1e0gA 3 45 338 382 3e-05 ... ref|NP_816427.1| endolysin [Enter...ococcus faecalis V583] gb|AAO82497.1| endolysin ... [Enterococcus faecalis V583] ... Length = 4

  17. ORF Alignment: NC_004578 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004578 gi|28871348 >1dlwA 1 114 25 138 3e-25 ... ref|NP_793967.1| protozoan/cyanob...acterial globin family protein [Pseudomonas ... syringae pv. tomato str. DC3000] gb|AAO57662.1| ... protozoa

  18. ORF Alignment: NC_004565 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004565 gi|28373188 >1epwA 1 1289 2 1313 0.0 ... ref|NP_783831.1| tetanus toxin tet...X [Clostridium tetani] emb|CAA28033.1| tetanus toxin ... precursor (AA 1-1315) [Clostridium tetani] ... ... emb|CAA29564.1| unnamed protein product [Clostridium ... tetani] gb|AAO37454.1| tetanus

  19. ORF Alignment: NC_004461 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004461 gi|27467238 >1kolA 35 391 30 342 2e-04 ... ref|NP_763875.1| xylitol dehydro...genase [Staphylococcus epidermidis ATCC 12228] ... gb|AAO03917.1| xylitol dehydrogenase [Staphylococc

  20. Experimental investigation on the bi-directional growing mechanism of the foils laminate approach in AAO fabrication

    Directory of Open Access Journals (Sweden)

    Chien Ming-Chun

    2006-01-01

    Full Text Available AbstractThe foils laminate approach can be implemented to grow bi-directional porous pattern from both the top and bottom surfaces of an aluminum foil. It was intuitively inferred that leakage of etchant from the clamped area can be a feasible cause to have the upward pores grow in the notches of the unpolished surface. This leakage hypothesis has been disproved by the leakage blocking and triple layers laminate experiments. It is further inferred that the non-uniformity of the thickness or material properties of the aluminum foil causes non-uniformed anodization rate along the sample surface. The fast oxidized areas create a pathway for leakage such that a shorter porous array from the back side is observed. Experiments with the process time being reduced by two hours validate this inference

  1. Histologic, serologic, and tribologic findings in failed metal-on-metal total hip arthroplasty: AAOS exhibit selection.

    Science.gov (United States)

    Pelt, Christopher E; Erickson, Jill; Clarke, Ian; Donaldson, Thomas; Layfield, Lester; Peters, Christopher L

    2013-11-06

    Despite multiple changes in second-generation metal-on-metal hip implants, greater-than-expected revision rates have led to alarm. We hypothesized that the finding of intraoperative metallosis would be associated with a high metal load on histologic analysis and that both would be associated with increased wear, greater serum metal ion levels, and predictable biologic responses in the histologic sections. We evaluated the implant positioning, serum ion levels, intraoperative findings of metallosis, wear characteristics of retrieved implants (tribology), histology, and outcomes in a series of eighteen large-diameter metal-on-metal total hip arthroplasties. The arthroplasties were divided into two groups on the basis of the intraoperative finding of metallosis and into two groups on the basis of the metal load score. Intraoperative metallosis was not associated with a high metal load score (p = 0.15). The finding of intraoperative metallosis was associated with greater serum metal ion levels, greater wear rates, and greater complication rates. Aseptic lymphocyte-dominated vasculitis-associated lesion (ALVAL) scores were similar between the metallosis and non-metallosis groups (p = 0.49) as well as between the high and low-metal-load groups (p = 0.56).

  2. Anticipation or ascertainment bias in schizophrenia? Penrose`s familial mental illness sample

    Energy Technology Data Exchange (ETDEWEB)

    Bassett, A.S. [Univ. of Toronto (Canada)]|[Queen Street Mental health Centre, Toronto (Canada); Husted, J. [Univ. of Waterloo, Ontario (Canada)

    1997-03-01

    Several studies have observed anticipation (earlier age at onset [AAO] in successive generations) in familial schizophrenia. However, whether true anticipation or ascertainment bias is the principal originating mechanism remains unclear. In 1944 L.S. Penrose collected AAO data on a large, representative sample of familial mental illness, using a broad ascertainment strategy. These data allowed examination of anticipation and ascertainment biases in five two-generation samples of affected relative pairs. The median intergenerational difference (MID) in AAO was used to assess anticipation. Results showed significant anticipation in parent-offspring pairs with schizophrenia (n = 137 pairs; MID 15 years; P = .0001) and in a positive control sample with Huntington disease (n = 11; P = .01). Broadening the diagnosis of the schizophrenia sample suggested anticipation of severity of illness. However, other analyses provided evidence for ascertainment bias, especially in later-AAO parents, in parent-offspring pairs. Aunt/uncle-niece/nephew schizophrenia pairs showed anticipation (n = 111; P = .0001), but the MID was 8 years and aunts/uncles had earlier median AAO than parents. Anticipation effects were greatest in pairs with late-AAO parents but remained significant in a subgroup of schizophrenia pairs with early parental AAO (n = 31; P = .03). A small control sample of other diseases had MID of 5 years but no significant anticipation (n = 9; F = .38). These results suggest that, although ascertainment-bias effects were observed in parent-offspring pairs, true anticipation appears to be inherent in the transmission of familial schizophrenia. The findings support investigations of unstable mutations and other mechanisms that may contribute to true anticipation in schizophrenia. 37 refs., 2 tabs.

  3. Efeito da cor e da presença de refúgio artificial sobre o desenvolvimento e sobrevivência de alevinos de Oreochromis niloticus (Linnaeus, 1758 - DOI: 10.4025/actascibiolsci.v26i1.1659 Effect of colour and presence of artificial haven on the development and survival of Oreochromis niloticus (Linnaeus, 1758 fry - DOI: 10.4025/actascibiolsci.v26i1.1659

    Directory of Open Access Journals (Sweden)

    Carmino Hayashi

    2004-04-01

    Full Text Available Com o objetivo de avaliar o desenvolvimento e a sobrevivência de alevinos revertidos de tilápias do Nilo (Oreochromis niloticus, cultivados sob condições de refúgios artificiais de diferentes colorações, realizou-se o presente trabalho, durante 28 dias, utilizando 240 alevinos de tilápia do Nilo com peso inicial médio de 0,51g ± 0,11g. Os animais foram distribuídos em 24 aquários com capacidade para 50L, em um delineamento experimental inteiramente casualizado, com 6 tratamentos (sem refúgios e com refúgios nas cores branca, azul, marrom, vermelho e verde e 4 repetições. Ao final do período experimental, foram analisadas as variáveis biomassa total média, fator de condição, uniformidade do lote e de sobrevivência. Observou-se que a uniformidade de peso e comprimento e o fator de condição foram influenciados pelas cores dos tratamentos, sendo que o tratamento com refúgio azul apresentou maior uniformidade. Concluiu-se, portanto, que a presença e a coloração do refúgio influenciam em parte do desenvolvimento de tilápias do NiloThe development and survival of sexually-reverted Nile tilapias (Oreochromis niloticus fry, bred in artificial havens of different colors, are provided. Research was carried out during 28 days, with 240 fry of the Nile tilapia, initial average weight 0.51 ± 0.11g. Animals were distributed in 24 50L-aquariums, in a randomized experimental design in six treatments (haven-less and havens in white, blue, brown, red and green and four replications. At the end of the experimental period, variable total biomass, condition factor, lot uniformity and survival were analyzed. Weight and length uniformity and factor of condition were affected by the colors of the treatments. Blue treatment had the best uniformity. Factor of condition was best in treatments with brown, red, blue and white havens. Actually they differed significantly from control and green treatments. It may be concluded that presence and

  4. Comparação do teor de taninos entre duas espécies de espinheira-santa (Maytenus aquifolium Mart.e Maytenus ilicifolia Mart. ex Reissekcultivadas no Horto Medicinal do Refúgio Biológico Bela Vista - RBBV da Itaipu Binacional - Foz do Iguaçu, PR - Brasil.

    Directory of Open Access Journals (Sweden)

    P.R. HOLNIK

    2015-09-01

    Full Text Available RESUMO As duas espécies de espinheira-santa Maytenus aquifolium Mart. e Maytenus ilicifolia Mart. ex Reissek pertencentes à família Celastraceae e têm sido intensamente exploradas nas populações nativas devido seu alto valor medicinal. O grande interesse pela espinheira-santa é para o tratamento de gastrites, úlceras gástricas e duodenais. O efeito antiulcerogênico está relacionado com a presença de polifenóis totais, mais especificamente com os taninos. Este trabalho teve como objetivo comparar o teor de taninos entre essas duas espécies cultivadas no Horto Medicinal do Refúgio Biológico Bela Vista - RBBV da Itaipu Binacional no município de Foz do Iguaçu, PR - Brasil. Foram realizadas duas coletas com intervalo de um mês para cada espécie e para a quantificação foi realizada a análise por espectrofotometria segundo a Farmacopeia Brasileira V. Os resultados foram analisados através do teste de variância (ANOVA e a diferença no teor de taninos foi evidenciada pelo teste Tukey, a 5% de nível de significância empregando-se o software SISVAR. Foram obtidos em média 0,61% para o lote 1 e 2 de Maytenus aquifolium e (3,90% para Maytenus ilicifolia, resultando em uma média de 84,35% de taninos a mais para Maytenus ilicifolia em comparação com Maytenus aquifolium concluindo assim que as espécies não devem ser intercambiáveis.

  5. Direitos Humanos, migração e refúgio: Temas pertinentes para a profissão de Serviço Social (Human Rights, Migration and Refuge... Doi: 10.5212/Emancipacao.v.16i1.0002

    Directory of Open Access Journals (Sweden)

    Lisarb Valéria Montes D'Oco

    2016-12-01

    Full Text Available Resumo: Este artigo tem como mote principal abordar as temáticas de direitos humanos, migração e refúgio e a sua relação com o Serviço Social. Elucidam-se a concepção de direitos humanos, de uma perspectiva histórica internacional, até os dias atuais, no Brasil e a relação dessa temática com os movimentos sociais, as legislações nacionais e internacionais e as políticas de direitos humanos no País. Posteriormente, situa-se o Serviço Social nessa temática, quanto às lutas pela sua defesa, à formação profissional e à produção teórica da categoria profissional. Pretende-se colaborar para a difusão dos direitos humanos como uma diretriz do trabalho dos profissionais do Serviço Social.Palavras-chave: Direitos Humanos. Migração. Serviço Social.Abstract: This article’s main theme addresses the issue of human rights, migration and refugee and their relation to social work. It elucidates the conception of human rights from an international and historical perspective until the present day in Brazil. It also clarifies the relation of this subject to social movements, national and international laws and human rights policies within Brazil. After that it contextualizes the social work in this subject, for the struggle for its defense, the professional formation and the theoretical production in the professional category. The article intended to cooperate in the dissemination of human rights as a guideline for the work of professional social workers.Keywords: Human Rights. Migration. Social Work.

  6. Technology Insertion (TI)/Industrial Process Improvement (IPI). Task Order no. 1 (Misc Manufacturing). Book 1. Database Documentation Book for OO-ALC MANPWW (Overview Layouts)

    Science.gov (United States)

    1989-12-15

    30󈧈 U0 ai 14 b4t mm Li=3 " 0 I 00 L40 8 to C 90 0cc0 0 00anOm 0 000000313 gb1 A 1. 1- 1.-.. In j u~l K -I - I IC W ta l- Pti00 00 a’ 3 0: at9 Us I4...OW-ORGN RCC-RE INSTR SK DUE-DATE CUST-ACCT-CDE JU7440 0# 3 O i** 1 SW CRiU FLAW. SMAY BOOT* 007440 02340 180 511 SW CRNR FLAME SPRAY BOOTH MADP 8/30...89 007440 00005 180 511 SW CRNR FLAME SPRAY BOOTH _ L19101 37 48w9 MANkWI MADPD 8/31/89 007440 02000 365 511 SW CRNR FLAME SPRAY BOOTH 0T7-I l/17/d

  7. ORF Alignment: NC_002976 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002976 gi|57867327 >1vpmA 2 152 7 157 1e-33 ... ref|NP_765118.1| hypothetical protein SE1563 [Stap... thioester ... hydrolase family protein [Staphylococcus epidermidis ... RP62A] gb|AAW54773.1| ...cytosolic long-chain acyl-CoA ... thioester hydrolase family protein [Stap...hylococcus ... epidermidis RP62A] gb|AAO05162.1| conserved hypothetical ... protein [Staphyloc...GNPVVTASTDSV Sbjct: 1 ... KSKKMSDAKCIKTRQVYPQDTNHHHTMFGGTLMANIDEIAAITAMKHAGNPVVTASTDSV 60 ... Query: 127 PTSVPDVEPETSVEKWFHETAP

  8. ORF Alignment: NC_004461 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004461 gi|27468481 >1vpmA 2 152 7 157 1e-33 ... ref|NP_765118.1| hypothetical protein SE1563 [Stap... thioester ... hydrolase family protein [Staphylococcus epidermidis ... RP62A] gb|AAW54773.1| ...cytosolic long-chain acyl-CoA ... thioester hydrolase family protein [Stap...hylococcus ... epidermidis RP62A] gb|AAO05162.1| conserved hypothetical ... protein [Staphyloc...GNPVVTASTDSV Sbjct: 1 ... KSKKMSDAKCIKTRQVYPQDTNHHHTMFGGTLMANIDEIAAITAMKHAGNPVVTASTDSV 60 ... Query: 127 PTSVPDVEPETSVEKWFHETAP

  9. Classification of Floating Chris Chemicals for the Development of a Spill Response Manual

    Science.gov (United States)

    1989-01-01

    is provided by gelling incoming spills since gelled materials do rot readily soak into the sand. An investigation conducted by Nichalovic et al. (1977...CLARIFIED OIL, MISC: CASHEW NUT SHELL (UNTREATED) OIL, MISC: CROTON OIL, EDIBLE: COTTONSEED OIL, MISC: COAL TAR OIL: DIESEL OCTYL EPOXY TALLATE OIL, FUEL

  10. ORF Alignment: NC_003197 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003197 gi|16767227 >1qd6C 1 240 50 289 e-101 ... ref|YP_152886.1| detergent-resist...erovar Typhi Ty2] ... ref|NP_457794.1| detergent-resistant phospholipase A... ... [Salmonella enterica subsp. enterica serovar Typhi str. ... CT18] gb|AAV79574.1| detergent...la typhimurium LT2] ... gb|AAO70868.1| detergent-resistant phospholipase A ... [Salmonella ent...erica subsp. enterica serovar Typhi Ty2] ... emb|CAD07935.1| detergent-resistant phospholipase A ...

  11. ORF Alignment: NC_004631 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004631 gi|29143666 >1qd6C 1 240 50 289 e-101 ... ref|YP_152886.1| detergent-resist...erovar Typhi Ty2] ... ref|NP_457794.1| detergent-resistant phospholipase A... ... [Salmonella enterica subsp. enterica serovar Typhi str. ... CT18] gb|AAV79574.1| detergent...la typhimurium LT2] ... gb|AAO70868.1| detergent-resistant phospholipase A ... [Salmonella ent...erica subsp. enterica serovar Typhi Ty2] ... emb|CAD07935.1| detergent-resistant phospholipase A ...

  12. ORF Alignment: NC_003198 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003198 gi|16762177 >1qd6C 1 240 50 289 e-101 ... ref|YP_152886.1| detergent-resist...erovar Typhi Ty2] ... ref|NP_457794.1| detergent-resistant phospholipase A... ... [Salmonella enterica subsp. enterica serovar Typhi str. ... CT18] gb|AAV79574.1| detergent...la typhimurium LT2] ... gb|AAO70868.1| detergent-resistant phospholipase A ... [Salmonella ent...erica subsp. enterica serovar Typhi Ty2] ... emb|CAD07935.1| detergent-resistant phospholipase A ...

  13. ORF Alignment: NC_006511 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_006511 gi|56415811 >1qd6C 1 240 50 289 e-101 ... ref|YP_152886.1| detergent-resist...erovar Typhi Ty2] ... ref|NP_457794.1| detergent-resistant phospholipase A... ... [Salmonella enterica subsp. enterica serovar Typhi str. ... CT18] gb|AAV79574.1| detergent...la typhimurium LT2] ... gb|AAO70868.1| detergent-resistant phospholipase A ... [Salmonella ent...erica subsp. enterica serovar Typhi Ty2] ... emb|CAD07935.1| detergent-resistant phospholipase A ...

  14. NCBI nr-aa BLAST: CBRC-DNOV-01-0482 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DNOV-01-0482 gb|AAO66447.1| CXCR4 [Macaca fascicularis] gb|AAO66448.1| CXCR4 [Macaca fasci...cularis] gb|AAO66449.1| CXCR4 [Macaca fascicularis] gb|AAO66450.1| CXCR4 [Macaca fascicularis] AAO66447.1 8e-54 71% ...

  15. CrossRef A study of upward going particles with the Extreme Energy Events telescopes

    CERN Document Server

    Abbrescia, M; Baldini, L; Ferroli, R Baldini; Batignani, G; Bencivenni, G; Bossini, E; Chiavassa, A; Cicalo, C; Cifarelli, L; Coccia, E; Corvaglia, A; De Gruttola, D; De Pasquale, S; Di Giovanni, A; D׳Incecco, M; Dreucci, M; Fabbri, F L; Fattibene, E; Ferraro, A; Forster, R; Frolov, V; Galeotti, P; Garbini, M; Gemme, G; Gnesi, I; Grazzi, S; Gustavino, C; Hatzifotiadu, D; La Rocca, P; Maggiora, A; Maron, G; Mazziotta, M N; Miozzi, S; Nania, R; Noferini, F; Nozzoli, F; Panareo, M; Panetta, M P; Paoletti, R; Perasso, L; Pilo, F; Piragino, G; Riggi, F; Righini, G C; Rodriguez, A R; Sartorelli, G; Scapparone, E; Schioppa, M; Scribano, A; Selvi, M; Serci, S; Siddi, E; Squarcia, S; Stori, L; Taiuti, M; Terreni, G; Vistoli, M C; Votano, L; Williams, M C S; Zani, S; Zichichi, A; Zuyeuski, R

    2016-01-01

    In this paper the first study of the upward going events detected by the telescopes of the Extreme Energy Event (EEE) project is reported. The EEE project consists of a detector array of Multigap Resistive Plate Chambers located at selected sites on the Italian territory. During autumn 2014 the first coordinated data taking period took place and around one billion candidate tracks were collected. Among them, of particular interest is the sample of particles which cross the telescopes from below. The results obtained demonstrate that the EEE telescopes can distinguish the electrons produced as decay products of cosmic muons stopped in the ground, or in the last chamber of the telescopes themselves, confirming the excellent performance of the system for the investigation of intriguing cosmic phenomena.

  16. Overcoming Drug Resistant Prostate Cancer with APE1/Ref 1 Blockade

    Science.gov (United States)

    2016-10-01

    were washed six times with PBS-Tween, blots were incubated with donkey anti- body against rabbit immunoglobulin G conjugated to horseradish peroxidase...formation of autophagosomes for cell protein digestion during stress . Cells in autophagy can either use the digested material for survival, or they...can be entered into the apoptotic cascade if the stress time period endures. During the induction of autophagy, the normally 730 McIlwain et al. The

  17. Kapital ja sotsiaalsed vajadused / Robin Blackburn ; ref. Valle-Sten Maiste

    Index Scriptorium Estoniae

    Blackburn, Robin

    2006-01-01

    Autori väitel püüdleb EL vaid siseturu laiendamise poole, pakkumata sotsiaalset turvalisust ja maksude ühtlustamist. Euroopa vajab märgatavalt efektiivsemaid korporatsioonide maksustamise viise, millele järgneks sotsiaalsete fondide võrgustiku rajamine. Sotsiaalsete fondide kaudu ei jaotataks ainult rikkust ümber, vaid investeeritaks ka loodus- ja tööskeskkonda. Vt. samas ka Valle-Sten Maiste art. "Naabrist rohkem pappi"

  18. The Rocket Electric Field Sounding (REFS) Program: Prototype Design and Successful First Launch

    Science.gov (United States)

    1992-01-15

    feedback loop of the first operational amplifier ( opamp ) charges up to a voltage that is proportional to the charge induced on the stator by the electric...field incident upon it. The 33 MOhm resistor in the feedback loop is there to provide bias current for the opamp . The resistor and capacitor pair must...0 to 15 PSI. It produces a change in bridge resistance that is proportional to pressure. 15 U00 x0 a r - 1S h 4. I S K I. S S : IN U if S 4 - I

  19. Synthetic sorbents for removal of sulfur dioxide in fluidized-bed coal combustors. [25 refs

    Energy Technology Data Exchange (ETDEWEB)

    Snyder, R.B.; Wilson, W.I.; Johnson, I.; Jonke, A.A.

    1977-06-01

    Synthetic sorbents have been investigated for use in place of limestone for SO/sub 2/ emission control in fluidized-bed coal combustors. Sorbents prepared by impregnation of porous alumina with alkali metal or alkaline earth oxides were studied. The most promising sorbent was found to be calcium oxide in alumina. However, the SO/sub 2/ reactivity of this synthetic sorbent was less than that for a moderately reactive limestone. Hence, a greater quantity of synthetic sorbent would be needed to meet SO/sub 2/ emission standards. The attrition resistance of this synthetic sorbent was found to be greater than that of natural stones; therefore, a larger number of cycles of use would be expected. It is estimated that the use of this synthetic sorbent would reduce the amount of waste sorbent to about one-sixth the amount expected using a moderately reactive once-through limestone. The cost of using this synthetic sorbent is estimated to be about three and a half times the cost expected using once-through limestone. This cost is considered to be too large in view of the expected modest decrease in environmental impact. The synthetic sorbents developed in this study are therefore not considered viable alternatives for limestone in fluidized-bed coal combustors.

  20. Scintillation properties of REF.sub.3./sub. (RE=Ce, Pr, Nd) single crystals

    Czech Academy of Sciences Publication Activity Database

    Víllora, E. G.; Shimamura, K.; Nakakita, S.; Nikl, Martin; Ichinose, N.

    2005-01-01

    Roč. 537, - (2005), s. 139-143 ISSN 0168-9002 Institutional research plan: CEZ:AV0Z10100521 Keywords : rare earth compounds * scintillator materials Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.224, year: 2005

  1. Austerlased reedeti ja müüdi maha / Stephan Zanzerl ; ref. Hille Simm

    Index Scriptorium Estoniae

    Zanzerl, Stephan

    2003-01-01

    Austria kodanikuinitsiatiivi "Kodumaa ja looduskeskkond" esindaja Stephan Zanzerli pöördumine Eesti rahva poole palvega hääletada Euroopa Liidu vastu. Euroopa Liidu negtiivsetest mõjudest Austria majandusele ja seadusandlusele

  2. Detecting Epistemic Vice in Higher Education Policy: Epistemic Insensibility in the Seven Solutions and the REF

    Science.gov (United States)

    Battaly, Heather

    2013-01-01

    This article argues that the Seven Solutions in the US, and the Research Excellence Framework in the UK, manifest the vice of epistemic insensibility. Section I provides an overview of Aristotle's analysis of moral vice in people. Section II applies Aristotle's analysis to epistemic vice, developing an account of epistemic insensibility. In so…

  3. Controllable self-assembly of NaREF4 upconversion nanoparticles and their distinctive fluorescence properties

    Science.gov (United States)

    Liu, Xiaoxia; Ni, Yaru; Zhu, Cheng; Fang, Liang; Kou, Jiahui; Lu, Chunhua; Xu, Zhongzi

    2016-07-01

    The paper presents the growth of hexagonal NaYF4:Yb3+, Tm3+ nanocrystals with tunable sizes induced by different contents of doped Yb3+ ions (10%-99.5%) using the thermal decomposition method. These nanoparticles, which have different sizes, are then self-assembled at the interface of cyclohexane and ethylene and transferred onto a normal glass slide. It is found that the size of nanoparticles directs their self-assembly. Due to the appropriate size of 40.5 nm, 15% Yb3+ ions doped nanoparticles are able to be self-assembled into an ordered inorganic monolayer membrane with a large area of about 10 × 10 μm2. More importantly, the obvious short-wave (300-500 nm) fluorescence improvement of the ordered 2D self-assembly structure is observed to be relative to disordered nanoparticles, which is because intrinsic absorption and scattering of upconversion nanoparticles leads to the self-loss of fluorescence, especially the short-wave fluorescence inside the disordered structure, and the relative emission of short-wave fluorescence is reduced. The construction of a 2D self-assembly structure can effectively avoid this and improve the radiated short-wave fluorescence, especially UV photons, and is able to direct the design of new types of solid-state optical materials in many fields.

  4. CrossRef Space-charge effects in Penning ion traps

    CERN Document Server

    Porobić, T; Breitenfeldt, M; Couratin, C; Finlay, P; Knecht, A; Fabian, X; Friedag, P; Fléchard, X; Liénard, E; Ban, G; Zákoucký, D; Soti, G; Van Gorp, S; Weinheimer, Ch; Wursten, E; Severijns, N

    2015-01-01

    The influence of space-charge on ion cyclotron resonances and magnetron eigenfrequency in a gas-filled Penning ion trap has been investigated. Off-line measurements with View the MathML source using the cooling trap of the WITCH retardation spectrometer-based setup at ISOLDE/CERN were performed. Experimental ion cyclotron resonances were compared with ab initio Coulomb simulations and found to be in agreement. As an important systematic effect of the WITCH experiment, the magnetron eigenfrequency of the ion cloud was studied under increasing space-charge conditions. Finally, the helium buffer gas pressure in the Penning trap was determined by comparing experimental cooling rates with simulations.

  5. Development of substrate-removal-free vertical ultraviolet light-emitting diode (RefV-LED

    Directory of Open Access Journals (Sweden)

    N. Kurose

    2014-02-01

    Full Text Available A vertical ultraviolet (UV light-emitting diode (LED that does not require substrate removal is developed. Spontaneous via holes are formed in n-AlN layer epitaxially grown on a high conductive n+Si substrate and the injected current flows directly from the p-electrode to high doped n+ Si substrate through p-AlGaN, multi-quantum wells, n-AlGaN and spontaneous via holes in n-AlN. The spontaneous via holes were formed by controlling feeding-sequence of metal-organic gas sources and NH3 and growth temperature in MOCVD. The via holes make insulating n-AlN to be conductive. We measured the current-voltage, current-light intensity and emission characteristics of this device. It exhibited a built-in voltage of 3.8 V and emission was stated at 350 nm from quantum wells with successive emission centered at 400 nm. This UV LED can be produced, including formation of n and p electrodes, without any resist process.

  6. Development of substrate-removal-free vertical ultraviolet light-emitting diode (RefV-LED)

    Energy Technology Data Exchange (ETDEWEB)

    Kurose, N., E-mail: kurose@fc.ritsumei.ac.jp; Aoyagi, Y. [The Research Organization of Science and Technology, Ritsumeikan University, 1-1-1, Noji-higashi, Kusatsu, Shiga 525-8577 (Japan); Shibano, K.; Araki, T. [Department of Science and Technology, Ritsumeikan University, 1-1-1, Noji-higashi, Kusatsu, Shiga 525-8577 (Japan)

    2014-02-15

    A vertical ultraviolet (UV) light-emitting diode (LED) that does not require substrate removal is developed. Spontaneous via holes are formed in n-AlN layer epitaxially grown on a high conductive n+Si substrate and the injected current flows directly from the p-electrode to high doped n{sup +} Si substrate through p-AlGaN, multi-quantum wells, n-AlGaN and spontaneous via holes in n-AlN. The spontaneous via holes were formed by controlling feeding-sequence of metal-organic gas sources and NH{sub 3} and growth temperature in MOCVD. The via holes make insulating n-AlN to be conductive. We measured the current-voltage, current-light intensity and emission characteristics of this device. It exhibited a built-in voltage of 3.8 V and emission was stated at 350 nm from quantum wells with successive emission centered at 400 nm. This UV LED can be produced, including formation of n and p electrodes, without any resist process.

  7. Current and future use of coal in the Northeast. [60 refs

    Energy Technology Data Exchange (ETDEWEB)

    Edelston, B.S.; Rubin, E.S.

    1976-05-01

    Some of the problems of and potential for coal utilization in the Northeast region (defined as New England, New York, Pennsylvania, New Jersey, Delaware, Maryland, and the District of Columbia are discussed. Coal utilization in the Northeast now occurs mainly in Pennsylvania, where coal is used extensively for steel manufacturing and electricity generation. Elsewhere in the region, coal use is limited for the most part to electric power generation, and increased future reliance on coal is likely to be associated principally with this use. At present, oil supplies most of the energy used to generate electricity in the Northeast. Recent trends in national and regional coal use are reviewed, and an overview of potential options for and constraints on future coal use are presented. The outlook for future coal supplies in the region for the reference years 1985 and 2000 is discussed. Supply estimates are shown tabularly. Regional availability of low-sulfur coal will depend on interregional economic factors as well as on technical constraints and public policy. The transportation system of the Northeast coals also constrain coal use. The potential demand for coal by electric utilities in the region is considered. Three coal demand scenarios are developed for 1985. The role of coal-derived synthetic fuels in the energy future of the Northeast is discussed. For the most part, processes producing low-Btu gas, high-Btu gas, and synthetic liquids from coal will contribute to the energy supply of the Northeast indirectly by augmenting national supplies of gas, oil, and electricity. In 1985, synthetic fuels production is likely to be small; by 2000, more substantial contributions could be available if a national policy for rapid coal synthetics development was pursued.

  8. THE REfERENT Of EGEUSASTHE (YOU HAVE TASTED) IN 1 ...

    African Journals Online (AJOL)

    In 1 Peter 2:2-3 the addressees are exhorted to “yearn for the unadulterated milk of. God's word ... like newborn babies” (ajrtigevnnhta brevf h). This exhortation is motivated by: “since you have tasted that the Lord is good” (ejg euvs asqe o{ti crhsto; o kuvrio~). This article attempts to establish the referent of ejg euvs asqe.

  9. Kütus, mida saadakse põllult / ref. Axel Novak

    Index Scriptorium Estoniae

    2006-01-01

    Bioetanooli autokütusena kasutamise probleemidest Saksamaal, Brasiilia positiivsest näitest biokütuste kasutamisel ning autotootjate huvist alternatiivkütuste kasutamise vastu. Skeem: Teraviljast alkoholini. Lisa: Etanooli liikumine - Stinnesi tarneahel. Vt. samas: Kärt Blumberg. Biodiisli müük Eestis võtab hoogu

  10. Decommissioning information management in decommissioning planning and operations at AECL (Ref 5054)

    International Nuclear Information System (INIS)

    Lemire, D.S.

    2006-01-01

    As the AECL Decommissioning program has grown over the past few years, particularly with regard to long-term planning, so has its need to manage the records and information required to support the program. The program encompasses a diverse variety of facilities, including prototype and research reactors, fuel processing facilities, research laboratories, waste processing facilities, buildings, structures, lands and waste storage areas, many of which have changed over time. The decommissioning program involves planning, assessing, monitoring and executing projects to decommission the facilities. The efficient and effective decommissioning planning, assessment, monitoring and execution for the facilities and projects are dependent on a sound information base, upon which decisions can be made. A vital part of this Information Base is the ongoing management of historical facility records, including decommissioning records, throughout the full life cycle of the facilities. This paper describes AECL's and particularly DP and O's approach to: 1) Establishing a decommissioning records and information framework, which identifies what records and information are relevant to decommissioning, prioritizing the decommissioning facilities, identifying sources of relevant information and providing a user-friendly, electronic, search and retrieval tool for facility information accessible to staff. 2) Systematically, gathering, assessing, archiving and identifying important information and making that information available to staff to support their ongoing decommissioning work. 3) Continually managing and enhancing the records and information base and its support infrastructure to ensure its long-term availability. 4) Executing special information enhancement projects, which transform historic records into information for analysis. (author)

  11. CrossRef Experimental verification of the HERD prototype at CERN SPS

    CERN Document Server

    Dong, Yongwei; Wang, Junjing; Xu, Ming; Albergo, Sebastiano; Ambroglini, Filippo; Ambrosi, Giovanni; Azzarello, Philipp; Bai, Yonglin; Bao, Tianwei; Baldini, Luca; Battiston, Roberto; Bernardini, Paolo; Chen, Zhen; D'Alessandro, Raffaello; Duranti, Matteo; D'Urso, Domenico; Fusco, Piergiorgio; Gao, Jiarui; Gao, Xiaohui; Gargano, Fabio; Giglietto, Nicola; Hu, Bingliang; Li, Ran; Li, Yong; Liu, Xin; Loparco, Francesco; Lu, Junguang; Marsella, Giovanni; Mazziotta, Mario N; De Mitri, Ivan; Mori, Nicola; Orsi, Silvio; Oscar, Adriani; Pearce, Mark; Pohl, Martin; Ryde, Felix; Shi, Dalian; Spillantini, Piero; Su, Meng; Sun, Xin; Surdo, Antonio; Walter, Roland; Wang, Bo; Wang, Le; Wang, Ruijie; Wang, Zhigang; Wu, Bobing; Wu, Xin; Yan, Peng; Zhang, Li; Zhang, Shuangnan

    2016-01-01

    The High Energy cosmic-Radiation Detection (HERD) facility is one of several space astronomy payloads of the cosmic light house program onboard China's Space Station, which is planned for operation starting around 2020 for about 10 years. Beam test with a HERD prototype, to verify the HERD specifications and the reading out method of wavelength shifting fiber and image intensified CCD, was taken at CERN SPS in November, 2015. The prototype is composed of an array of 5*5*10 LYSO crystals, which is 1/40th of the scale of HERD calorimeter. Experimental results on the performances of the calorimeter are discussed. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

  12. NCBI nr-aa BLAST: CBRC-VPAC-01-0807 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-VPAC-01-0807 gb|AAO73490.1| CX3CR1 [Macaca fascicularis] gb|AAO73491.1| CX3CR1 [Maca...ca fascicularis] gb|AAO73498.1| CX3CR1 [Macaca mulatta] gb|AAO73500.1| CX3CR1 [Macaca mulatta] gb|AAO73501.1| CX3CR1 [Macaca mulatta] AAO73490.1 5e-67 81% ...

  13. NCBI nr-aa BLAST: CBRC-STRI-01-0392 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-STRI-01-0392 gb|AAO73490.1| CX3CR1 [Macaca fascicularis] gb|AAO73491.1| CX3CR1 [Maca...ca fascicularis] gb|AAO73498.1| CX3CR1 [Macaca mulatta] gb|AAO73500.1| CX3CR1 [Macaca mulatta] gb|AAO73501.1| CX3CR1 [Macaca mulatta] AAO73490.1 1e-60 85% ...

  14. Deslocamento miscível de nitrato e fosfato proveniente de água residuária da suinocultura em colunas de solo Miscible displacement of nitrate and phosphate from swine wastewater in soil columns

    Directory of Open Access Journals (Sweden)

    Marcelo H. Anami

    2008-02-01

    Full Text Available A fertirrigação com águas residuárias da suinocultura vem sendo muito difundida no País, principalmente na região sul do Brasil, entretanto, o alto potencial poluidor dos dejetos pode tornar-se uma ameaça de contaminação de solos e águas superficiais e subterrâneas se utilizados em quantidades excessivas. Neste trabalho o objetivo principal foi avaliar o processo de lixiviação de íons nitrato e fosfato em colunas de solo, obtendo-se os coeficientes de dispersão hidrodinâmico e o fator de retardamento para a determinação do potencial de contaminação dos lençóis de água subterrâneos. Verificou-se, ainda, o efeito da aplicação de águas residuárias da suinocultura tratada com reatores anaeróbios sobre as propriedades físico-químicas do solo, cujos resultados indicaram que o potencial de contaminação dos lençóis de água subterrâneos pelo íon nitrato é elevado, ao contrário do que ocorre com o íon fosfato, que apresentou baixo potencial de contaminação em função da sua alta reatividade.Fertigation with wastewater from swine is very much used, mainly in the southern region of Brazil. However, the high polluting potential of these wastewaters represents a threat of soil contamination of surface and underground waters if used in excessive amounts. The objective of this work was to evaluate the leaching process of nitrate and phosphate ions in soil columns, getting the hydrodynamic dispersion coefficient and factor of retardation and potential of contamination of underground water. The effect of wastewater application on physical and chemical properties of the soil was verified. The results showed that the potential for contamination of underground water by nitrate ions is high, in contrast to what occurs with phosphate ions that presented low potential of contamination due to their high reactivity.

  15. Maristem—Stem Cells of Marine/Aquatic Invertebrates: From Basic Research to Innovative Applications

    Directory of Open Access Journals (Sweden)

    Loriano Ballarin

    2018-02-01

    Full Text Available The “stem cells” discipline represents one of the most dynamic areas in biomedicine. While adult marine/aquatic invertebrate stem cell (MISC biology is of prime research and medical interest, studies on stem cells from organisms outside the classical vertebrate (e.g., human, mouse, and zebrafish and invertebrate (e.g., Drosophila, Caenorhabditis models have not been pursued vigorously. Marine/aquatic invertebrates constitute the largest biodiversity and the widest phylogenetic radiation on Earth, from morphologically simple organisms (e.g., sponges, cnidarians, to the more complex mollusks, crustaceans, echinoderms, and protochordates. These organisms contain a kaleidoscope of MISC-types that allow the production of a large number of novel bioactive-molecules, many of which are of significant potential interest for human health. MISCs further participate in aging and regeneration phenomena, including whole-body regeneration. For years, the European MISC-community has been highly fragmented and has established scarce ties with biomedical industries in an attempt to harness MISCs for human welfare. Thus, it is important to (i consolidate the European community of researchers working on MISCs; (ii promote and coordinate European research on MISC biology; (iii stimulate young researchers to embark on research in MISC-biology; (iv develop, validate, and share novel MISC tools and methodologies; (v establish the MISC discipline as a forefront interest of biomedical disciplines, including nanobiomedicine; and (vi establish collaborations with industries to exploit MISCs as sources of bioactive molecules. In order to fill the recognized gaps, the EC-COST Action 16203 “MARISTEM” has recently been launched. At its initial stage, the consortium unites 26 scientists from EC countries, Cooperating countries, and Near Neighbor Countries.

  16. Inpatients’ opinions on a hospital in Portugal [v1; ref status: indexed, http://f1000r.es/xb

    Directory of Open Access Journals (Sweden)

    Carina C Silva

    2013-02-01

    Full Text Available Background: Little is known about the relationship between the opinions of inpatients and the degree to which hospitals are improving in performance over time. The aim of this study was to determine the personal assessment level of inpatients or their representatives regarding aspects of health care in an internal medicine ward. Methods: We carried out a questionnaire in September 2011 with 284 discharged patients and patient representatives, focusing on their opinions about the department, health professionals and amenities, with response options ranging from 1 (very bad to 5 (very good. The relationships between domains from the questionnaire and socio-demographic factors were examined using a t-test and one-way ANOVA. Results: The response rate was 78%. The patients showed a slightly higher mean score (m for factors in the medical care domain than did the patient representatives (m = 4.51 vs. m = 4.27; p = 0.014. The mean score of all the items in all domains was 4.24; this allowed us to determine the difference from the overall mean (DIFM for medical care (DIFM = 0.18; p = 0.000, foods (DIFM = –0.31; p = 0.000, diagnostic tests (DIFM = –0.15; p = 0.036 and transport (DIFM = –0.41; p = 0.000. Respondents with a medium or higher educational level gave lower scores to the domains food (m = 3.74; p = 0.004, diagnostic tests (m = 3.72; p = 0.04 and transport (m = 3.62; p = 0.025 than those with lower educational levels. The domains facilities (m = 2.4; p = 0.04 and diagnostic tests (m = 3.63; p = 0.009 were given lower scores by those aged <50 years compared with older respondents. Conclusions: Our findings suggest that the evaluation of the responders will allow the hospital management to make improvements in the quality of care.

  17. ProgRef v4 : um software para coleta de dados em programas de reforço com humanos

    OpenAIRE

    Rodrigo Morande Becker

    2011-01-01

    Os avanços científico e tecnológico estão cada vez mais interdependentes. A Análise Experimental do Comportamento como uma ciência não pode se colocar distante de meios que facilitem e aprimorem a coleta e a análise de dados. Um computador de uso pessoal é uma ótima ferramenta para auxiliar na pesquisa tanto básica quanto aplicada. A presente dissertação esta inserida nesse contexto ao propor o desenvolvimento de um software para coleta e análise de dados de programas de reforço com humanos. ...

  18. On genomics, kin, and privacy [v1; ref status: indexed, http://f1000r.es/35l

    Directory of Open Access Journals (Sweden)

    Amalio Telenti

    2014-03-01

    Full Text Available The storage of greater numbers of exomes or genomes raises the question of loss of privacy for the individual and for families if genomic data are not properly protected. Access to genome data may result from a personal decision to disclose, or from gaps in protection. In either case, revealing genome data has consequences beyond the individual, as it compromises the privacy of family members. Increasing availability of genome data linked or linkable to metadata through online social networks and services adds one additional layer of complexity to the protection of genome privacy.  The field of computer science and information technology offers solutions to secure genomic data so that individuals, medical personnel or researchers can access only the subset of genomic information required for healthcare or dedicated studies.

  19. Methods for analysis of trace elements in coal, coal fly ash, soil, and plant samples. [59 refs

    Energy Technology Data Exchange (ETDEWEB)

    Slates, R.V.

    1976-11-01

    Results of a literature search are presented, and analytical methods are proposed for studies of trace elements in coal, coal ash residue, soil, and vegetation. Increased trace element levels in soils and plants collected near power plants have been reported by several investigators. Many sample dissolution and analysis techniques were used in the reported studies. A nine-laboratory comparison of trace element analyses for a variety of methods showed excessive variation relative to quoted uncertainty limits. Analysis results from a subsequent four-laboratory comparison of instrumental nuclear techniques for trace element analysis agreed with the National Bureau of Standards certified values for all nine elements determined. Instrumental neutron activation analysis, spark source mass spectrometry, and atomic absorption spectrometry are proposed as primary analysis methods for coal, coal ash, soil, and plants in a Savannah River Laboratory study of trace elements. Bomb procedures are proposed for dissolution of samples.

  20. Interactive lectures: Clickers or personal devices? [v1; ref status: indexed, http://f1000r.es/54w

    Directory of Open Access Journals (Sweden)

    Lesley J. Morrell

    2015-03-01

    Full Text Available Audience response systems (‘clickers’ are frequently used to promote participation in large lecture classes, and evidence suggests that they convey a number of benefits to students, including improved academic performance and student satisfaction. The limitations of these systems (such as limited access and cost can be overcome using students’ personal electronic devices, such as mobile phones, tablets and laptops together with text message, web- or app-based polling systems. Using questionnaires, we compare student perceptions of clicker and smartphone based polling systems. We find that students prefer interactive lectures generally, but those that used their own device preferred those lectures over lectures using clickers. However, device users were more likely to report using their devices for other purposes (checking email, social media etc. when they were available to answer polling questions. These students did not feel that this distracted them from the lecture, instead, concerns over the use of smartphones centred around increased battery usage and inclusivity for students without access to suitable technology. Our results suggest that students generally preferred to use their own devices over clickers, and that this may be a sensible way to overcome some of the limitations associated with clickers, although issues surrounding levels of distraction and the implications for retention and recall of information need further investigation.

  1. Interactive lectures: Clickers or personal devices? [v1; ref status: indexed, http://f1000r.es/54w

    OpenAIRE

    Lesley J. Morrell; Domino A. Joyce

    2015-01-01

    Audience response systems (?clickers?) are frequently used to promote participation in large lecture classes, and evidence suggests that they convey a number of benefits to students, including improved academic performance and student satisfaction. The limitations of these systems (such as limited access and cost) can be overcome using students? personal electronic devices, such as mobile phones, tablets and laptops together with text message, web- or app-based polling systems. Using question...

  2. Development of a system for receiving, crushing and screening recycled fuel (REF) material; Kierraetyspolttoaineen vastaanotto-, murskaus- ja seulontajaerjestelmaen kehittaeminen

    Energy Technology Data Exchange (ETDEWEB)

    Nurmi, A.; Kurki, T.; Wrang, T. [BMH Wood Technology Oy, Rauma (Finland)

    1995-12-31

    The goal of this project is to develop a system to which source sorted combustible industrial, office and municipal waste material can be dumped to be handled in such way that it can be burnt in modern fluidized bed and circulating bed boilers. One drawback of present handling systems is the fact that most of them are more or less inapplicable for handling plastic materials, especially thin plastic films and sheets. Reducing plastic waste into a particle size of 50 mm required by modern fluidized bed boilers has proved to be very difficult. An essential part of this project is the development of waste material screening after primary and/or secondary crushing. The idea is to separate plastic particles larger than the maximum allowable size from the crushed material and then feed them to a separate low-capacity plastic crusher. The main stages of the project are: (1) Study and analysis on existing technology and equipment, (2) Development of system components, (3) Development of the system, (4) Building a pilot/demonstration plant, (5) Tests and analysis and (6) Decisions on further actions

  3. Computer-aided drug discovery [v1; ref status: indexed, http://f1000r.es/5ij

    Directory of Open Access Journals (Sweden)

    Jürgen Bajorath

    2015-08-01

    Full Text Available Computational approaches are an integral part of interdisciplinary drug discovery research. Understanding the science behind computational tools, their opportunities, and limitations is essential to make a true impact on drug discovery at different levels. If applied in a scientifically meaningful way, computational methods improve the ability to identify and evaluate potential drug molecules, but there remain weaknesses in the methods that preclude naïve applications. Herein, current trends in computer-aided drug discovery are reviewed, and selected computational areas are discussed. Approaches are highlighted that aid in the identification and optimization of new drug candidates. Emphasis is put on the presentation and discussion of computational concepts and methods, rather than case studies or application examples. As such, this contribution aims to provide an overview of the current methodological spectrum of computational drug discovery for a broad audience.

  4. CrossRef Large numbers of cold positronium atoms created in laser-selected Rydberg states using resonant charge exchange

    CERN Document Server

    McConnell, R; Kolthammer, WS; Richerme, P; Müllers, A; Walz, J; Grzonka, D; Zielinski, M; Fitzakerley, D; George, MC; Hessels, EA; Storry, CH; Weel, M

    2016-01-01

    Lasers are used to control the production of highly excited positronium atoms (Ps*). The laser light excites Cs atoms to Rydberg states that have a large cross section for resonant charge-exchange collisions with cold trapped positrons. For each trial with 30 million trapped positrons, more than 700 000 of the created Ps* have trajectories near the axis of the apparatus, and are detected using Stark ionization. This number of Ps* is 500 times higher than realized in an earlier proof-of-principle demonstration (2004 Phys. Lett. B 597 257). A second charge exchange of these near-axis Ps* with trapped antiprotons could be used to produce cold antihydrogen, and this antihydrogen production is expected to be increased by a similar factor.

  5. Comprehensive comparisons of the current human, mouse, and rat RefSeq, Ensembl, EST, and FANTOM3 datasets

    DEFF Research Database (Denmark)

    Nordström, Karl J V; Mirza, Majd A I; Larsson, Thomas P

    2006-01-01

    . The results indicate large discrepancies between the datasets, as considerable numbers of unique transcripts can be found in each dataset. Despite the high number of ncRNA (38,129 in mouse) there are also almost 20,000 EST clusters in both mouse and humans with more than one EST that do not overlap any...

  6. Immunohistochemical visualization of mouse interneuron subtypes [v1; ref status: indexed, http://f1000r.es/4em

    Directory of Open Access Journals (Sweden)

    Simon Molgaard

    2014-10-01

    Full Text Available The activity of excitatory neurons is controlled by a small, but highly diverse population of inhibitory interneurons. These cells show a high level of physiological, morphological and neurochemical heterogeneity, and play highly specific roles in neuronal circuits. In the mammalian hippocampus, these are divided into 21 different subtypes of GABAergic interneurons based on their expression of different markers, morphology and their electrophysiological properties. Ideally, all can be marked using an antibody directed against the inhibitory neurotransmitter GABA, but parvalbumin, calbindin, somatostatin, and calretinin are also commonly used as markers to narrow down the specific interneuron subtype. Here, we describe a journey to find the necessary immunological reagents for studying GABAergic interneurons of the mouse hippocampus. Based on web searches there are several hundreds of different antibodies on the market directed against these four markers. Searches in the literature databases allowed us to narrow it down to a subset of antibodies most commonly used in publications. However, in our hands the most cited ones did not work for immunofluorescence stainings of formaldehyde fixed tissue sections and cultured hippocampal neurons, and we had to immunostain our way through thirteen different commercial antibodies before finally finding a suitable antibody for each of the four markers. The antibodies were evaluated based on signal-to-noise ratios as well as if positive cells were found in layers of the hippocampus where they have previously been described. Additionally, the antibodies were also tested on sections from mouse spinal cord with similar criteria for specificity of the antibodies. Using the antibodies with a high rating on pAbmAbs, stainings with high signal-to-noise ratios and location of the immunostained cells in accordance with the literature could be obtained, making these antibodies suitable choices for studying the GABAergic system.

  7. CrossRef Optimizing charge breeding techniques for ISOL facilities in Europe: Conclusions from the EMILIE project

    CERN Document Server

    Delahaye, P; Angot, J; Cam, J F; Traykov, E; Ban, G; Celona, L; Choinski, J; Gmaj, P; Jardin, P; Koivisto, H; Kolhinen, V; Lamy, T; Maunoury, L; Patti, G; Thuillier, T; Tarvainen, O; Vondrasek, R; Wenander, F

    2016-01-01

    The present paper summarizes the results obtained from the past few years in the framework of the Enhanced Multi-Ionization of short-Lived Isotopes for Eurisol (EMILIE) project. The EMILIE project aims at improving the charge breeding techniques with both Electron Cyclotron Resonance Ion Sources (ECRIS) and Electron Beam Ion Sources (EBISs) for European Radioactive Ion Beam (RIB) facilities. Within EMILIE, an original technique for debunching the beam from EBIS charge breeders is being developed, for making an optimal use of the capabilities of CW post-accelerators of the future facilities. Such a debunching technique should eventually resolve duty cycle and time structure issues which presently complicate the data-acquisition of experiments. The results of the first tests of this technique are reported here. In comparison with charge breeding with an EBIS, the ECRIS technique had lower performance in efficiency and attainable charge state for metallic ion beams and also suffered from issues related to beam c...

  8. Nanotechnology-supported THz medical imaging [v1; ref status: indexed, http://f1000r.es/ws

    Directory of Open Access Journals (Sweden)

    Andreas Stylianou

    2013-03-01

    Full Text Available Over the last few decades, the achievements and progress in the field of medical imaging have dramatically enhanced the early detection and treatment of many pathological conditions. The development of new imaging modalities, especially non-ionising ones, which will improve prognosis, is of crucial importance. A number of novel imaging modalities have been developed but they are still in the initial stages of development and serious drawbacks obstruct them from offering their benefits to the medical field. In the 21st century, it is believed that nanotechnology will highly influence our everyday life and dramatically change the world of medicine, including medical imaging. Here we discuss how nanotechnology, which is still in its infancy, can improve Terahertz (THz imaging, an emerging imaging modality, and how it may find its way into real clinical applications. THz imaging is characterised by the use of non-ionising radiation and although it has the potential to be used in many biomedical fields, it remains in the field of basic research. An extensive review of the recent available literature shows how the current state of this emerging imaging modality can be transformed by nanotechnology. Innovative scientific concepts that use nanotechnology-based techniques to overcome some of the limitations of the use of THz imaging are discussed. We review a number of drawbacks, such as a low contrast mechanism, poor source performance and bulky THz systems, which characterise present THz medical imaging and suggest how they can be overcome through nanotechnology. Better resolution and higher detection sensitivity can also be achieved using nanotechnology techniques.

  9. MODIS/Terra+Aqua BRDF/Albedo Nadir BRDF-Adjusted Ref Daily L3 Global - 500m V006

    Data.gov (United States)

    National Aeronautics and Space Administration — The MODIS MCD43A4 Version 6 Nadir Bidirectional reflectance distribution function Adjusted Reflectance (NBAR) data set is a daily 16-day product. The Julian date in...

  10. Digital teaching tools and global learning communities [v1; ref status: indexed, http://f1000r.es/533

    OpenAIRE

    Mary Williams; Patti Lockhart; Cathie Martin

    2015-01-01

    In 2009, we started a project to support the teaching and learning of university-level plant sciences, called Teaching Tools in Plant Biology. Articles in this series are published by the plant science journal, The Plant Cell (published by the American Society of Plant Biologists). Five years on, we investigated how the published materials are being used through an analysis of the Google Analytics pageviews distribution and through a user survey. Our results suggest that this project has had ...

  11. Advances in understanding cartilage remodeling [v1; ref status: indexed, http://f1000r.es/5e6

    Directory of Open Access Journals (Sweden)

    Yefu Li

    2015-08-01

    Full Text Available Cartilage remodeling is currently among the most popular topics in osteoarthritis research. Remodeling includes removal of the existing cartilage and replacement by neo-cartilage. As a loss of balance between removal and replacement of articular cartilage develops (particularly, the rate of removal surpasses the rate of replacement, joints will begin to degrade. In the last few years, significant progress in molecular understanding of the cartilage remodeling process has been made. In this brief review, we focus on the discussion of some current “controversial” observations in articular cartilage degeneration: (1 the biological effect of transforming growth factor-beta 1 on developing and mature articular cartilages, (2 the question of whether aggrecanase 1 (ADAMTS4 and aggrecanase 2 (ADAMTS5 are key enzymes in articular cartilage destruction, and (3 chondrocytes versus chondron in the development of osteoarthritis. It is hoped that continued discussion and investigation will follow to better clarify these topics. Clarification will be critical for those in search of novel therapeutic targets for the treatment of osteoarthritis.

  12. Bond-girl Eva Green: "Daniel ei ole sugugi halb" / Eva Green ; ref. Viktoria Ladõnskaja

    Index Scriptorium Estoniae

    Green, Eva

    2006-01-01

    Ajakirjanikud vaatasid Londonis uut Bondi-filmi "007 : Casino Royale" ja kohtusid pressikonverentsil peaosatäitjatega. Prantsusmaal elav rootsi-alžeeria päritolu näitlejanna Eva Green räägib oma rollist ja koostööst Bondi-kehastaja Daniel Craigiga

  13. Classification and Dose-Response Characterization of Environmental Chemicals Based On Structured Toxicity Information From ToxRefDB

    Science.gov (United States)

    Thirty years and over a billion of today’s dollars worth of pesticide registration toxicity studies, historically stored as hardcopy and scanned documents, have been digitized into highly standardized and structured toxicity data, within the U.S. Environmental Protection Agency’s...

  14. CrossRef Energy Reconstruction in a High Granularity Semi-Digital Hadronic Calorimeter for ILC Experiments

    CERN Document Server

    Mannai, S; Cortina, E; Laktineh, I

    2016-01-01

    Abstract: The Semi-Digital Hadronic CALorimeter (SDHCAL) is one of the two hadronic calorimeter options proposed by the International Large Detector (ILD) project for the future International Linear Collider (ILC) experiments. It is a sampling calorimeter with 48 active layers made of Glass Resistive Plate Chambers (GRPCs) and their embedded electronics. A fine lateral segmentation is obtained thanks to pickup pads of 1 cm2. This ensures the high granularity required for the application of the Particle Flow Algorithm (PFA) in order to improve the jet energy resolution in the ILC experiments. The performance of the SDHCAL technological prototype was tested successfully in several beam tests at CERN. The main point to be discussed here concerns the energy reconstruction in SDHCAL. Based on Monte Carlo simulation of the SDHCAL prototype using the GEANT4 package, we present different energy reconstruction methods to study the energy linearity and resolution of the detector response to single hadrons. In particula...

  15. Monitoring drug promiscuity over time [v2; ref status: indexed, http://f1000r.es/4oa

    OpenAIRE

    Ye Hu; Jürgen Bajorath

    2014-01-01

    Drug promiscuity and polypharmacology are much discussed topics in pharmaceutical research. Experimentally, promiscuity can be studied by profiling of compounds on arrays of targets. Computationally, promiscuity rates can be estimated by mining of compound activity data. In this study, we have assessed drug promiscuity over time by systematically collecting activity records for approved drugs. For 518 diverse drugs, promiscuity rates were determined over different time intervals. Significant ...

  16. Monitoring drug promiscuity over time [v1; ref status: indexed, http://f1000r.es/4bh

    OpenAIRE

    Ye Hu; Jürgen Bajorath

    2014-01-01

    Drug promiscuity and polypharmacology are much discussed topics in pharmaceutical research. Experimentally, promiscuity can be studied by profiling of compounds on arrays of targets. Computationally, promiscuity rates can be estimated by mining of compound activity data. In this study, we have assessed drug promiscuity over time by systematically collecting activity records for approved drugs. For 518 diverse drugs, promiscuity rates were determined over different time intervals. Significant ...

  17. Paging Doctor Google! Heuristics vs. technology [v2; ref status: indexed, http://f1000r.es/113

    Directory of Open Access Journals (Sweden)

    Kenar D Jhaveri

    2013-04-01

    Full Text Available The most dramatic development in medical decision-making technology has been the advent of the Internet. This has had an impact not only on clinicians, but has also become an important resource for patients who often approach their doctors with medical information they have obtained from the Internet.  Increasingly, medical students, residents and attending physicians have been using the Internet as a tool for diagnosing and treating disease. Internet-based resources that are available take various forms, including informational websites, online journals and textbooks, and social media.  Search engines such as Google have been increasingly used to help in making diagnoses of disease entities. Do these search methods fare better than experienced heuristic methods? In a small study, we examined the comparative role of heuristics versus the 'Google' mode of thinking. Internal medicine residents were asked to “google” key words to come up with a diagnosis. Their results were compared to experienced nephrology faculty and fellows in training using heuristics and no additional help of internet. Overall, with the aid of Google, the novices (internal medicine residents correctly diagnosed renal diseases less often than the experts (the attendings but with the same frequency as the intermediates (nephrology fellows.  However, in a subgroup analysis of both common diseases and rare diseases, the novices correctly diagnosed renal diseases less often than the experts but more often than the intermediates in each analysis.  The novices correctly diagnosed renal diseases with the same frequency as nephrology fellows in training.

  18. Magnetic Resonance Imaging in Neuropsychiatric Lupus [v1; ref status: indexed, http://f1000r.es/5eh

    Directory of Open Access Journals (Sweden)

    Nicolae Sarbu

    2015-06-01

    Full Text Available Neuropsychiatric lupus is a major diagnostic challenge, and a main cause of morbidity and mortality in patients with systemic lupus erythematosus (SLE. Magnetic resonance imaging (MRI is, by far, the main tool for assessing the brain in this disease. Conventional and advanced MRI techniques are used to help establishing the diagnosis, to rule out alternative diagnoses, and recently, to monitor the evolution of the disease. This review explores the neuroimaging findings in SLE, including the recent advances in new MRI methods.

  19. Self-organization of signal transduction [v1; ref status: indexed, http://f1000r.es/zg

    Directory of Open Access Journals (Sweden)

    Gabriele Scheler

    2013-04-01

    Full Text Available We propose a model of parameter learning for signal transduction, where the objective function is defined by signal transmission efficiency. We apply this to learn kinetic rates as a form of evolutionary learning, and look for parameters which satisfy the objective. This is a novel approach compared to the usual technique of adjusting parameters only on the basis of experimental data. The resulting model is self-organizing, i.e. perturbations in protein concentrations or changes in extracellular signaling will automatically lead to adaptation. We systematically perturb protein concentrations and observe the response of the system. We find compensatory or co-regulation of protein expression levels. In a novel experiment, we alter the distribution of extracellular signaling, and observe adaptation based on optimizing signal transmission. We also discuss the relationship between signaling with and without transients. Signaling by transients may involve maximization of signal transmission efficiency for the peak response, but a minimization in steady-state responses. With an appropriate objective function, this can also be achieved by concentration adjustment. Self-organizing systems may be predictive of unwanted drug interference effects, since they aim to mimic complex cellular adaptation in a unified way.

  20. Management of thrombocythemia [v1; ref status: indexed, http://f1000r.es/4ez

    Directory of Open Access Journals (Sweden)

    Krisstina Gowin

    2014-09-01

    Full Text Available Essential thrombocythemia is a clonal myeloproliferative neoplasm characterized by an elevated platelet count, the potential for both microvascular and macrovascular sequelae, and a risk for transformation to myelofibrosis or acute myeloid leukemia. A systematic and detailed initial analysis is essential for accurate diagnosis of essential thrombocythemia, as many etiologies are reactive and benign. Once a diagnosis has been made, risk stratification and symptom assessment are vital to guide the subsequent therapy. Treatment may be required in high-risk disease, such as in cases of advanced age or prior thrombotic events. Systemic therapy is aimed at reducing the thrombotic risk and includes daily low dose aspirin and in some patients, cytoreductive therapy.  Currently, the first line cytoreductive therapy includes hydroxyurea or pegylated interferon, with a phase III clinical trial underway comparing these two important agents. Anagrelide and clinical trials are reserved for refractory or intolerant patients. Looking to the future, new therapies including Janus kinase 2 (JAK2 and telomerase inhibitors are promising and may become valuable to the treatment armamentarium for those afflicted with essential thrombocythemia.

  1. Radiological imaging in patients with low back pain and sciatica[6 figs., 14 refs]; Billeddiagnostikk ved lumbago og isjas

    Energy Technology Data Exchange (ETDEWEB)

    Dullerud, R. [Aker Sykehus, Oslo (Norway)

    1999-05-01

    Low back pain and sciatica are among the most common medical problems in Western countries, affecting up to 80% of the population at some time during their lives. Plain radiography is still a sensitive method in degenerative spinal disease and for the identification of spondylolysis and destructions as well as transitional vertebra and other anomalies in the lumbosacral region. In lumbar disk herniation CT and MR have higher sensitivity than lumbar myelography and should be used as the primary imaging methods. Myelography is still the method of choice in lumbar spinal stenosis. Myelography should also be considered in patients with poor consistency between CT and MR findings and the clinical presentation. Postoperatively MR is superior to CT and myelography for distinguishing between scar tissue and recurrent disk herniation.

  2. Data publication consensus and controversies [v3; ref status: indexed, http://f1000r.es/4ja

    Directory of Open Access Journals (Sweden)

    John Kratz

    2014-10-01

    Full Text Available The movement to bring datasets into the scholarly record as first class research products (validated, preserved, cited, and credited has been inching forward for some time, but now the pace is quickening. As data publication venues proliferate, significant debate continues over formats, processes, and terminology. Here, we present an overview of data publication initiatives underway and the current conversation, highlighting points of consensus and issues still in contention. Data publication implementations differ in a variety of factors, including the kind of documentation, the location of the documentation relative to the data, and how the data is validated. Publishers may present data as supplemental material to a journal article, with a descriptive “data paper,” or independently. Complicating the situation, different initiatives and communities use the same terms to refer to distinct but overlapping concepts. For instance, the term published means that the data is publicly available and citable to virtually everyone, but it may or may not imply that the data has been peer-reviewed. In turn, what is meant by data peer review is far from defined; standards and processes encompass the full range employed in reviewing the literature, plus some novel variations. Basic data citation is a point of consensus, but the general agreement on the core elements of a dataset citation frays if the data is dynamic or part of a larger set. Even as data publication is being defined, some are looking past publication to other metaphors, notably “data as software,” for solutions to the more stubborn problems.

  3. Data publication consensus and controversies [v2; ref status: indexed, http://f1000r.es/3hi

    Directory of Open Access Journals (Sweden)

    John Kratz

    2014-05-01

    Full Text Available The movement to bring datasets into the scholarly record as first class research products (validated, preserved, cited, and credited has been inching forward for some time, but now the pace is quickening. As data publication venues proliferate, significant debate continues over formats, processes, and terminology. Here, we present an overview of data publication initiatives underway and the current conversation, highlighting points of consensus and issues still in contention. Data publication implementations differ in a variety of factors, including the kind of documentation, the location of the documentation relative to the data, and how the data is validated. Publishers may present the data as supplemental material to a journal article, with a descriptive “data paper,” or independently. Complicating the situation, different initiatives and communities use the same terms to refer distinct but overlapping concepts. For instance, the term “published” means that the data is publicly available and citable to virtually everyone, but it may or may not imply that the data has been peer-reviewed. In turn, what is meant by data peer review is far from defined; standards and processes encompass the full range employed in reviewing the literature, plus some novel variations. Basic data citation is a point of consensus, but the general agreement on the core elements of a dataset citation frays if the data is dynamic or part of a larger set. Even as data publication is being defined, some are looking past publication to other metaphors, notably “data as software,” for solutions to the more stubborn problems.

  4. A letter to the Master Clinician [v2; ref status: indexed, http://f1000r.es/2zh

    Directory of Open Access Journals (Sweden)

    Kenar D. Jhaveri

    2014-02-01

    Full Text Available In this commentary, the author writes a letter to the Master Clinician about his concerns regarding the teaching responsibilities of current faculty members during ward rounds. This short essay highlights the transition that has been noticed in medical training in the last decade.

  5. A Computer Simulation of Vehicle and Actuator Dynamics for a Hexapod Walking Robot

    Science.gov (United States)

    1994-03-01

    define P1 3.14159265358979323846 #define PIF 3.14159f /* angle measurement conversions */ float degjo~rad(float deg); float rad-tofdeg(float rad...double degto~rad(double deg); double rad_to_deg(double rad); #endif 154 H1 rile "misc.C’ #include "misc.H" /* angle measurement conversions ~ float

  6. National Defense Stockpile Program. Phase 1. Development and Analyses

    Science.gov (United States)

    1990-03-01

    percent respectively for each year. Examples include appliances , furniture, jewelry, power tools and sporting equipment (NIPA categories 3, 5-16 and 18...8. Mattresses & Bedding 45. Telephone & Telegraph 9. Appliances 46. Domestic Services 10. China, Glassware & Utensils 47. Misc. Household Services 11...Jewelry & Watches 53. Misc. Transportation 17. Opthalmic & Orthopedic Goods 54. Rail Transportation 18. Books & Maps 55. Airline Transportation 19. Boats

  7. 76 FR 56196 - Agency Information Collection Activities; Proposed Collection; Comment Request

    Science.gov (United States)

    2011-09-12

    ... annual hours. Consumer Response Center Consumers can submit complaints about fraud and other practices to... consumer complaints and fraud complaints. In addition, the FTC has expanded the information required on its... Misc. and fraud-related consumer complaints (phone) 262,000 6.1 26,724 Misc. and fraud-related consumer...

  8. Rages or Temper Tantrums? The Behavioral Organization, Temporal Characteristics, and Clinical Significance of Angry-Agitated Outbursts in Child Psychiatry Inpatients

    Science.gov (United States)

    Potegal, Michael; Carlson, Gabrielle; Margulies, David; Gutkovitch, Zinoviy; Wall, Melanie

    2009-01-01

    Angry, agitated outbursts (AAOs) are a common precipitant of children's psychiatric hospitalization. In the hospital, AAOs present both management and diagnostic challenges, e.g., while they have recently been described as manic "rages", older studies suggest that they may be exacerbated temper tantrums. Factor analyses of 109 AAOs had by 46…

  9. NCBI nr-aa BLAST: CBRC-DNOV-01-3215 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DNOV-01-3215 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  10. NCBI nr-aa BLAST: CBRC-TBEL-01-2154 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TBEL-01-2154 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  11. NCBI nr-aa BLAST: CBRC-ETEL-01-0353 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-ETEL-01-0353 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  12. NCBI nr-aa BLAST: CBRC-SARA-01-1608 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-SARA-01-1608 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  13. NCBI nr-aa BLAST: CBRC-FCAT-01-0282 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-FCAT-01-0282 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  14. NCBI nr-aa BLAST: CBRC-OLAT-16-0022 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-OLAT-16-0022 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  15. NCBI nr-aa BLAST: CBRC-PABE-01-0133 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PABE-01-0133 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  16. NCBI nr-aa BLAST: CBRC-ACAR-01-0569 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-ACAR-01-0569 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  17. NCBI nr-aa BLAST: CBRC-XTRO-01-2431 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-XTRO-01-2431 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  18. NCBI nr-aa BLAST: CBRC-EEUR-01-1511 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-EEUR-01-1511 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  19. NCBI nr-aa BLAST: CBRC-BTAU-01-3054 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-BTAU-01-3054 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  20. NCBI nr-aa BLAST: CBRC-RMAC-01-0015 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-RMAC-01-0015 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  1. NCBI nr-aa BLAST: CBRC-GGAL-23-0008 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-GGAL-23-0008 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  2. NCBI nr-aa BLAST: CBRC-HSAP-01-0032 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-HSAP-01-0032 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  3. NCBI nr-aa BLAST: CBRC-CFAM-02-0024 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CFAM-02-0024 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  4. NCBI nr-aa BLAST: CBRC-RNOR-05-0237 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-RNOR-05-0237 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  5. NCBI nr-aa BLAST: CBRC-PTRO-01-0019 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PTRO-01-0019 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  6. NCBI nr-aa BLAST: CBRC-OANA-01-1293 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-OANA-01-1293 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  7. NCBI nr-aa BLAST: CBRC-TGUT-26-0004 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TGUT-26-0004 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  8. NCBI nr-aa BLAST: CBRC-CJAC-01-1490 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CJAC-01-1490 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  9. NCBI nr-aa BLAST: CBRC-TNIG-22-0071 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TNIG-22-0071 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  10. NCBI nr-aa BLAST: CBRC-MMUS-04-0074 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MMUS-04-0074 ref|NP_001832.1| cannabinoid receptor 2 (macrophage) [Homo sapien...s] sp|P34972|CNR2_HUMAN Cannabinoid receptor 2 (CB2) (CB-2) (CX5) emb|CAA52376.1| CB2 (peripheral) cannabino...id receptor [Homo sapiens] emb|CAD22548.1| peripheral cannabinoid receptor CB2 [Homo sapiens] emb|CAD22549.1| peripheral cann...abinoid receptor CB2 [Homo sapiens] gb|AAO92299.1| cannabinoid r...eceptor 2 [Homo sapiens] emb|CAI14799.1| cannabinoid receptor 2 (macrophage) [Homo sapiens] emb|CAJ42137.1| cann

  11. California Satellite Data

    Data.gov (United States)

    National Aeronautics and Space Administration — Citation: ####################### If using this dataset please cite the following in your work: @misc{VotDasNemSri2010 , author = "Petr Votava and Kamalika Das and...

  12. 1116-IJBCS-Article-Joseph Djeugap Fovo

    African Journals Online (AJOL)

    hp

    ulaval.ca; Fax : (237) 33 45. 15 66, BP 222 ..... Berger RD. 1980. Measuring disease intensity. In. Proc. EC. Stakman. Commemorative Symposium on Crop. Loss Assessments, St. Paul (ed). University of Minesota Misc : Minesota. Campbell CL ...

  13. Stroke, tPA, and Physician Decision-Making

    Science.gov (United States)

    ... hospital rooms have on physician decision-making. It ap- peared as if these do not have a ... misc/ addir. xhtml# reprintsus Neurology ® is the official journal of the American Academy of Neurology. Published continuously ...

  14. 2009 - Color - Barre Montpelier area (0.3m)

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) This dataset (MISC_0_3M_CLR_2009)includes truecolor ortho imagery covering the Barre-Monteplier (Capital Region) of Vermont. VCGI reprojected the...

  15. 2008 - Color - Northern Quarter of VT (0.3m)

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) This dataset (MISC_0_3M_CLR_2008) includes truecolor ortho imagery covering an area north and south of the VT/Canadian border. VCGI extracted the...

  16. American River Watershed Investigation, California. Volume 7. Appendix S. Part 2

    Science.gov (United States)

    1991-12-01

    productivity and diversity of tree, shrub and forbs provides abundant fruits, seeds, nectar , and forage for wildlife species. Natomas Cross Canal--Sacramento...abundant fruits, seeds, and nectar resources for species such as hummingbirds, scrub jay, black-headed grosbeak, rufous-sided towhee, Virginia opossum...pasture, native pasture Rice Rice Row Crop Truck berry, onions, garlic tomatoes, misc. truck crop, asparagus, melon , field crop, beans, misc. field

  17. Fabrication of ultra thin anodic aluminium oxide membranes by low anodization voltages

    Science.gov (United States)

    Pastore, I.; Poplausks, R.; Apsite, I.; Pastare, I.; Lombardi, F.; Erts, D.

    2011-06-01

    Formation of ultrathin anodised aluminium oxide (AAO) membranes with high aspect ratio by Al anodization in sulphuric and oxalic acids at low potentials was investigated. Low anodization potentials ensure slow electrochemical reaction speeds and formation of AAO membranes with pore diameter and thickness below 20 nm and 70 nm respectively. Minimum time necessary for formation of continuous AAO membranes was determined. AAO membrane pore surface was covered with polymer Paraloid B72TM to transport it to the selected substrate. The fabricated ultra thin AAO membranes could be used to fabricate nanodot arrays on different surfaces.

  18. The effects of anaesthesia on the developing brain: a summary of the clinical evidence [v2; ref status: indexed, http://f1000r.es/1mv

    Directory of Open Access Journals (Sweden)

    Clara KY Yu

    2013-08-01

    Full Text Available Introduction: There is data amassing in the literature regarding the potentially adverse effects of anaesthesia exposure on the developing human brain. The purpose of this article is to summarise current relevant data from clinical studies in this area. Methods: Articles from journals written in English were searched for using PubMed, Ovid and Medline. Keywords used included: brain (newborn, infant, child and neonate, neurodegeneration, apoptosis, toxicity, neurocognitive impairment (developmental impairment and learning disorders and anaesthesia (intravenous, inhalational and sedation. Results: From the initial search, 23 articles were identified as potentially relevant, with publication dates spanning from 1978 to 2012.  Twelve studies were deemed irrelevant to the research questions. The results of neurocognitive assessment from eight of the remaining eleven studies had showed some differences in the performances of children exposed to anaesthesia. The control population in these studies was highly variable. The age at which the subjects were exposed to anaesthesia ranged from prenatal to 4 years in the majority of studies with one including children aged up to 12 years when exposed. Discussion: Although there is clinical data suggesting a possible detrimental effect, the evidence is best considered preliminary and inconclusive at this stage. Many of the outcome measures were lacking in specificity and standardization in most cases. Parents should be counselled to not avoid necessary invasive procedures for fear of a currently ill-defined risk.  However, deferral of elective procedures beyond the first few years of life should be contemplated.

  19. A revised method for measuring distraction by tactile stimulation [v1; ref status: indexed, http://f1000r.es/42o

    Directory of Open Access Journals (Sweden)

    Jacqueline R. Schechter

    2014-08-01

    Full Text Available Sensory hypersensitivity (SH refers to the tendency to attend to subtle stimuli, to persist in attending to them, and to find them noxious. SH is relatively common in several developmental disorders including Tourette Syndrome and Chronic Tic Disorder (TS/CTD. This study was an attempt to quantify the extent to which a mild tactile stimulus distracts one’s attention in TS/CTD. Fourteen adults with TS/CTD and 14 tic-free control subjects completed questionnaires regarding SH and ADHD, and TS/CTD subjects completed self-report measures of current and past tic disorder symptoms and of current obsessions and compulsions. All subjects performed a sustained attention choice reaction time task during alternating blocks in which a mildly annoying stimulus (von Frey hair was applied to the ankle (“ON” or was not applied (“OFF”. We present here the clinical and cognitive task data for each subject.

  20. Tooth eruption sequence and dental crowding: a case-control study [v1; ref status: indexed, http://f1000r.es/2ng

    Directory of Open Access Journals (Sweden)

    Vahid Moshkelgosha

    2014-06-01

    Full Text Available When cases of dental crowding are identified and diagnosed promptly, interceptive orthodontics is particularly successful. Aim: To assess the differences in the eruption sequence of the mandibular canine and first premolar teeth in children with and without dental crowding. Materials and Methods: Children who attended the Shiraz Dental School's orthodontic clinic (Iran from September to December 2012 were enrolled in this case-control study. Tooth size arch length discrepancy (TSALD of all 8-10 year olds was calculated from patients’ dental models. Thirty-six children were randomly selected from those with TSALD of equal or less than 4mm (those with crowding. Each selected case was matched for sex and age with another child (as control with TSALD>−4mm attending the same clinic, in the same time period. The existing panoramic radiographs were traced and the eruption percentages were measured for mandibular canine and first premolar teeth. The mean difference between canine and first premolar eruption percentages was compared between the case and control groups using the SPSS (version PASW 18 software and a paired sample t-test. Results: Canine and first premolar eruption percentages in the case group were 65.82±13.00 and 78.92±10.15 percent, respectively. The mean eruption percentages for canines and first premolars of the control group were 74.12±14.55 and 75.47±11.60 percent, respectively. There was a significant difference in pre-eruptive positions of canine and first premolar teeth in those with moderate to severe crowding when compared to the control group (p<0.001. Conclusion: These findings may improve the early diagnosis of children with high risk of developing moderate to severe crowding during mixed dentition.

  1. An a posteriori measure of network modularity [v3; ref status: indexed, http://f1000r.es/2ju

    Directory of Open Access Journals (Sweden)

    Timothée Poisot

    2013-12-01

    Full Text Available Measuring the modularity of networks, and how it deviates from random expectations, important to understand their structure and emerging properties. Several measures exist to assess modularity, which when applied to the same network, can return both different modularity values (i.e. different estimates of how modular the network is and different module compositions (i.e. different groups of species forming said modules. More importantly, as each optimization method uses a different optimization criterion, there is a need to have an a posteriori measure serving as an equivalent of a goodness-of-fit. In this article, I propose such a measure of modularity, which is simply defined as the ratio of interactions established between members of the same modules vs. members of different modules. I apply this measure to a large dataset of 290 ecological networks representing host–parasite (bipartite and predator–prey (unipartite interactions, to show how the results are easy to interpret and present especially to a broad audience not familiar with modularity analyses, but still can reveal new features about modularity and the ways to measure it.

  2. Epidemiology and patterns of musculoskeletal motorcycle injuries in the USA [v1; ref status: indexed, http://f1000r.es/444

    Directory of Open Access Journals (Sweden)

    Sean T. Burns

    2015-05-01

    Full Text Available Introduction: Motorcycles have become an increasingly popular mode of transportation despite their association with a greater risk for injury compared with automobiles. Whereas the recent incidence of annual passenger vehicle fatalities in the United States of America (USA has progressively declined, motorcycle fatalities have steadily increased in the past 11 years. Although motorcycle injuries (MIs have been studied, to the author’s knowledge there are no published reports on MIs in the USA during this 11-year period. Methods: Study data were derived from a prospectively collected Level I trauma center database. Data sampling included motorcycle crash injury evaluations for the 10-year period ending on 31 August 2008. This retrospective analysis included patient demographic and medical data, helmet use, Glasgow coma scale (GCS score, injury severity score (ISS, length of hospital stay (LOS, specific injury diagnosis, and death. Data statistics were analyzed using the Spearman correlation coefficient, Kruskal-Wallis tests, and logistic regression. Results: The study identified 1252 motorcycle crash injuries. Helmets were worn by 40.7% of patients for which helmet data were available. The rates of the most common orthopedic injuries were tibia/fibula (19.01%, spine (16.21%, and forearm (10.14% fractures. The most common non-orthopedic motorcycle crash injuries were concussions (21.09%, skull fractures (8.23%, face fractures (13.66%, and hemo- and pneumothorax (8.79%. There was a significant correlation between greater age and higher ISS (r=0.21, P<0.0001 and longer LOS (r=0.22, P<0.0001. Older patients were also less likely to wear a helmet (OR=0.99, 95% CI: 0.98, 0.997, associated with a significantly higher risk for death (after adjustment for helmet use OR=1.03, 95% CI: 1.00, 1.05. All patients without helmets had a significantly lower GCS score (P=0.0001 and a higher mortality rate (after adjustment for patient demographic data OR=2.28, 95% CI: 1.13, 4.58.  Conclusion: Compared with historical reports, the prevalence of skull, face, spine, and pelvis fractures have increased in American motorcycle crashes. Compared to recent European studies, the incidence of USA skull and face fractures is much higher, while the incidence of USA spine and pelvis fractures is more comparable; however, this is not associated with increased in-hospital mortality.

  3. Expectant fathers’ knowledge of maternal morbidity: a Sri Lankan experience [v1; ref status: indexed, http://f1000r.es/zj

    Directory of Open Access Journals (Sweden)

    Amaya Weekrakkody

    2013-05-01

    Full Text Available Background: Male partners play an important and vital role in the decision-making process regarding pregnant women’s health. The purpose of the present study was to assess the knowledge and awareness of expectant fathers about Gestational Diabetes Mellitus (GDM, Pregnancy Induced Hypertension (PIH, and anaemia during pregnancy. Methods: A cross sectional descriptive study was carried out among expectant fathers whose partners were attending antenatal clinics at the Anuradhapura Teaching Hospital, Sri Lanka. All consenting participants were interviewed by investigators using an interviewer administered questionnaire to collect data on knowledge of risk factors, symptoms, complications and their control. Statistical analysis was performed using the Kruskal Wallis test.  Results: Of the 246 expectant fathers studied, 192 (78% were aware of GDM, 183 (74.4% and 154 (62.6% were aware of PIH and anaemia during pregnancy, respectively. The total number of answers provided by expectant fathers ranged from 0 to 33 (of 41 questions. There were 44 fathers who could not answer even a single question. For GDM, anaemia, and PIH, the percentages of expectant fathers who failed to provide at least a single correct answer were 24.8%, 40.2%, and 31.3%, respectively. The median number of total correct answers provided increased steadily along with the average income (chi-square 31.24, p<0.001 and educational level (chi-square 33.57, p<0.001. Expectant fathers in the 25-34 age group had significantly higher scores, compared to younger and older fathers (chi-square 15.11, p=0.001. Fathers experiencing the second pregnancy of their spouses also had higher scores. Conclusions: Expectant father’s knowledge of the selected morbidities was limited. To improve maternal health, any health promotional programmes should include expectant fathers.

  4. GASOLINE: a Cytoscape app for multiple local alignment of PPI networks [v2; ref status: indexed, http://f1000r.es/4f7

    Directory of Open Access Journals (Sweden)

    Giovanni Micale

    2014-09-01

    Full Text Available Comparing protein interaction networks can reveal interesting patterns of interactions for a specific function or process in distantly related species. In this paper we present GASOLINE, a Cytoscape app for multiple local alignments of PPI (protein-protein interaction networks. The app is based on the homonymous greedy and stochastic algorithm. GASOLINE starts with the identification of sets of similar nodes, called seeds of the alignment. Alignments are then extended in a greedy manner and finally refined. Both the identification of seeds and the extension of alignments are performed through an iterative Gibbs sampling strategy. GASOLINE is a Cytoscape app for computing and visualizing local alignments, without requiring any post-processing operations. GO terms can be easily attached to the aligned proteins for further functional analysis of alignments. GASOLINE can perform the alignment task in few minutes, even for a large number of input networks.

  5. GeneMANIA: Fast gene network construction and function prediction for Cytoscape [v1; ref status: indexed, http://f1000r.es/3rv

    Directory of Open Access Journals (Sweden)

    Jason Montojo

    2014-07-01

    Full Text Available The GeneMANIA Cytoscape app enables users to construct a composite gene-gene functional interaction network from a gene list. The resulting network includes the genes most related to the original list, and functional annotations from Gene Ontology. The edges are annotated with details about the publication or data source the interactions were derived from. The app leverages GeneMANIA’s database of 1800+ networks, containing over 500 million interactions spanning 8 organisms: A. thaliana, C. elegans, D. melanogaster, D. rerio, H. sapiens, M. musculus, R. norvegicus, and S. cerevisiae. Users may also import their own organisms, networks, and expression profiles. The app is compatible with Cytoscape versions 2 and 3.

  6. Biological network analysis with CentiScaPe: centralities and experimental dataset integration [v2; ref status: indexed, http://f1000r.es/55u

    Directory of Open Access Journals (Sweden)

    Giovanni Scardoni

    2015-07-01

    Full Text Available The growing dimension and complexity of the available experimental data generating biological networks have increased the need for tools that help in categorizing nodes by their topological relevance. Here we present CentiScaPe, a Cytoscape app specifically designed to calculate centrality indexes used for the identification of the most important nodes in a network. CentiScaPe is a comprehensive suite of algorithms dedicated to network nodes centrality analysis, computing several centralities for undirected, directed and weighted networks. The results of the topological analysis can be integrated with data set from lab experiments, like expression or phosphorylation levels for each protein represented in the network. Our app opens new perspectives in the analysis of biological networks, since the integration of topological analysis with lab experimental data enhance the predictive power of the bioinformatics analysis.

  7. BridgeDb app: unifying identifier mapping services for Cytoscape [v1; ref status: indexed, http://f1000r.es/3qb

    Directory of Open Access Journals (Sweden)

    Jianjiong Gao

    2014-07-01

    Full Text Available The BridgeDb app for Cytoscape allows users to map and annotate identifiers of genes, proteins and metabolites in the context of biological networks. The app greatly simplifies the identifier mapping process in Cytoscape by providing a unified interface to different mapping resources and services. The app also provides a programming interface via Cytoscape Commands that can be utilized for identifier mapping by other Cytoscape apps. In this article we provide a technical guide to the BridgeDb app for mapping identifiers in Cytoscape.

  8. Non-invasive imaging to monitor lupus nephritis and neuropsychiatric systemic lupus erythematosus [v1; ref status: indexed, http://f1000r.es/5gh

    Directory of Open Access Journals (Sweden)

    Joshua Thurman

    2015-06-01

    Full Text Available Systemic lupus erythematosus (SLE is an autoimmune disease that can affect multiple different organs, including the kidneys and central nervous system (CNS. Conventional radiological examinations in SLE patients include volumetric/ anatomical computed tomography (CT, magnetic resonance imaging (MRI and ultrasound (US. The utility of these modalities is limited, however, due to the complexity of the disease. Furthermore, CT and MRI contrast agents are contraindicated in patients with renal impairment. Various radiologic methods are currently being developed to improve disease characterization in patients with SLE beyond simple anatomical endpoints. Physiological non-contrast MRI protocols have been developed to assess tissue oxygenation, glomerular filtration, renal perfusion, interstitial diffusion, and inflammation-driven fibrosis in lupus nephritis (LN patients. For neurological symptoms, vessel size imaging (VSI, an MRI approach utilizing T2-relaxing iron oxide nanoparticles has shown promise as a diagnostic tool. Molecular imaging probes (mostly for MRI and nuclear medicine imaging have also been developed for diagnosing SLE with high sensitivity, and for monitoring disease activity. This paper reviews the challenges in evaluating disease activity in patients with LN and neuropsychiatric systemic lupus erythematosus (NPSLE. We describe novel MRI and positron-emission tomography (PET molecular imaging protocols using targeted iron oxide nanoparticles and radioactive ligands, respectively, for detection of SLE-associated inflammation.

  9. Case Report: Gollop-Wolfgang Complex in a 5 month old baby [v3; ref status: indexed, http://f1000r.es/53y

    Directory of Open Access Journals (Sweden)

    Ihtesham A. Qureshi

    2015-02-01

    Full Text Available Skeletal dysplasias are disorders associated with a generalized abnormality in the skeleton. The Gollop-Wolfgang complex (GWC is a limb deficiency disorder and an unusual limb malformation with highly variable manifestations. Here we report an interesting case of a 5-month old male baby from India with Gollop-Wolfgang Complex showing bifurcation of the right femur, ectrodactyly of both feet, ectrodactyly of left hand, syndactyly of right hand and unusual presentation of bilateral fibular agenesis and caudal (Sacrococcygeal agenesis. The etiology of GWC in this 5 month old male baby could possibly be attributed to spontaneous gene mutation. The clinical, radiographic findings and the unusual presentation are presented in detail.

  10. Cladonia lichens on extensive green roofs: evapotranspiration, substrate temperature, and albedo [v1; ref status: indexed, http://f1000r.es/2ha

    Directory of Open Access Journals (Sweden)

    Amy Heim

    2013-12-01

    Full Text Available Green roofs are constructed ecosystems that provide ecosystem services in urban environments. Shallow substrate green roofs subject the vegetation layer to desiccation and other environmental extremes, so researchers have evaluated a variety of stress-tolerant vegetation types for green roof applications. Lichens can be found in most terrestrial habitats.  They are able to survive extremely harsh conditions, including frequent cycles of desiccation and rehydration, nutrient-poor soil, fluctuating temperatures, and high UV intensities. Extensive green roofs (substrate depth <20cm exhibit these harsh conditions, making lichens possible candidates for incorporation into the vegetation layer on extensive green roofs.  In a modular green roof system, we tested the effect of Cladonia lichens on substrate temperature, water loss, and albedo compared to a substrate-only control. Overall, the Cladonia modules had significantly cooler substrate temperatures during the summer and significantly warmer temperatures during the fall.  Additionally, the Cladonia modules lost significantly less water than the substrate-only control. This implies that they may be able to benefit neighboring vascular plant species by reducing water loss and maintaining favorable substrate temperatures.

  11. Cladonia lichens on extensive green roofs: evapotranspiration, substrate temperature, and albedo [v2; ref status: indexed, http://f1000r.es/2v4

    Directory of Open Access Journals (Sweden)

    Amy Heim

    2014-01-01

    Full Text Available Green roofs are constructed ecosystems that provide ecosystem services in urban environments. Shallow substrate green roofs subject the vegetation layer to desiccation and other environmental extremes, so researchers have evaluated a variety of stress-tolerant vegetation types for green roof applications. Lichens can be found in most terrestrial habitats.  They are able to survive extremely harsh conditions, including frequent cycles of desiccation and rehydration, nutrient-poor soil, fluctuating temperatures, and high UV intensities. Extensive green roofs (substrate depth <20cm exhibit these harsh conditions, making lichens possible candidates for incorporation into the vegetation layer on extensive green roofs.  In a modular green roof system, we tested the effect of Cladonia lichens on substrate temperature, water loss, and albedo compared to a substrate-only control. Overall, the Cladonia modules had significantly cooler substrate temperatures during the summer and significantly warmer temperatures during the fall.  Additionally, the Cladonia modules lost significantly less water than the substrate-only control. This implies that they may be able to benefit neighboring vascular plant species by reducing water loss and maintaining favorable substrate temperatures.

  12. Case Report: Reversible cabergoline-associated cardiac valvulopathy post drug discontinuation [v1; ref status: indexed, http://f1000r.es/2jm

    Directory of Open Access Journals (Sweden)

    Chris G. Yedinak

    2014-07-01

    Full Text Available We present a case of a 21 year old male patient diagnosed with a 2.2 cm prolactin-secreting adenoma in contact with the optic chiasm. The patient was treated with up to 6mg/week of cabergoline (total cumulative dose 814 mg and developed mild valvulopathy. Valvulopathy was subsequently reversed after discontinuation of cabergoline therapy.

  13. Clinical applications of microRNAs [v2; ref status: indexed, http://f1000r.es/1o3

    Directory of Open Access Journals (Sweden)

    Per Hydbring

    2013-08-01

    Full Text Available MicroRNAs represent a class of small RNAs derived from polymerase II controlled transcriptional regions. The primary transcript forms one or several bulging double stranded hairpins which are processed by Drosha and Dicer into hetero-duplexes. The targeting microRNA strand of the duplex is incorporated into the RNA Induced Silencing Complex from where it silences up to hundreds of mRNA transcript by inducing mRNA degradation or blocking protein translation. Apart from involvement in a variety of biological processes, microRNAs were early recognized for their potential in disease diagnostics and therapeutics. Due to their stability, microRNAs could be used as biomarkers. Currently, there are microRNA panels helping physicians determining the origins of cancer in disseminated tumors. The development of microRNA therapeutics has proved more challenging mainly due to delivery issues. However, one drug is already in clinical trials and several more await entering clinical phases. This review summarizes what has been recognized pre-clinically and clinically on diagnostic microRNAs. In addition, it highlights individual microRNA drugs in running platforms driven by four leading microRNA-therapeutic companies.

  14. shRNA-seq data analysis with edgeR [v1; ref status: indexed, http://f1000r.es/38s

    Directory of Open Access Journals (Sweden)

    Zhiyin Dai

    2014-04-01

    Full Text Available Pooled short hairpin RNA sequencing (shRNA-seq screens are becoming increasingly popular in functional genomics research, and there is a need to establish optimal analysis tools to handle such data. Our open-source shRNA processing pipeline in edgeR provides a complete analysis solution for shRNA-seq screen data, that begins with the raw sequence reads and ends with a ranked lists of candidate shRNAs for downstream biological validation. We first summarize the raw data contained in a fastq file into a matrix of counts (samples in the columns, hairpins in the rows with options for allowing mismatches and small shifts in hairpin position. Diagnostic plots, normalization and differential representation analysis can then be performed using established methods to prioritize results in a statistically rigorous way, with the choice of either the classic exact testing methodology or a generalized linear modelling that can handle complex experimental designs. A detailed users’ guide that demonstrates how to analyze screen data in edgeR along with a point-and-click implementation of this workflow in Galaxy are also provided. The edgeR package is freely available from http://www.bioconductor.org.

  15. Sub-strains of Drosophila Canton-S differ markedly in their locomotor behavior [v1; ref status: indexed, http://f1000r.es/3is

    Directory of Open Access Journals (Sweden)

    Julien Colomb

    2014-07-01

    Full Text Available We collected five sub-strains of the standard laboratory wild-type Drosophila melanogaster Canton Special (CS and analyzed their walking behavior in Buridan's paradigm using the CeTrAn software. According to twelve different aspects of their behavior, the sub-strains fit into three groups. The group separation appeared not to be correlated with the origin of the stocks. We conclude that founder effects but not laboratory selection likely influenced the gene pool of the sub-strains. The flies’ stripe fixation was the parameter that varied most. Our results suggest that differences in the genome of laboratory stocks can render comparisons between nominally identical wild-type stocks meaningless. A single source for control strains may settle this problem.

  16. Progress and challenges in the computational prediction of gene function using networks [v1; ref status: indexed, http://f1000r.es/SqmJUM

    Directory of Open Access Journals (Sweden)

    Paul Pavlidis

    2012-09-01

    Full Text Available In this opinion piece, we attempt to unify recent arguments we have made that serious confounds affect the use of network data to predict and characterize gene function. The development of computational approaches to determine gene function is a major strand of computational genomics research. However, progress beyond using BLAST to transfer annotations has been surprisingly slow. We have previously argued that a large part of the reported success in using "guilt by association" in network data is due to the tendency of methods to simply assign new functions to already well-annotated genes. While such predictions will tend to be correct, they are generic; it is true, but not very helpful, that a gene with many functions is more likely to have any function. We have also presented evidence that much of the remaining performance in cross-validation cannot be usefully generalized to new predictions, making progressive improvement in analysis difficult to engineer. Here we summarize our findings about how these problems will affect network analysis, discuss some ongoing responses within the field to these issues, and consolidate some recommendations and speculation, which we hope will modestly increase the reliability and specificity of gene function prediction.

  17. DataUp: A tool to help researchers describe and share tabular data [v2; ref status: indexed, http://f1000r.es/48u

    Directory of Open Access Journals (Sweden)

    Carly Strasser

    2014-09-01

    Full Text Available Scientific datasets have immeasurable value, but they lose their value over time without proper documentation, long-term storage, and easy discovery and access. Across disciplines as diverse as astronomy, demography, archeology, and ecology, large numbers of small heterogeneous datasets (i.e., the long tail of data are especially at risk unless they are properly documented, saved, and shared. One unifying factor for many of these at-risk datasets is that they reside in spreadsheets. In response to this need, the California Digital Library (CDL partnered with Microsoft Research Connections and the Gordon and Betty Moore Foundation to create the DataUp data management tool for Microsoft Excel. Many researchers creating these small, heterogeneous datasets use Excel at some point in their data collection and analysis workflow, so we were interested in developing a data management tool that fits easily into those work flows and minimizes the learning curve for researchers. The DataUp project began in August 2011. We first formally assessed the needs of researchers by conducting surveys and interviews of our target research groups: earth, environmental, and ecological scientists. We found that, on average, researchers had very poor data management practices, were not aware of data centers or metadata standards, and did not understand the benefits of data management or sharing. Based on our survey results, we composed a list of desirable components and requirements and solicited feedback from the community to prioritize potential features of the DataUp tool. These requirements were then relayed to the software developers, and DataUp was successfully launched in October 2012.

  18. Connecting undergraduate science education with the needs of today’s graduates [v1; ref status: indexed, http://f1000r.es/4pl

    Directory of Open Access Journals (Sweden)

    Viviane Callier

    2014-11-01

    Full Text Available Undergraduate science programs are not providing graduates with the knowledgebase and skills they need to be successful on today’s job market. Curricular changes relevant to today’s marketplace and more opportunities for internships and work experience during students’ secondary education would facilitate a smoother transition to the working world and help employers find graduates that possess both the hard and soft skills needed in the workplace. In this article, we discuss these issues and offer solutions that would generate more marketplace-ready undergraduates.

  19. The reproductive season of scleractinian corals in Socotra, Yemen [v1; ref status: indexed, http://f1000r.es/36f

    Directory of Open Access Journals (Sweden)

    Andrew H. Baird

    2014-03-01

    Full Text Available Determining when corals reproduce has clear management and economic implications. Here we document the reproductive condition of corals in the genus Acropora on the island of Socotra in Yemen during February 2014. Twenty percent of colonies (n = 143 contained mature gametes and 28% had immature gametes indicating that spawning will occur in both February and March in 2014, confirming previous anecdotal reports of coral spawning at this time in Socotra. Acropora typically reproduce in synchrony with many other broadcast spawning scleractinian corals, and we therefore predict that many other species are reproductively active at this time of year.

  20. Association of spirochetal infection with Morgellons disease [v1; ref status: indexed, http://f1000r.es/8g

    OpenAIRE

    Marianne J Middelveen; Divya Burugu; Akhila Poruri; Jennie Burke; Peter J Mayne; Eva Sapi; Douglas G Kahn; Raphael B Stricker

    2013-01-01

    Morgellons disease (MD) is an emerging multisystem illness characterized by skin lesions with unusual filaments embedded in or projecting from epithelial tissue. Filament formation results from abnormal keratin and collagen expression by epithelial-based keratinocytes and fibroblasts. Recent research comparing MD to bovine digital dermatitis, an animal infectious disease with similar skin features, provided clues that spirochetal infection could play an important role in the human disease as ...

  1. How do eubacterial organisms manage aggregation-prone proteome? [v1; ref status: indexed, http://f1000r.es/3k3

    Directory of Open Access Journals (Sweden)

    Rishi Das Roy

    2014-06-01

    Full Text Available Eubacterial genomes vary considerably in their nucleotide composition. The percentage of genetic material constituted by guanosine and cytosine (GC nucleotides ranges from 20% to 70%.  It has been posited that GC-poor organisms are more dependent on protein folding machinery. Previous studies have ascribed this to the accumulation of mildly deleterious mutations in these organisms due to population bottlenecks. This phenomenon has been supported by protein folding simulations, which showed that proteins encoded by GC-poor organisms are more prone to aggregation than proteins encoded by GC-rich organisms. To test this proposition using a genome-wide approach, we classified different eubacterial proteomes in terms of their aggregation propensity and chaperone-dependence using multiple machine learning models. In contrast to the expected decrease in protein aggregation with an increase in GC richness, we found that the aggregation propensity of proteomes increases with GC content. A similar and even more significant correlation was obtained with the GroEL-dependence of proteomes: GC-poor proteomes have evolved to be less dependent on GroEL than GC-rich proteomes. We thus propose that a decrease in eubacterial GC content may have been selected in organisms facing proteostasis problems.

  2. Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV [v1; ref status: indexed, http://f1000r.es/4io

    Directory of Open Access Journals (Sweden)

    Andrew C. R. Martin

    2014-10-01

    Full Text Available The JavaScript Sequence Alignment Viewer (JSAV is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and ’dotifying’ repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

  3. FALCON: a software package for analysis of nestedness in bipartite networks [v1; ref status: indexed, http://f1000r.es/3z8

    Directory of Open Access Journals (Sweden)

    Stephen J. Beckett

    2014-08-01

    Full Text Available Nestedness is a statistical measure used to interpret bipartite interaction data in several ecological and evolutionary contexts, e.g. biogeography (species-site relationships and species interactions (plant-pollinator and host-parasite networks. Multiple methods have been used to evaluate nestedness, which differ in how the metrics for nestedness are determined. Furthermore, several different null models have been used to calculate statistical significance of nestedness scores. The profusion of measures and null models, many of which give conflicting results, is problematic for comparison of nestedness across different studies. We developed the FALCON software package to allow easy and efficient comparison of nestedness scores and statistical significances for a given input network, using a selection of the more popular measures and null models from the current literature. FALCON currently includes six measures and five null models for nestedness in binary networks, and two measures and four null models for nestedness in weighted networks. The FALCON software is designed to be efficient and easy to use. FALCON code is offered in three languages (R, MATLAB, Octave and is designed to be modular and extensible, enabling users to easily expand its functionality by adding further measures and null models. FALCON provides a robust methodology for comparing the strength and significance of nestedness in a given bipartite network using multiple measures and null models. It includes an “adaptive ensemble” method to reduce undersampling of the null distribution when calculating statistical significance. It can work with binary or weighted input networks. FALCON is a response to the proliferation of different nestedness measures and associated null models in the literature. It allows easy and efficient calculation of nestedness scores and statistical significances using different methods, enabling comparison of results from different studies and thereby supporting theoretical study of the causes and implications of nestedness in different biological contexts.

  4. Defining the functional states of Th17 cells [v1; ref status: indexed, http://f1000r.es/51y

    Directory of Open Access Journals (Sweden)

    Youjin Lee

    2015-05-01

    Full Text Available The molecular mechanisms governing T helper (Th cell differentiation and function have revealed a complex network of transcriptional and protein regulators. Cytokines not only initiate the differentiation of CD4 Th cells into subsets but also influence the identity, plasticity and effector function of a T cell. Of the subsets, Th17 cells, named for producing interleukin 17 (IL-17 as their signature cytokine, secrete a cohort of other cytokines, including IL-22, IL-21, IL-10, IL-9, IFNγ, and GM-CSF.  In recent years, Th17 cells have emerged as key players in host defense against both extracellular pathogens and fungal infections, but they have also been implicated as one of the main drivers in the pathogenesis of autoimmunity, likely mediated in part by the cytokines that they produce. Advances in high throughput genomic sequencing have revealed unexpected heterogeneity in Th17 cells and, as a consequence, may have tremendous impact on our understanding of their functional diversity. The assortment in gene expression may also identify different functional states of Th17 cells. This review aims to understand the interplay between the cytokine regulators that drive Th17 cell differentiation and functional states in Th17 cells.

  5. Response to Dr Stevens' letter ref. Visitisen et al: "Short-term effects of night shift work on breast cancer risk: a cohort study of payroll data"

    DEFF Research Database (Denmark)

    Kolstad, Henrik A; Garde, Anne Helene; Hansen, Åse Marie

    2017-01-01

    : a cohort study of payroll data". Scand J Work Environ Health. 2017;43(1):95. http://dx.doi.org/10.5271/sjweh.3607 2. Vistisen HT, Garde AH, Frydenberg M, Christiansen P, Hansen AM, Hansen J, Bonde JP, Kolstad HA. Short-term effects of night shift work on breast cancer risk: A cohort study of payroll data....... Scand J Work Environ Health. 2017;43(1):59-67. http://dx.doi.org/10.5271/sjweh.3603. 3. Ijaz S, Verbeek J, Seidler A, Lindbohm ML, Ojajarvi A, Orsini N, Costa G, Neuvonen K. Night-shift work and breast cancer--a systematic review and meta-analysis. Scand J Work Environ Health. 2013 Sep 1......;39(5):431-47. http://dx.doi.org/10.5271/sjweh.3371....

  6. Functional characterization of Candida albicans Hos2 histone deacetylase [v2; ref status: indexed, http://f1000r.es/3i2

    Directory of Open Access Journals (Sweden)

    G Karthikeyan

    2014-05-01

    Full Text Available Candida albicans is a mucosal commensal organism capable of causing superficial (oral and vaginal thrush infections in immune normal hosts, but is a major pathogen causing systemic and mucosal infections in immunocompromised individuals. Azoles have been very effective anti-fungal agents and the mainstay in treating opportunistic mold and yeast infections. Azole resistant strains have emerged compromising the utility of this class of drugs. It has been shown that azole resistance can be reversed by the co-administration of a histone deacetylase (HDAC inhibitor, suggesting that resistance is mediated by epigenetic mechanisms possibly involving Hos2, a fungal deacetylase. We report here the cloning and functional characterization of HOS2 (HighOsmolarity Sensitive, a gene coding for fungal histone deacetylase from C. albicans. Inhibition studies showed that Hos2 is susceptible to pan inhibitors such as trichostatin A (TSA and suberoylanilide hydroxamic acid (SAHA, but is not inhibited by class I inhibitors such as MS-275. This in vitro enzymatic assay, which is amenable to high throughput could be used for screening potent fungal Hos2 inhibitors that could be a potential anti-fungal adjuvant. Purified Hos2 protein consistently deacetylated tubulins, rather than histones from TSA-treated cells. Hos2 has been reported to be a putative NAD+ dependent histone deacetylase, a feature of sirtuins. We assayed for sirtuin activation with resveratrol and purified Hos2 protein and did not find any sirtuin activity.

  7. AGRIS: providing access to agricultural research data exploiting open data on the web [v1; ref status: indexed, http://f1000r.es/599

    Directory of Open Access Journals (Sweden)

    Fabrizio Celli

    2015-05-01

    Full Text Available AGRIS is the International System for Agricultural Science and Technology. It is supported by a large community of data providers, partners and users. AGRIS is a database that aggregates bibliographic data, and through this core data, related content across online information systems is retrieved by taking advantage of Semantic Web capabilities. AGRIS is a global public good and its vision is to be a responsive service to its user needs by facilitating contributions and feedback regarding the AGRIS core knowledgebase, AGRIS’s future and its continuous development. Periodic AGRIS e-consultations, partner meetings and user feedback are assimilated to the development of the AGRIS application and content coverage. This paper outlines the current AGRIS technical set-up, its network of partners, data providers and users as well as how AGRIS’s responsiveness to clients’ needs inspires the continuous technical development of the application. The paper concludes by providing a use case of how the AGRIS stakeholder input and the subsequent AGRIS e-consultation results influence the development of the AGRIS application, knowledgebase and service delivery.

  8. Creating 3D visualizations of MRI data: A brief guide [v1; ref status: indexed, http://f1000r.es/5o8

    Directory of Open Access Journals (Sweden)

    Christopher R. Madan

    2015-08-01

    Full Text Available While magnetic resonance imaging (MRI data is itself 3D, it is often difficult to adequately present the results papers and slides in 3D. As a result, findings of MRI studies are often presented in 2D instead. A solution is to create figures that include perspective and can convey 3D information; such figures can sometimes be produced by standard functional magnetic resonance imaging (fMRI analysis packages and related specialty programs. However, many options cannot provide functionality such as visualizing activation clusters that are both cortical and subcortical (i.e., a 3D glass brain, the production of several statistical maps with an identical perspective in the 3D rendering, or animated renderings. Here I detail an approach for creating 3D visualizations of MRI data that satisfies all of these criteria. Though a 3D ‘glass brain’ rendering can sometimes be difficult to interpret, they are useful in showing a more overall representation of the results, whereas the traditional slices show a more local view. Combined, presenting both 2D and 3D representations of MR images can provide a more comprehensive view of the study’s findings.

  9. Capsaicin from chili (Capsicum spp. inhibits vascular smooth muscle cell proliferation [v1; ref status: indexed, http://f1000r.es/4yk

    Directory of Open Access Journals (Sweden)

    Rongxia Liu

    2015-01-01

    Full Text Available Accelerated vascular smooth muscle cell (VSMC proliferation is implied in cardiovascular disease and significantly contributes to vessel lumen reduction following surgical interventions such as percutaneous transluminal coronary angioplasty or bypass surgery. Therefore, identification and characterization of compounds and mechanisms able to counteract VSMC proliferation is of potential therapeutic relevance. This work reveals the anti-proliferative effect of the natural product capsaicin from Capsicum spp. by quantification of metabolic activity and DNA synthesis in activated VSMC. The observed in vitro activity profile of capsaicin warrants further research on its mechanism of action and potential for therapeutic application.

  10. An open ecosystem engagement strategy through the lens of global food safety [v1; ref status: indexed, http://f1000r.es/527

    Directory of Open Access Journals (Sweden)

    Paul Stacey

    2015-05-01

    Full Text Available The Global Food Safety Partnership (GFSP is a public/private partnership established through the World Bank to improve food safety systems through a globally coordinated and locally-driven approach. This concept paper aims to establish a framework to help GFSP fully leverage the potential of open models.   In preparing this paper the authors spoke to many different GFSP stakeholders who asked questions about open models such as: what is it? what’s in it for me? why use an open rather than a proprietary model? how will open models generate equivalent or greater sustainable revenue streams compared to the current “traditional” approaches?  This last question came up many times with assertions that traditional service providers need to see opportunity for equivalent or greater revenue dollars before they will buy-in. This paper identifies open value propositions for GFSP stakeholders and proposes a framework for creating and structuring that value.   Open Educational Resources (OER were the primary open practice GFSP partners spoke to us about, as they provide a logical entry point for collaboration. Going forward, funders should consider requiring that educational resources and concomitant data resulting from their sponsorship should be open, as a public good. There are, however, many other forms of open practice that bring value to the GFSP. Nine different open strategies and tactics (Appendix A are described, including: open content (including OER and open courseware, open data, open access (research, open government, open source software, open standards, open policy, open licensing and open hardware. It is recommended that all stakeholders proactively pursue "openness" as an operating principle.   This paper presents an overall GFSP Open Ecosystem Engagement Strategy within which specific local case examples can be situated. Two different case examples, China and Colombia, are presented to show both project-based and crowd-sourced, direct-to-public paths through this ecosystem.

  11. MODIS/Terra+Aqua BRDF/Albedo Nadir BRDF-Adjusted Ref Band5 Daily L3 Global 30ArcSec CMG V006

    Data.gov (United States)

    National Aeronautics and Space Administration — The MCD43D66 Version 6 Bidirectional Reflectance Distribution Function and Albedo (BRDF/Albedo) Nadir BRDF Adjusted Reflectance (NBAR) data set is a daily 16-day...

  12. MODIS/Terra+Aqua BRDF/Albedo Nadir BRDF-Adjusted Ref Band4 Daily L3 Global 30ArcSec CMG V006

    Data.gov (United States)

    National Aeronautics and Space Administration — The MCD43D65 Version 6 Bidirectional Reflectance Distribution Function and Albedo (BRDF/Albedo) Nadir BRDF Adjusted Reflectance (NBAR) data set is a daily 16-day...

  13. MODIS/Terra+Aqua BRDF/Albedo Nadir BRDF-Adjusted Ref Band1 Daily L3 Global 30ArcSec CMG V006

    Data.gov (United States)

    National Aeronautics and Space Administration — The MCD43D62 Version 6 Bidirectional Reflectance Distribution Function and Albedo (BRDF/Albedo) Nadir BRDF Adjusted Reflectance (NBAR) data set is a daily 16-day...

  14. MODIS/Terra+Aqua BRDF/Albedo Nadir BRDF-Adjusted Ref Band6 Daily L3 Global 30ArcSec CMG V006

    Data.gov (United States)

    National Aeronautics and Space Administration — The MCD43D67 Version 6 Bidirectional Reflectance Distribution Function and Albedo (BRDF/Albedo) Nadir BRDF Adjusted Reflectance (NBAR) data set is a daily 16-day...

  15. MODIS/Terra+Aqua BRDF/Albedo Nadir BRDF-Adjusted Ref Band3 Daily L3 Global 30ArcSec CMG V006

    Data.gov (United States)

    National Aeronautics and Space Administration — The MCD43D64 Version 6 Bidirectional Reflectance Distribution Function and Albedo (BRDF/Albedo) Nadir BRDF Adjusted Reflectance (NBAR) data set is a daily 16-day...

  16. MODIS/Terra+Aqua BRDF/Albedo Nadir BRDF-Adjusted Ref Band7 Daily L3 Global 30ArcSec CMG V006

    Data.gov (United States)

    National Aeronautics and Space Administration — The MCD43D68 Version 6 Bidirectional Reflectance Distribution Function and Albedo (BRDF/Albedo) Nadir BRDF Adjusted Reflectance (NBAR) data set is a daily 16-day...

  17. Minoxidil induced hypertrichosis in a 2 year-old child [v1; ref status: indexed, http://f1000r.es/1vw

    Directory of Open Access Journals (Sweden)

    Ingrid Herskovitz

    2013-10-01

    Full Text Available We report a case of a 2 year-old male patient who developed generalized hypertrichosis after 2 months of treatment with 5% minoxidil foam for alopecia areata. This report highlights the danger of prescribing  topical minoxidil to young children and the need to correctly instruct caretakers about its administration.

  18. Astrocytes require insulin-like growth factor I to protect neurons against oxidative injury [v1; ref status: indexed, http://f1000r.es/2lf

    Directory of Open Access Journals (Sweden)

    Laura Genis

    2014-01-01

    Full Text Available Oxidative stress is a proposed mechanism in brain aging, making the study of its regulatory processes an important aspect of current neurobiological research. In this regard, the role of the aging regulator insulin-like growth factor I (IGF-I in brain responses to oxidative stress remains elusive as both beneficial and detrimental actions have been ascribed to this growth factor. Because astrocytes protect neurons against oxidative injury, we explored whether IGF-I participates in astrocyte neuroprotection and found that blockade of the IGF-I receptor in astrocytes abrogated their rescuing effect on neurons. The protection mediated by IGF-I against oxidative stress (H2O2 in astrocytes is probably needed for these cells to provide adequate neuroprotection. Indeed, in astrocytes but not in neurons, IGF-I helps decrease the pro-oxidant protein thioredoxin-interacting protein 1 and normalizes the levels of reactive oxygen species. Furthermore, IGF-I cooperates with trophic signals produced by astrocytes in response to H2O2 such as stem cell factor (SCF to protect neurons against oxidative insult. After stroke, a condition associated with brain aging where oxidative injury affects peri-infarcted regions, a simultaneous increase in SCF and IGF-I expression was found in the cortex, suggesting that a similar cooperative response takes place in vivo. Cell-specific modulation by IGF-I of brain responses to oxidative stress may contribute in clarifying the role of IGF-I in brain aging.

  19. Guiding Ebola patients to suitable health facilities: an SMS-based approach [v1; ref status: indexed, http://f1000r.es/51l

    Directory of Open Access Journals (Sweden)

    Mohamad-Ali Trad

    2015-02-01

    Full Text Available Access to appropriate health services is a fundamental problem in developing countries, where patients do not have access to information and to the nearest health service facility. We propose building a recommendation system based on simple SMS text messaging to help Ebola patients readily find the closest health service with available and appropriate resources. The system will map people’s reported symptoms to likely Ebola case definitions and suitable health service locations. In addition to providing a valuable individual service to people with curable diseases, the proposed system will also predict population-level disease spread risk for infectious diseases using crowd-sourced symptoms from the population. Health workers will be able to better plan and anticipate responses to the current Ebola outbreak in West Africa. Patients will have improved access to appropriate health care. This system could also be applied in other resource poor or rich settings.

  20. Folie a deux: a case report [v1; ref status: indexed, http://f1000r.es/SD4pSL

    Directory of Open Access Journals (Sweden)

    Sobia Haqqi

    2012-09-01

    Full Text Available Folie a deux, to date, remains a rare, yet a challenging psychiatric diagnosis. We discuss two cases that were identified in our out-patient clinics. One case was lost to follow up, while the other one showed improvement over time with appropriate management. Conclusion: As with any rare disorder, recognition and correct referral for rare diagnosis like folie a deux is of paramount importance.

  1. Dynamics of Ebola epidemics in West Africa 2014 [v2; ref status: indexed, http://f1000r.es/5fh

    Directory of Open Access Journals (Sweden)

    Robin J. Evans

    2015-05-01

    Full Text Available This paper investigates the dynamics of Ebola virus transmission in West Africa during 2014. The reproduction numbers for the total period of epidemic and for different consequent time intervals are estimated based on a simple linear model. It contains one major parameter - the average infectious period that defines the dynamics of epidemics. Numerical implementations are carried out on data collected from three countries Guinea, Sierra Leone and Liberia as well as the total data collected worldwide. Predictions are provided by considering different scenarios involving the average times of infectiousness for the next few months and the end of the current epidemic is estimated according to each scenario.

  2. Understanding the direct and indirect costs of patients with schizophrenia [v2; ref status: indexed, http://f1000r.es/5ow

    Directory of Open Access Journals (Sweden)

    Kazuhiro Tajima-Pozo

    2015-08-01

    Full Text Available Background: Schizophrenia is a disabling mental disorder with high prevalence and that usually  requires long-term follow-up and expensive lifelong treatment. The cost of schizophrenia treatment consumes a significant amount of the health services' budget in western countries. Objective: The aim of the study was to find out about the costs related to schizophrenia across different european countries and compare them. Results: Schizophrenia treatment costs an estimated 18 billion euros annually worldwide. The direct costs associated with medical help are only part of the total expenditure. The indirect costs are an equally (or even moreimportant part of the total cost. These expenses are related to the lack of productivity of schizophrenic patients and the cost that relatives have to bear as a result of taking care of their affected relatives. Conclusions: Although data on the cost of schizophrenia may vary slightly between different european countries, the general conclusion that can be drawn is that schizophrenia is a very costly disorder. Not only because of direct costs related to medical procedures, but also due to the non-medical (indirect costs. Together this suggests the need to investigate cost-efficient strategies that could provide a better outcome for schizophrenic patients, as well as the people who care for them.

  3. The nature and prevalence of chronic pain in homeless persons: an observational study [v1; ref status: indexed, http://f1000r.es/o6

    Directory of Open Access Journals (Sweden)

    Rebecca Fisher

    2013-07-01

    Full Text Available Background: Homeless people are known to suffer disproportionately with health problems that reduce physical functioning and quality of life, and shorten life expectancy. They suffer from a wide range of diseases that are known to be painful, but little information is available about the nature and prevalence of chronic pain in this vulnerable group. This study aimed to estimate the prevalence of chronic pain among homeless people, and to examine its location, effect on activities of daily living, and relationship with alcohol and drugs. Methods: We conducted face-to-face interviews with users of homeless shelters in four major cities in the United Kingdom, in the winters of 2009-11. Participants completed the Brief Pain Inventory, Short Form McGill Pain questionnaire, Leeds Assessment of Neuropathic Symptoms and Signs, and detailed their intake of prescribed and unprescribed medications and alcohol. We also recorded each participant’s reasons for homelessness, and whether they slept rough or in shelters. Findings: Of 168 shelter users approached, 150 (89.3% participated: 93 participants (63% reported experiencing pain lasting longer than three months; the mean duration of pain experienced was 82.2 months. The lower limbs were most frequently affected. Opioids appeared to afford a degree of analgesia for some, but whilst many reported symptoms suggestive of neuropathic pain, very few were taking anti-neuropathic drugs. Interpretation: The prevalence of chronic pain in the homeless appears to be substantially higher than the general population, is poorly controlled, and adversely affects general activity, walking and sleeping. It is hard to discern whether chronic pain is a cause or effect of homelessness, or both. Pain is a symptom, but in this challenging group it might not always be possible to treat the underlying cause. Exploring the diagnosis and treatment of neuropathic pain may offer a means of improving the quality of these vulnerable people’s lives.

  4. Case Report: Neuropathic pain in a patient with congenital insensitivity to pain [v2; ref status: indexed, http://f1000r.es/5iu

    Directory of Open Access Journals (Sweden)

    Daniel W. Wheeler

    2015-06-01

    Full Text Available We report a unique case of a woman with Channelopathy-associated Insensitivity to Pain (CIP Syndrome, who developed features of neuropathic pain after sustaining pelvic fractures and an epidural hematoma that impinged on the right fifth lumbar (L5 nerve root. Her pelvic injuries were sustained during painless labor, which culminated in a Cesarean section. She had been diagnosed with CIP as child, which was later confirmed when she was found to have null mutations of the SCN9A gene that encodes the voltage-gated sodium channel Nav1.7. She now complains of troubling continuous buzzing in both legs and a vice-like squeezing in the pelvis on walking. Quantitative sensory testing showed that sensory thresholds to mechanical stimulation of the dorsum of both feet had increased more than 10-fold on both sides compared with tests performed before her pregnancy. These findings fulfill the diagnostic criteria for neuropathic pain. Notably, she mostly only experiences the negative symptoms (such as numbness and tingling, but also electric shocks, and she has not reported sharp or burning sensations, although the value of verbal descriptors is somewhat limited in a person who has never felt pain before. However, her case strongly suggests that at least some of the symptoms of neuropathic pain can persist despite the absence of the Nav1.7 channel. Pain is a subjective experience and this case sheds light on the transmission of neuropathic pain in humans that cannot be learned from knockout mice.

  5. A novel pseudoderivative-based mutation operator for real-coded adaptive genetic algorithms [v2; ref status: indexed, http://f1000r.es/1td

    Directory of Open Access Journals (Sweden)

    Maxinder S Kanwal

    2013-11-01

    Full Text Available Recent development of large databases, especially those in genetics and proteomics, is pushing the development of novel computational algorithms that implement rapid and accurate search strategies. One successful approach has been to use artificial intelligence and methods, including pattern recognition (e.g. neural networks and optimization techniques (e.g. genetic algorithms. The focus of this paper is on optimizing the design of genetic algorithms by using an adaptive mutation rate that is derived from comparing the fitness values of successive generations. We propose a novel pseudoderivative-based mutation rate operator designed to allow a genetic algorithm to escape local optima and successfully continue to the global optimum. Once proven successful, this algorithm can be implemented to solve real problems in neurology and bioinformatics. As a first step towards this goal, we tested our algorithm on two 3-dimensional surfaces with multiple local optima, but only one global optimum, as well as on the N-queens problem, an applied problem in which the function that maps the curve is implicit. For all tests, the adaptive mutation rate allowed the genetic algorithm to find the global optimal solution, performing significantly better than other search methods, including genetic algorithms that implement fixed mutation rates.

  6. Sub-strains of Drosophila Canton-S differ markedly in their locomotor behavior [v2; ref status: indexed, http://f1000r.es/57i

    Directory of Open Access Journals (Sweden)

    Julien Colomb

    2015-04-01

    Full Text Available We collected five sub-strains of the standard laboratory wild-type Drosophila melanogaster Canton Special (CS and analyzed their walking behavior in Buridan's paradigm using the CeTrAn software. According to twelve different aspects of their behavior, the sub-strains fit into three groups. The group separation appeared not to be correlated with the origin of the stocks. We conclude that founder effects but not laboratory selection likely influenced the gene pool of the sub-strains. The flies’ stripe fixation was the parameter that varied most. Our results suggest that differences in the genome of laboratory stocks can render comparisons between nominally identical wild-type stocks meaningless. A single source for control strains may settle this problem.

  7. A novel mouse model of creatine transporter deficiency [v2; ref status: indexed, http://f1000r.es/4zb

    Directory of Open Access Journals (Sweden)

    Laura Baroncelli

    2015-01-01

    Full Text Available Mutations in the creatine (Cr transporter (CrT gene lead to cerebral creatine deficiency syndrome-1 (CCDS1, an X-linked metabolic disorder characterized by cerebral Cr deficiency causing intellectual disability, seizures, movement  and behavioral disturbances, language and speech impairment ( OMIM #300352. CCDS1 is still an untreatable pathology that can be very invalidating for patients and caregivers. Only two murine models of CCDS1, one of which is an ubiquitous knockout mouse, are currently available to study the possible mechanisms underlying the pathologic phenotype of CCDS1 and to develop therapeutic strategies. Given the importance of validating phenotypes and efficacy of promising treatments in more than one mouse model we have generated a new murine model of CCDS1 obtained by ubiquitous deletion of 5-7 exons in the Slc6a8 gene. We showed a remarkable Cr depletion in the murine brain tissues and cognitive defects, thus resembling the key features of human CCDS1. These results confirm that CCDS1 can be well modeled in mice. This CrT−/y murine model will provide a new tool for increasing the relevance of preclinical studies to the human disease.

  8. A novel mouse model of creatine transporter deficiency [v1; ref status: indexed, http://f1000r.es/4f8

    Directory of Open Access Journals (Sweden)

    Laura Baroncelli

    2014-09-01

    Full Text Available Mutations in the creatine (Cr transporter (CrT gene lead to cerebral creatine deficiency syndrome-1 (CCDS1, an X-linked metabolic disorder characterized by cerebral Cr deficiency causing intellectual disability, seizures, movement  and behavioral disturbances, language and speech impairment ( OMIM #300352. CCDS1 is still an untreatable pathology that can be very invalidating for patients and caregivers. Only two murine models of CCDS1, one of which is an ubiquitous knockout mouse, are currently available to study the possible mechanisms underlying the pathologic phenotype of CCDS1 and to develop therapeutic strategies. Given the importance of validating phenotypes and efficacy of promising treatments in more than one mouse model we have generated a new murine model of CCDS1 obtained by ubiquitous deletion of 5-7 exons in the Slc6a8 gene. We showed a remarkable Cr depletion in the murine brain tissues and cognitive defects, thus resembling the key features of human CCDS1. These results confirm that CCDS1 can be well modeled in mice. This CrT−/y murine model will provide a new tool for increasing the relevance of preclinical studies to the human disease.

  9. Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues [v2; ref status: indexed, http://f1000r.es/2dl

    Directory of Open Access Journals (Sweden)

    Liliana Florea

    2013-11-01

    Full Text Available Alternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. However, despite many efforts, the repertoire of gene splicing variation is still incompletely characterized, even in humans. Here we describe a new computational system, ASprofile, and its application to RNA-seq data from Illumina’s Human Body Map project (>2.5 billion reads.  Using the system, we identified putative alternative splicing events in 16 different human tissues, which provide a dynamic picture of splicing variation across the tissues. We detected 26,989 potential exon skipping events representing differences in splicing patterns among the tissues. A large proportion of the events (>60% were novel, involving new exons (~3000, new introns (~16000, or both. When tracing these events across the sixteen tissues, only a small number (4-7% appeared to be differentially expressed (‘switched’ between two tissues, while 30-45% showed little variation, and the remaining 50-65% were not present in one or both tissues compared.  Novel exon skipping events appeared to be slightly less variable than known events, but were more tissue-specific. Our study represents the first effort to build a comprehensive catalog of alternative splicing in normal human tissues from RNA-seq data, while providing insights into the role of alternative splicing in shaping tissue transcriptome differences. The catalog of events and the ASprofile software are freely available from the Zenodo repository (http://zenodo.org/record/7068; doi:10.5281/zenodo.7068 and from our web site http://ccb.jhu.edu/software/ASprofile.

  10. Bayesian prediction of microbial oxygen requirement [v1; ref status: indexed, http://f1000r.es/1m6

    Directory of Open Access Journals (Sweden)

    Dan B. Jensen

    2013-09-01

    Full Text Available Background: Prediction of the optimal habitat conditions for a given bacterium, based on genome sequence alone would be of value for scientific as well as industrial purposes. One example of such a habitat adaptation is the requirement for oxygen. In spite of good genome data availability, there have been only a few prediction attempts of bacterial oxygen requirements, using genome sequences. Here, we describe a method for distinguishing aerobic, anaerobic and facultative anaerobic bacteria, based on genome sequence-derived input, using naive Bayesian inference. In contrast, other studies found in literature only demonstrate the ability to distinguish two classes at a time. Results: The results shown in the present study are as good as or better than comparable methods previously described in the scientific literature, with an arguably simpler method, when results are directly compared. This method further compares the performance of a single-step naive Bayesian prediction of the three included classifications, compared to a simple Bayesian network with two steps. A two-step network, distinguishing first respiring from non-respiring organisms, followed by the distinction of aerobe and facultative anaerobe organisms within the respiring group, is found to perform best. Conclusions: A simple naive Bayesian network based on the presence or absence of specific protein domains within a genome is an effective and easy way to predict bacterial habitat preferences, such as oxygen requirement.

  11. Longhorned beetle (Coleoptera: Cerambycidae diversity in a fragmented temperate forest landscape [v2; ref status: indexed, http://f1000r.es/yz

    Directory of Open Access Journals (Sweden)

    Daniel M Pavuk

    2013-03-01

    Full Text Available Longhorned beetles (Coleoptera: Cerambycidae are an important component of temperate forest ecosystems.  We trapped longhorned beetles in forests in northwest Ohio during 2008 to test the hypothesis that larger forests have greater species diversity than smaller forests.  Large forests had a significantly greater cerambycid species richness than small forests (t = 3.16. P = 0.02, and there was a significant relationship between forest size and cerambycid species richness.

  12. MODIS/Terra+Aqua BRDF/Albedo Nadir BRDF-Adjusted Ref Band2 Daily L3 Global 30ArcSec CMG V006

    Data.gov (United States)

    National Aeronautics and Space Administration — The MCD43D63 Version 6 Bidirectional Reflectance Distribution Function and Albedo (BRDF/Albedo) Nadir BRDF Adjusted Reflectance (NBAR) data set is a daily 16-day...

  13. Connecting the pieces: Using ORCIDs to improve research impact and repositories [v1; ref status: indexed, http://f1000r.es/5du

    Directory of Open Access Journals (Sweden)

    Mohamed Baessa

    2015-07-01

    Full Text Available Quantitative data are crucial in the assessment of research impact in the academic world. However, as a young university created in 2009, King Abdullah University of Science and Technology (KAUST needs to aggregate bibliometrics from researchers coming from diverse origins, not necessarily with the proper affiliations. In this context, the University has launched an institutional repository in September 2012 with the objectives of creating a home for the intellectual outputs of KAUST researchers. Later, the university adopted the first mandated institutional open access policy in the Arab region, effective June 31, 2014. Several projects were then initiated in order to accurately identify the research being done by KAUST authors and bring it into the repository in accordance with the open access policy. Integration with ORCID has been a key element in this process and the best way to ensure data quality for researcher’s scientific contributions. It included the systematic inclusion and creation, if necessary, of ORCID identifiers in the existing repository system, an institutional membership in ORCID, and the creation of dedicated integration tools. In addition and in cooperation with the Office of Research Evaluation, the Library worked at implementing a Current Research Information System (CRIS as a standardized common resource to monitor KAUST research outputs. We will present our findings about the CRIS implementation, the ORCID API, the repository statistics as well as our approach in conducting the assessment of research impact in terms of usage by the global research community.

  14. Finding small molecules for the ‘next Ebola’ [v1; ref status: indexed, http://f1000r.es/542

    Directory of Open Access Journals (Sweden)

    Sean Ekins

    2015-02-01

    Full Text Available The current Ebola virus epidemic may provide some suggestions of how we can better prepare for the next pathogen outbreak. We propose several cost effective steps that could be taken that would impact the discovery and use of small molecule therapeutics including: 1. text mine the literature, 2. patent assignees and/or inventors should openly declare their relevant filings, 3. reagents and assays could be commoditized, 4. using manual curation to enhance database links, 5. engage database and curation teams, 6. consider open science approaches, 7. adapt the “box” model for shareable reference compounds, and 8. involve the physician’s perspective.

  15. The Binding Ring Illusion: assimilation affects the perceived size of a circular array [v2; ref status: indexed, http://f1000r.es/12q

    Directory of Open Access Journals (Sweden)

    J Daniel McCarthy

    2013-04-01

    Full Text Available Our perception of an object’s size arises from the integration of multiple sources of visual information including retinal size, perceived distance and its size relative to other objects in the visual field. This constructive process is revealed through a number of classic size illusions such as the Delboeuf Illusion, the Ebbinghaus Illusion and others illustrating size constancy. Here we present a novel variant of the Delbouef and Ebbinghaus size illusions that we have named the Binding Ring Illusion. The illusion is such that the perceived size of a circular array of elements is underestimated when superimposed by a circular contour – a binding ring – and overestimated when the binding ring slightly exceeds the overall size of the array. Here we characterize the stimulus conditions that lead to the illusion, and the perceptual principles that underlie it. Our findings indicate that the perceived size of an array is susceptible to the assimilation of an explicitly defined superimposed contour. Our results also indicate that the assimilation process takes place at a relatively high level in the visual processing stream, after different spatial frequencies have been integrated and global shape has been constructed. We hypothesize that the Binding Ring Illusion arises due to the fact that the size of an array of elements is not explicitly defined and therefore can be influenced (through a process of assimilation by the presence of a superimposed object that does have an explicit size.

  16. Internet-delivered eye movement desensitization and reprocessing (iEMDR: an open trial [v2; ref status: indexed, http://f1000r.es/zr

    Directory of Open Access Journals (Sweden)

    Jay Spence

    2013-05-01

    Full Text Available Recent research indicates internet-delivered cognitive behavioural therapy (iCBT can reduce symptoms of post traumatic stress disorder (PTSD. This study examined the efficacy of an internet-delivered treatment protocol that combined iCBT and internet-delivered eye movement desensitization and reprocessing (iEMDR, in an uncontrolled trial. Eleven of the 15 participants completed post-treatment questionnaires. Large effect sizes were found from pre-treatment to 3-month follow-up (d = 1.03 – 1.61 on clinician-assessed and self-reported measures of PTSD, anxiety and distress, with moderate effect sizes (d = 0.59 – 0.70 found on measures of depression and disability. At post-treatment, 55% of the participants no longer met criteria for PTSD and this was sustained at follow-up. Symptom worsening occurred in 3 of 15 (20% of the sample from pre- to post-treatment; however, these participants reported overall symptom improvement by follow-up. Future research directions for iEMDR are discussed.

  17. Misleading hepatitis B testing in the setting of intravenous immunoglobulin [v1; ref status: indexed, http://f1000r.es/25r

    Directory of Open Access Journals (Sweden)

    Christelle M Ilboudo

    2013-11-01

    Full Text Available Intravenous immunoglobulin (IVIG is commonly used for a wide range of diagnoses, by multiple pediatric subspecialists. We report two cases of hepatitis B screening results post IVIG infusion, where positive anti-Hepatitis B core antigen serology tests indicated possible occult hepatitis infection, leading to a delay in care. However, serial antibody testing showed results consistent with the passive transfer of antibodies.

  18. Levels of the DNA repair enzyme human apurinic/apyrimidinic endonuclease (APE1, APEX, Ref-1) are associated with the intrinsic radiosensitivity of cervical cancers.

    OpenAIRE

    Herring, C. J.; West, C. M.; Wilks, D. P.; Davidson, S. E.; Hunter, R. D.; Berry, P.; Forster, G.; MacKinnon, J.; Rafferty, J. A.; Elder, R. H.; Hendry, J. H.; Margison, G. P.

    1998-01-01

    A study was made of the relationship between the intrinsic radiosensitivity of human cervical tumours and the expression of the DNA repair enzyme human apurinic/apyrimidinic endonuclease (HAP1). The radiosensitivity of clonogenic cells in tumour biopsies was measured as surviving fraction at 2 Gy (SF2) using a soft agar assay. HAP1 expression levels were determined after staining of formalin-fixed paraffin-embedded tumour sections with a rabbit antiserum raised against recombinant HAP1. Both ...

  19. Association between digital dermatoglyphics and handedness among Sinhalese in Sri Lanka [v3; ref status: indexed, http://f1000r.es/278

    Directory of Open Access Journals (Sweden)

    Buddhika TB Wijerathne

    2013-11-01

    Full Text Available Background The relationship between handedness and digital dermatoglyphic patterns has never been investigated in the Sinhalese population. The goal of this study is to establish the above mentioned relationship, which would positively aid personal identification.  Findings One hundred forty Sinhalese students (70 right-handed and 70 left-handed were studied for their digital dermatoglyphic pattern distribution. The results show that a statistically significant correlation exists for; digit 5 (Ulnar loop; P= 0.0449 and radial loop; P= 0.0248 by Fisher’s exact test of the right hand in female, digit 1 (radial loop; P=0.0248 by Fisher’s exact test and digit 2 (Ulnar loop; P=0.0306 of the left hand in females, digit 3 (Ulnar loop; P= 0.0486 and whorl; P= 0.0356 by Fisher’s exact test and digit 4 (Ulnar loop; P= 0.0449 and whorl; P= 0.0301 by Fisher’s exact test of the right hand in males, digit 4 (whorl; P=0.0160 by Fisher’s exact test of the left hand in males. Conclusions  Statistically significant differences in handedness and digital dermatoglyphic patterns were evident among Sinhalese people. Further study with a larger sample size is recommended.

  20. Association between digital dermatoglyphics and handedness among Sinhalese in Sri Lanka [v2; ref status: indexed, http://f1000r.es/1ft

    Directory of Open Access Journals (Sweden)

    Buddhika TB Wijerathne

    2013-07-01

    Full Text Available Background The relationship between handedness and digital dermatoglyphic patterns has never been investigated in the Sinhalese population. The goal of this study is to establish the above mentioned relationship, which would positively aid personal identification.  Findings One hundred forty Sinhalese students (70 right-handed and 70 left-handed were studied for their digital dermatoglyphic pattern distribution. The results show that a statistically significant correlation exists for; digit 5 (Ulnar loop; P= 0.0449 and radial loop; P= 0.0248 by Fisher’s exact test of the right hand in female, digit 1 (radial loop; P=0.0248 by Fisher’s exact test and digit 2 (Ulnar loop; P=0.0306 of the left hand in females, digit 3 (Ulnar loop; P= 0.0486 and whorl; P= 0.0356 by Fisher’s exact test and digit 4 (Ulnar loop; P= 0.0449 and whorl; P= 0.0301 by Fisher’s exact test of the right hand in males, digit 4 (whorl; P=0.0160 by Fisher’s exact test of the left hand in males. Conclusions  Statistically significant differences in handedness and digital dermatoglyphic patterns were evident among Sinhalese people. Further study with a larger sample size is recommended.

  1. Modeling enzootic raccoon rabies from land use patterns - Georgia (USA 2006-2010 [v2; ref status: indexed, http://f1000r.es/34t

    Directory of Open Access Journals (Sweden)

    John E. Duke

    2014-03-01

    Full Text Available We analyzed how land-use patterns and changes in urbanization influence reported rabid raccoons in Georgia from 2006 - 2010.  Using Geographical Information Systems and rabies surveillance data, multivariate analysis was conducted on 15 land-use variables that included natural topography, agricultural development, and urbanization to model positive raccoon rabies cases while controlling for potential raccoon submission bias associated with higher human population densities.  Low intensity residential development was positively associated with reported rabid raccoons while a negative association was found with evergreen forest.  Evergreen forests may offer a barrier effect where resources are low and raccoon populations are not supported.  Areas with pure stands of upland evergreen forest might be utilized in baiting strategies for oral rabies vaccination programs where fewer or no baits may be needed.  Their use as a barrier should be considered carefully in a cost-effective strategy for oral rabies vaccination (ORV programs to contain the western spread of this important zoonotic disease.

  2. Modeling enzootic raccoon rabies from land use patterns - Georgia (USA 2006-2010 [v1; ref status: indexed, http://f1000r.es/2i3

    Directory of Open Access Journals (Sweden)

    John E. Duke

    2013-12-01

    Full Text Available We analyzed how land-use patterns and changes in urbanization influence reported rabid raccoons in Georgia from 2006 - 2010.  Using Geographical Information Systems and rabies surveillance data, multivariate analysis was conducted on 15 land-use variables that included natural topography, agricultural development, and urbanization to model positive raccoon rabies cases while controlling for potential raccoon submission bias associated with higher human population densities.  Low intensity residential development was positively associated with reported rabid raccoons while a negative association was found with evergreen forest.  Evergreen forests may offer a barrier effect where resources are low and raccoon populations are not supported.  Areas with pure stands of upland evergreen forest might be utilized in baiting strategies for oral rabies vaccination programs where fewer or no baits may be needed.  Their use as a barrier should be considered carefully in a cost-effective strategy for oral rabies vaccination (ORV programs to contain the western spread of this important zoonotic disease.

  3. Methodological framework to identify possible adverse drug reactions using population-based administrative data [v1; ref status: indexed, http://f1000r.es/3ys

    Directory of Open Access Journals (Sweden)

    Brian Sauer

    2014-10-01

    Full Text Available Purpose: We present a framework for detecting possible adverse drug reactions (ADRs using the Utah Medicaid administrative data. We examined four classes of ADRs associated with treatment of dementia by acetylcholinesterase inhibitors (AChEIs: known reactions (gastrointestinal, psychological disturbances, potential reactions (respiratory disturbance, novel reactions (hepatic, hematological disturbances, and death. Methods: Our cohort design linked drug utilization data to medical claims from Utah Medicaid recipients. We restricted the analysis to 50 years-old and older beneficiaries diagnosed with dementia-related diseases. We compared patients treated with AChEI to patients untreated with anti-dementia medication therapy. We attempted to remove confounding by establishing propensity-score-matched cohorts for each outcome investigated; we then evaluated the effects of drug treatment by conditional multivariable Cox-proportional-hazard regression. Acute and transient effects were evaluated by a crossover design using conditional logistic regression. Results: Propensity-matched analysis of expected reactions revealed that AChEI treatment was associated with gastrointestinal episodes (Hazard Ratio [HR]: 2.02; 95%CI: 1.28-3.2, but not psychological episodes, respiratory disturbance, or death. Among the unexpected reactions, the risk of hematological episodes was higher (HR: 2.32; 95%CI: 1.47-3.6 in patients exposed to AChEI. AChEI exposure was not associated with an increase in hepatic episodes. We also noted a trend, identified in the case-crossover design, toward increase odds of experiencing acute hematological events during AChEI exposure (Odds Ratio: 3.0; 95% CI: 0.97 - 9.3. Conclusions: We observed an expected association between AChEIs treatment and gastrointestinal disturbances and detected a signal of possible hematological ADR after treatment with AChEIs in this pilot study. Using this analytic framework may raise awareness of potential ADEs and generate hypotheses for future investigations. Early findings, or signal detection, are considered hypothesis generating since confirmatory studies must be designed to determine if the signal represents a true drug safety problem.

  4. agINFRA: a research data hub for agriculture, food and the environment [v2; ref status: indexed, http://f1000r.es/5hk

    Directory of Open Access Journals (Sweden)

    Andreas Drakos

    2015-06-01

    Full Text Available The agINFRA project (www.aginfra.eu was a European Commission funded project under the 7th Framework Programme that aimed to introduce agricultural scientific communities to the vision of open and participatory data-intensive science. agINFRA has now evolved into the European hub for data-powered research on agriculture, food and the environment, serving the research community through multiple roles. Working on enhancing the interoperability between heterogeneous data sources, the agINFRA project has left a set of grid- and cloud- based services that can be reused by future initiatives and adopted by existing ones, in order to facilitate the dissemination of agricultural research, educational and other types of data. On top of that, agINFRA provided a set of domain-specific recommendations for the publication of agri-food research outcomes. This paper discusses the concept of the agINFRA project and presents its major outcomes, as adopted by existing initiatives activated in the context of agricultural research and education.

  5. The Resource Identification Initiative: A cultural shift in publishing [v1; ref status: indexed, http://f1000r.es/5fj

    Directory of Open Access Journals (Sweden)

    Anita Bandrowski

    2015-05-01

    Full Text Available A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to allow humans and algorithms to identify the exact resources that are reported or answer basic questions such as “What other studies used resource X?” To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (including software and databases. RRIDs represent accession numbers assigned by an authoritative database, e.g., the model organism databases, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal (www.scicrunch.org/resources. RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are generally accurate in performing the task of identifying resources and supportive of the goals of the project. We also show that identifiability of the resources pre- and post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on reproducibility relating to research resources.

  6. An object oriented implementation of the Yeadon human inertia model [v2; ref status: indexed, http://f1000r.es/558

    Directory of Open Access Journals (Sweden)

    Christopher Dembia

    2015-04-01

    Full Text Available We present an open source software implementation of a popular mathematical method developed by M.R. Yeadon for calculating the body and segment inertia parameters of a human body. The software is written in a high level open source language and provides three interfaces for manipulating the data and the model: a Python API, a command-line user interface, and a graphical user interface. Thus the software can fit into various data processing pipelines and requires only simple geometrical measures as input.

  7. On the intrinsic disorder status of the major players in programmed cell death pathways [v1; ref status: indexed, http://f1000r.es/1me

    Directory of Open Access Journals (Sweden)

    Alexey V Uversky

    2013-09-01

    Full Text Available Earlier computational and bioinformatics analysis of several large protein datasets across 28 species showed that proteins involved in regulation and execution of programmed cell death (PCD possess substantial amounts of intrinsic disorder. Based on the comprehensive analysis of these datasets by a wide array of modern bioinformatics tools it was concluded that disordered regions of PCD-related proteins are involved in a multitude of biological functions and interactions with various partners, possess numerous posttranslational modification sites, and have specific evolutionary patterns (Peng et al. 2013. This study extends our previous work by providing information on the intrinsic disorder status of some of the major players of the three major PCD pathways: apoptosis, autophagy, and necroptosis. We also present a detailed description of the disorder status and interactomes of selected proteins that are involved in the p53-mediated apoptotic signaling pathways.

  8. Assessing the bipotency of in vitro-derived neuromesodermal progenitors [v1; ref status: indexed, http://f1000r.es/58z

    Directory of Open Access Journals (Sweden)

    Anestis Tsakiridis

    2015-04-01

    Full Text Available Retrospective clonal analysis in the mouse has demonstrated that the posterior spinal cord neurectoderm and paraxial mesoderm share a common bipotent progenitor. These neuromesodermal progenitors (NMPs are the source of new axial structures during embryonic rostrocaudal axis elongation and are marked by the simultaneous co-expression of the transcription factors T(Brachyury (T(Bra and Sox2. NMP-like cells have recently been derived from pluripotent stem cells in vitro following combined stimulation of Wnt and fibroblast growth factor (FGF signaling. Under these conditions the majority of cultures consist of T(Bra/Sox2 co-expressing cells after 48-72 hours of differentiation. Although the capacity of these cells to generate posterior neural and paraxial mesoderm derivatives has been demonstrated at the population level, it is unknown whether a single in vitro-derived NMP can give rise to both neural and mesodermal cells. Here we demonstrate that T(Bra positive cells obtained from mouse epiblast stem cells (EpiSCs after culture in NMP-inducing conditions can generate both neural and mesodermal clones. This finding suggests that, similar to their embryonic counterparts, in vitro-derived NMPs are truly bipotent and can thus be exploited as a model for studying the molecular basis of developmental cell fate decisions.

  9. JSim, an open-source modeling system for data analysis [v1; ref status: indexed, http://f1000r.es/2fk

    Directory of Open Access Journals (Sweden)

    Erik Butterworth

    2013-12-01

    Full Text Available JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter sets, and for making comparisons among different models running simultaneously or separately. Interactive use is supported by a large collection of graphical user interfaces for model writing and compilation diagnostics, defining input functions, model runs, selection of algorithms solving ordinary and partial differential equations, run-time multidimensional graphics, parameter optimization (8 methods, sensitivity analysis, and Monte Carlo simulation for defining confidence ranges. JSim uses Mathematical Modeling Language (MML a declarative syntax specifying algebraic and differential equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc. are accessed through procedure calls. MML syntax is simple, basically defining the parameters and variables, then writing the equations in a straightforward, easily read and understood mathematical form. This makes JSim good for teaching modeling as well as for model analysis for research.   For high throughput applications, JSim can be run as a batch job.  JSim can automatically translate models from the repositories for Systems Biology Markup Language (SBML and CellML models. Stochastic modeling is supported. MML supports assigning physical units to constants and variables and automates checking dimensional balance as the first step in verification testing. Automatic unit scaling follows, e.g. seconds to minutes, if needed. The JSim Project File sets a standard for reproducible modeling analysis: it includes in one file everything for analyzing a set of experiments: the data, the models, the data fitting, and evaluation of parameter confidence ranges. JSim is open source; it and about 400 human readable open source physiological/biophysical models are available at http://www.physiome.org/jsim/.

  10. JSim, an open-source modeling system for data analysis [v3; ref status: indexed, http://f1000r.es/3n0

    Directory of Open Access Journals (Sweden)

    Erik Butterworth

    2014-07-01

    Full Text Available JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter sets, and for making comparisons among different models running simultaneously or separately. Interactive use is supported by a large collection of graphical user interfaces for model writing and compilation diagnostics, defining input functions, model runs, selection of algorithms solving ordinary and partial differential equations, run-time multidimensional graphics, parameter optimization (8 methods, sensitivity analysis, and Monte Carlo simulation for defining confidence ranges. JSim uses Mathematical Modeling Language (MML a declarative syntax specifying algebraic and differential equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc. are accessed through procedure calls. MML syntax is simple, basically defining the parameters and variables, then writing the equations in a straightforward, easily read and understood mathematical form. This makes JSim good for teaching modeling as well as for model analysis for research.   For high throughput applications, JSim can be run as a batch job.  JSim can automatically translate models from the repositories for Systems Biology Markup Language (SBML and CellML models. Stochastic modeling is supported. MML supports assigning physical units to constants and variables and automates checking dimensional balance as the first step in verification testing. Automatic unit scaling follows, e.g. seconds to minutes, if needed. The JSim Project File sets a standard for reproducible modeling analysis: it includes in one file everything for analyzing a set of experiments: the data, the models, the data fitting, and evaluation of parameter confidence ranges. JSim is open source; it and about 400 human readable open source physiological/biophysical models are available at http://www.physiome.org/jsim/.

  11. Porting and using PanGIA for Cytoscape 3: challenges and solutions [v1; ref status: indexed, http://f1000r.es/3r3

    Directory of Open Access Journals (Sweden)

    David Welker

    2014-07-01

    Full Text Available Much of the biologically significant functionality in Cytoscape is contained within third-party add-ons, called plugins in Cytoscape 2 and apps in Cytoscape 3. In the transition from Cytoscape 2 to Cystoscape 3, some of the underlying assumptions upon which plugins relied changed, requiring a significant porting effort for plugins to work as Cytoscape 3 apps. PanGIA is a Cytoscape add-on (http://apps.cytoscape.org/apps/pangia designed to analyze and visualize genetic interaction data in light of physical interaction data. In order to convert the PanGIA plugin to an app, various challenges, including those related to a transformed data model, concurrency, and randomization had to be overcome. In the process, the ability to control randomization was added to the GUI, a feature which was not only integral to the porting process, but which also ensures more easily reproducible scientific analysis for PanGIA users. Most authors of Cytoscape 2 plugins will face similar challenges porting their software to work with Cytoscape 3, and this paper gives details of how the PanGIA port addressed them.

  12. Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7 [v1; ref status: indexed, http://f1000r.es/508

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    Markus Knipp

    2015-02-01

    Full Text Available Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole. The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

  13. Cytoscape: the network visualization tool for GenomeSpace workflows [v2; ref status: indexed, http://f1000r.es/47f

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    Barry Demchak

    2014-08-01

    Full Text Available Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013.

  14. Cytoscape: the network visualization tool for GenomeSpace workflows [v1; ref status: indexed, http://f1000r.es/3ph

    Directory of Open Access Journals (Sweden)

    Barry Demchak

    2014-07-01

    Full Text Available Modern genomic analysis often requires workflows incorporating multiple best-ofbreed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded it over 850 times since the release of its first version in September, 2013.

  15. Cancer quasispecies and stem-like adaptive aneuploidy [v1; ref status: indexed, http://f1000r.es/29s

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    Domenico Napoletani

    2013-12-01

    Full Text Available In this paper we develop a theoretical frame to understand self-regulation of aneuploidy rate in cancer and stem cells. This is accomplished building upon quasispecies theory, by leaving its formal mathematical structure intact, but by drastically changing the meaning of its objects. In particular, we propose a novel definition of chromosomal master sequence, as a sequence of physically distinct whole or fragmented chromosomes, whose length is taken to be the sum of the copy numbers of each whole or fragmented chromosome. This fundamental change in the functional objects of quasispecies theory allows us to show that previously measured aneuploidy rates in cancer populations are already close to a formally derived aneuploid error threshold, and that any value of aneuploidy rate larger than the aneuploid error threshold would lead to a loss of fitness of a tumor population. Finally, we make a phenomenological analysis of existing experimental evidence to argue that single clone cancer cells, derived from an aneuploid cancer subpopulation, are capable of self-regulating their aneuploidy rate and of adapting it to distinct environments, namely primary and metastatic microenvironments. We also discuss the potential origin of this self-regulatory ability in the wider context of developmental and comparative biology and we hypothesize the existence of a diversification factor, i.e. a cellular mechanism that regulates adaptation of aneuploidy rates, active in all embryo, adult and cancer stem cells.

  16. Dentin reactions to caries are misinterpreted by histological “gold standards” [v1; ref status: indexed, http://f1000r.es/2my

    Directory of Open Access Journals (Sweden)

    Priscila Florentino Silva

    2014-01-01

    Full Text Available Dentin reactions to caries, crucial for pathogenesis and for the determination of the severity of caries lesions, are believed to be reasonably detected by stereomicroscopy (SM and polarized light microscopy in quinoline (PLMQ, but accuracies are not available. Here, stereomicroscopy of wet (SW and dry (SD ground sections of natural occlusal caries lesions resulted in moderate (0.7, for normal dentin and low accuracies (< 0.6, for carious and sclerotic dentin as validated by contrast-corrected microradiography. Accuracies of PLMQ were moderate for both normal (0.71 and carious dentin (0.71. The hypothesis that detection of dentin reactions by SM and PLMQ would be influenced by the contrast quality of micrographic images was rejected. Dentin reactions were scored by SW, SD, PLMQ, and three types of microradiographic images with varying contrast qualities and each technique was compared against the one that resulted in the highest number of scores for each dentin reaction. Large differences resulted, mainly related to the detection of sclerotic dentin by both SW and SD, and normal and carious dentin by PLMQ. It is concluded that contrast-corrected microradiography should be preferred as the gold standard and SM and PLMQ should be avoided, but the relationship of PLMQ with dentin mineralization deserves further investigation.

  17. Mobile phones affect multiple sperm quality traits: a meta-analysis [v1; ref status: indexed, http://f1000r.es/ny

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    Madhukar Shivajirao Dama

    2013-02-01

    Full Text Available As mobile phone usage is growing rapidly, there is a need for a comprehensive analysis of the literature to inform scientific debates about the adverse effects of mobile phone radiation on sperm quality traits. Therefore, we conducted a meta-analysis of the eligible published research studies on human males of reproductive age. Eleven studies were eligible for this analysis. Based on the meta-analysis, mobile phone use was significantly associated with deterioration in semen quality (Hedges’s g = -0.547; 95% CI: -0.713, -0.382; p < 0.001. The traits particularly affected adversely were sperm concentration, sperm morphology, sperm motility, proportion of non-progressive motile sperm (%, proportion of slow progressive motile sperm (%, and sperm viability. Direct exposure of spermatozoa to mobile phone radiation with in vitro study designs also significantly deteriorated the sperm quality (Hedges’s g = -2.233; 95% CI: -2.758, -1.708; p < 0.001, by reducing straight line velocity, fast progressive motility, Hypo-osmotic swelling (HOS test score, major axis (µm, minor axis (µm, total sperm motility, perimeter (µm, area (µm2, average path velocity, curvilinear velocity, motile spermatozoa, and  acrosome reacted spermatozoa (%. The strength of evidence for the different outcomes varied from very low to very high. The analysis shows that mobile phone use is possibly associated with a number of deleterious effects on the spermatozoa.

  18. Fused embryos and pre-metamorphic conjoined larvae in a broadcast spawning reef coral [v2; ref status: indexed, http://f1000r.es/54p

    Directory of Open Access Journals (Sweden)

    Lei Jiang

    2015-03-01

    Full Text Available Fusion of embryos or larvae prior to metamorphosis is rarely known to date in colonial marine organisms. Here, we document for the first time that the embryos of the broadcast spawning coral Platygyra daedalea could fuse during blastulation and further develop into conjoined larvae, and the settlement of conjoined larvae immediately resulted in inborn juvenile colonies. Fusion of embryos might be an adaptive strategy to form pre-metamorphic chimeric larvae and larger recruits, thereby promoting early survival. However, future studies are needed to explore whether and to what extent fusion of coral embryos occurs in the field, and fully evaluate its implications.

  19. Ankylosis of the hips and knees due to sickle cell disease [v1; ref status: indexed, http://f1000r.es/S7w2Gz

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    Saad Saleh Abdullah Al Elayan

    2012-10-01

    Full Text Available This is a case report of a 29-year-old Saudi male with sickle cell disease (SCD with severe stiffness of his joints, mainly both knees and hips, secondary to complications of SCD. He was severely crippled: unable to sit, stand or walk, and was bedridden for 8 years when he was presented to us. Radiographs showed fusion of both knees and hips. There was no evidence of active osteomyelitis by Gallium scan. The patient’s hemoglobin S decreased to levels below 30% by exchange transfusion. Bilateral total hip replacement, as well as unilateral total knee replacement, was carried out to improve his level of function. There is only one reported case of such severe and multiple joint complications in a single patient suffering from SCD. The increased life expectancy that medical advances have offered to the sickle-cell patients has led to the appearance of sickle-cell-related complications, which were previously only seen rarely. These complications were successfully managed and the patient was able to move and transfer using a wheel chair.

  20. Case Report: A case report of acromegaly associated with primary aldosteronism [v1; ref status: indexed, http://f1000r.es/2ny

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    Joanna Matrozova

    2014-02-01

    Full Text Available We describe a patient with a rare combination of acromegaly and primary aldosteronism. A 37 year-old female patient was diagnosed with acromegaly on the basis of typical clinical, hormonal and image characteristics. She presented also with one of the most common co-morbidities – arterial hypertension. The patient has been regularly followed-up and after three surgical interventions, irradiation and adjuvant treatment with a dopamine agonist, acromegaly was finally controlled in 2008 (20 years after diagnosis. Arterial hypertension however, remained a therapeutic problem even after prescription of four antihypertensive drugs. She had normal biochemical parameters, except for low potassium levels 3.2 (3.5-5.6 mmol/l. This raised the suspicion of primary hyperaldosteronism, confirmed by a high aldosterone to plasma rennin activity ratio, high aldosterone level after a Captopril challenge test and visualization of a 35 mm left adrenal nodule on a CT scan. After an operation, the patient recovered from hypokalemia and antihypertensive therapy was reduced to a small dose of a Ca blocker. Co-morbid arterial hypertension is common in acromegaly, though it is rare for this to be caused by Conn’s adenoma. The association of Conn’s adenoma with acromegaly has been interpreted in two lines: as a component of multiple endocrine neoplasia type (MEN1 syndrome or as a direct mitogenic effect of hyperactivated GH-IGF1 axis.

  1. Association of spirochetal infection with Morgellons disease [v1; ref status: indexed, http://f1000r.es/8g

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    Marianne J Middelveen

    2013-01-01

    Full Text Available Morgellons disease (MD is an emerging multisystem illness characterized by skin lesions with unusual filaments embedded in or projecting from epithelial tissue. Filament formation results from abnormal keratin and collagen expression by epithelial-based keratinocytes and fibroblasts. Recent research comparing MD to bovine digital dermatitis, an animal infectious disease with similar skin features, provided clues that spirochetal infection could play an important role in the human disease as it does in the animal illness. Based on histological staining, immunofluorescent staining, electron microscopic imaging and polymerase chain reaction, we report the detection of Borrelia spirochetes in dermatological tissue of  four randomly-selected MD patients. The association of MD with spirochetal infection provides evidence that this infection may be a significant factor in the illness and refutes claims that MD lesions are self-inflicted and that people suffering from this disorder are delusional. Molecular characterization of the Borrelia spirochetes found in MD patients is warranted.

  2. High efficiency generalized transduction in Escherichia coli O157:H7 [v1; ref status: indexed, http://f1000r.es/8f

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    Martin G Marinus

    2013-01-01

    Full Text Available Genetic manipulation in enterohemorrhagic E. coli O157:H7 is currently restricted to recombineering, a method that utilizes the recombination system of bacteriophage lambda, to introduce gene replacements and base changes inter alia into the genome. Bacteriophage 933W is a prophage in E. coli O157:H7 strain EDL933, which encodes the genes (stx2AB for the production of Shiga toxin which is the basis for the potentially fatal Hemolytic Uremic Syndrome in infected humans. We replaced the stx2AB genes with a kanamycin cassette using recombineering. After induction of the prophage by ultra-violet light, we found that bacteriophage lysates were capable of transducing to wildtype, point mutations in the lactose, arabinose and maltose genes. The lysates could also transduce tetracycline resistant cassettes. Bacteriophage 933W is also efficient at transducing markers in E. coli K-12. Co-transduction experiments indicated that the maximal amount of transferred DNA was likely the size of the bacteriophage genome, 61 kB. All tested transductants, in both E. coli K-12 and O157:H7, were kanamycin-sensitive indicating that the transducing particles contained host DNA.

  3. A novel envelope mediated post entry restriction of murine leukaemia virus in human cells is Ref1/TRIM5α independent

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    McKnight Áine

    2010-10-01

    Full Text Available Abstract Background 'Intrinsic' resistance to retroviral infection was first recognised with the Friend virus susceptibility gene (Fv1, which determines susceptibility to murine leukaemia virus (MLV infection in different murine species. Similarly, the tripartite motif (TRIM family of proteins determine lentiviral restriction in a primate host-species specific manner. For example rhesus TRIM5α (rhTRIM5α can potently restrict HIV-1 infection while human TRIM5α (huTRIM5α only has a mild effect on SIVmac and HIV-1 infectivity (Lv1. Human TRIM5α is able to restrict MLV-N virus replication, but is ineffective against MLV-B or MLV-NB virus infection. Lv2 restriction of some HIV-2 viruses is seen in human cells. Like Lv1, Lv2 is a post-entry restriction factor, whose viral determinants have been mapped to the viral capsid (CA. Unlike Lv1, however, Lv2 is determined by envelope (Env in addition to CA. Here we present evidence of a novel Env determined post entry restriction to infection in human cells of pseudotyped MLV-B and MLV-NB cores. Results We generated retroviral vectors pseudotyped with various gamma and lentiviral Envs on MLV-B and -NB CAs containing a green fluorescent protein (GFP reporter. Flow cytometry was used to determine transduction efficiencies in NP2/CD4/CXCR4 (glioma cell line stably transduced with the HIV receptors and HeLa/CD4 cell lines. The HeLa/CD4 cell line restricted both MLV CAs in an Env dependent manner, compared to NP2/CD4/CXCR4 cells. Quantitative polymerase chain reaction (QT-PCR analysis of reverse transcription (RT transcripts demonstrates that this restriction occurs at a post entry and RT level. siRNA knockdown of huTRIM5α ruled out a direct role for this cellular component in mediating this restriction. We describe a previously unobserved Env determined restriction of MLV-B and MLV-NB CAs in HeLa/CD4 cells when pseudotyped with HIV-2 and RD114 Envs, but not gibbon ape leukaemia virus (GALV, HIV-1 or Amphotrophic (Ampho Envs. Conclusions Our data further demonstrate the variability of Env and CA mediated susceptibility to post entry host cell restriction. We discuss the relevance of these findings in light of the growing evidence supporting the complexities involved in innate host immunity to retroviral infection.

  4. Does excitatory fronto-extracephalic tDCS lead to improved working memory performance? [v1; ref status: indexed, http://f1000r.es/216

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    Níall Lally

    2013-10-01

    Full Text Available Evidence suggests that excitatory transcranial direct current stimulation (tDCS may improve performance on a wide variety of cognitive tasks. Due to the non-invasive and inexpensive nature of the method, harnessing its potential could be particularly useful for the treatment of neuropsychiatric illnesses involving cognitive dysfunction. However, questions remain regarding the efficacious stimulation parameters. Here, using a double-blind between-subjects design, we explored whether 1 mA excitatory (anodal left dorsolateral prefrontal cortex stimulation with a contralateral extracephalic reference electrode, leads to enhanced working memory performance across two days, relative to sham stimulation. Participants performed the 3-back, a test of working memory, at baseline, and during and immediately following stimulation on two days, separated by 24-48 hours. Active stimulation did not significantly enhance performance versus sham over the course of the experiment. However, exploratory comparisons did reveal a significant effect of stimulation group on performance during the first stimulation phase only, with active stimulation recipients performing better than sham. While these results do not support the hypothesis that dorsolateral prefrontal cortex tDCS boosts working memory, they raise the possibility that its effects may be greatest during early learning stages.

  5. Case Report: Urgent endovascular treatment of subclavian artery injury after blunt trauma [v1; ref status: indexed, http://f1000r.es/4x8

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    Taka-aki Nakada

    2014-12-01

    Full Text Available Subclavian arterial injury is rare and potentially life-threatening, particularly when it leads to arterial occlusion, causing limb ischemia, retrograde thromboembolization and cerebral infarction within hours after injury. Here we report a blunt trauma case with subclavian arterial injury, upper extremity ischemia, and the need for urgent treatment to salvage the limb and prevent cerebral infarction. A 41-year-old man had a left, open, mid-shaft clavicle fracture and left subclavian artery injury accompanied by a weak pulse in the left radial artery, decreased blood pressure of the left arm compared to the right, and left hand numbness. Urgent debridement and irrigation of the open clavicle fracture was followed by angiography for the subclavian artery injury. The left distal subclavian artery had a segmental dissection with a thrombus. Urgent endovascular treatment using a self-expanding nitinol stent successfully restored the blood flow and blood pressure to the left upper extremity. Endovascular treatment is a viable option for cases of subclavian artery injury where there is a risk of extremity ischemia and cerebral infarction.

  6. Cocaine self-administration in rats lacking a functional trpc4 gene [v1; ref status: indexed, http://f1000r.es/w9

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    Kristin C Rasmus

    2013-04-01

    Full Text Available The canonical transient receptor potential (TRPC family of Ca2+ permeable, non-selective cation channels is abundantly expressed throughout the brain, and plays a pivotal role in modulating cellular excitability. Unlike other TRPC channels, TRPC4 subtype expression in the adult rodent brain is restricted to a network of structures that receive dopaminergic innervation, suggesting an association with motivation- and reward-related behaviors. We hypothesized that these channels may play a critical role in dopamine-dependent drug-seeking behaviors. Here, we gathered data testing trpc4 knockout (KO rats and wild-type (WT littermates in the acquisition of a natural sucrose reward (10 days, and cocaine self-administration (13 days at 0.5 mg/kg/infusion. Rats lacking the trpc4 gene (trpc4-KO learned to lever press for sucrose to a similar degree as their WT controls. However, when they were switched to cocaine, the trpc4-KO rats had substantially reduced cocaine-paired lever pressing compared to WT controls. No obvious group differences in inactive lever pressing were observed, for any time, during cocaine self-administration.

  7. Matched molecular pair-based data sets for computer-aided medicinal chemistry [v2; ref status: indexed, http://f1000r.es/309

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    Ye Hu

    2014-02-01

    Full Text Available Matched molecular pairs (MMPs are widely used in medicinal chemistry to study changes in compound properties including biological activity, which are associated with well-defined structural modifications. Herein we describe up-to-date versions of three MMP-based data sets that have originated from in-house research projects. These data sets include activity cliffs, structure-activity relationship (SAR transfer series, and second generation MMPs based upon retrosynthetic rules. The data sets have in common that they have been derived from compounds included in the ChEMBL database (release 17 for which high-confidence activity data are available. Thus, the activity data associated with MMP-based activity cliffs, SAR transfer series, and retrosynthetic MMPs cover the entire spectrum of current pharmaceutical targets. Our data sets are made freely available to the scientific community.

  8. A computational analysis of the long-term regulation of arterial pressure [v2; ref status: indexed, http://f1000r.es/2hm

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    Daniel A. Beard

    2013-12-01

    Full Text Available The asserted dominant role of the kidneys in the chronic regulation of blood pressure and in the etiology of hypertension has been debated since the 1970s. At the center of the theory is the observation that the acute relationships between arterial pressure and urine production—the acute pressure-diuresis and pressure-natriuresis curves—physiologically adapt to perturbations in pressure and/or changes in the rate of salt and volume intake. These adaptations, modulated by various interacting neurohumoral mechanisms, result in chronic relationships between water and salt excretion and pressure that are much steeper than the acute relationships. While the view that renal function is the dominant controller of arterial pressure has been supported by computer models of the cardiovascular system known as the “Guyton-Coleman model”, no unambiguous description of a computer model capturing chronic adaptation of acute renal function in blood pressure control has been presented. Here, such a model is developed with the goals of: 1. representing the relevant mechanisms in an identifiable mathematical model; 2. identifying model parameters using appropriate data; 3. validating model predictions in comparison to data; and 4. probing hypotheses regarding the long-term control of arterial pressure and the etiology of primary hypertension. The developed model reveals: long-term control of arterial blood pressure is primarily through the baroreflex arc and the renin-angiotensin system; and arterial stiffening provides a sufficient explanation for the etiology of primary hypertension associated with ageing. Furthermore, the model provides the first consistent explanation of the physiological response to chronic stimulation of the baroreflex.

  9. A computational analysis of the long-term regulation of arterial pressure [v1; ref status: indexed, http://f1000r.es/1xq

    Directory of Open Access Journals (Sweden)

    Daniel A. Beard

    2013-10-01

    Full Text Available The asserted dominant role of the kidneys in the chronic regulation of blood pressure and in the etiology of hypertension has been debated since the 1970s. At the center of the theory is the observation that the acute relationships between arterial pressure and urine production—the acute pressure-diuresis and pressure-natriuresis curves—physiologically adapt to perturbations in pressure and/or changes in the rate of salt and volume intake. These adaptations, modulated by various interacting neurohumoral mechanisms, result in chronic relationships between water and salt excretion and pressure that are much steeper than the acute relationships. While the view that renal function is the dominant controller of arterial pressure has been supported by computer models of the cardiovascular system known as the “Guyton-Coleman model”, no unambiguous description of a computer model capturing chronic adaptation of acute renal function in blood pressure control has been presented. Here, such a model is developed with the goals of: 1. capturing the relevant mechanisms in an identifiable mathematical model; 2. identifying model parameters using appropriate data; 3. validating model predictions in comparison to data; and 4. probing hypotheses regarding the long-term control of arterial pressure and the etiology of primary hypertension. The developed model reveals: long-term control of arterial blood pressure is primarily through the baroreflex arc and the renin-angiotensin system; and arterial stiffening provides a sufficient explanation for the etiology of primary hypertension associated with ageing. Furthermore, the model provides the first consistent explanation of the physiological response to chronic stimulation of the baroreflex.

  10. An evolutionarily significant unicellular strategy in response to starvation in Dictyostelium social amoebae [v2; ref status: indexed, http://f1000r.es/4kb

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    Darja Dubravcic

    2014-12-01

    Full Text Available The social amoeba Dictyostelium discoideum is widely studied for its multicellular development program as a response to starvation. Aggregates of up to 106 cells form fruiting bodies containing (i dormant spores (~80% that can persist for months in the absence of nutrients, and (ii dead stalk cells (~20% that promote the dispersion of the spores towards nutrient-rich areas. It is often overlooked that not all cells aggregate upon starvation. Using a new quantitative approach based on time-lapse fluorescence microscopy and a low ratio of reporting cells, we have quantified this fraction of non-aggregating cells. In realistic starvation conditions, up to 15% of cells do not aggregate, which makes this third cell fate a significant component of the population-level response of social amoebae to starvation. Non-aggregating cells have an advantage over cells in aggregates since they resume growth earlier upon arrival of new nutrients, but have a shorter lifespan under prolonged starvation. We find that phenotypic heterogeneities linked to cell nutritional state bias the representation of cells in the aggregating vs. non-aggregating fractions, and thus affect population partitioning. Next, we report that the fraction of non-aggregating cells depends on genetic factors that regulate the timing of starvation, signal sensing efficiency and aggregation efficiency. In addition, interactions between clones in mixtures of non-isogenic cells affect the partitioning of each clone into both fractions. We further build a numerical model to test the evolutionary significance of the non-aggregating cell fraction. The partitioning of cells into aggregating and non-aggregating fractions is optimal in fluctuating environments with an unpredictable duration of starvation periods. Our study highlights the unicellular component of the response of social amoebae to starvation, and thus extends its evolutionary and ecological framework.

  11. Prism adaptation does not alter configural processing of faces [v1; ref status: indexed, http://f1000r.es/1wk

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    Janet H. Bultitude

    2013-10-01

    Full Text Available Patients with hemispatial neglect (‘neglect’ following a brain lesion show difficulty responding or orienting to objects and events on the left side of space. Substantial evidence supports the use of a sensorimotor training technique called prism adaptation as a treatment for neglect. Reaching for visual targets viewed through prismatic lenses that induce a rightward shift in the visual image results in a leftward recalibration of reaching movements that is accompanied by a reduction of symptoms in patients with neglect. The understanding of prism adaptation has also been advanced through studies of healthy participants, in whom adaptation to leftward prismatic shifts results in temporary neglect-like performance. Interestingly, prism adaptation can also alter aspects of non-lateralised spatial attention. We previously demonstrated that prism adaptation alters the extent to which neglect patients and healthy participants process local features versus global configurations of visual stimuli. Since deficits in non-lateralised spatial attention are thought to contribute to the severity of neglect symptoms, it is possible that the effect of prism adaptation on these deficits contributes to its efficacy. This study examines the pervasiveness of the effects of prism adaptation on perception by examining the effect of prism adaptation on configural face processing using a composite face task. The composite face task is a persuasive demonstration of the automatic global-level processing of faces: the top and bottom halves of two familiar faces form a seemingly new, unknown face when viewed together. Participants identified the top or bottom halves of composite faces before and after prism adaptation. Sensorimotor adaptation was confirmed by significant pointing aftereffect, however there was no significant change in the extent to which the irrelevant face half interfered with processing. The results support the proposal that the therapeutic effects of prism adaptation are limited to dorsal stream processing.

  12. MODIS/Terra+Aqua BRDF/Albedo Nadir BRDF-Adjusted Ref Daily L3 Global 0.05Deg CMG V006

    Data.gov (United States)

    National Aeronautics and Space Administration — The MODIS MCD43C4 Version 6 Nadir Bidirectional reflectance distribution function Adjusted Reflectance (NBAR) data set is a daily 16-day product. The Julian date in...

  13. False memory susceptibility is correlated with categorisation ability in humans [v1; ref status: indexed, http://f1000r.es/3ty

    Directory of Open Access Journals (Sweden)

    Kathryn Hunt

    2014-07-01

    Full Text Available Our memory is often surprisingly inaccurate, with errors ranging from misremembering minor details of events to generating illusory memories of entire episodes. The pervasiveness of such false memories generates a puzzle: in the face of selection pressure for accuracy of memory, how could such systematic failures have persisted over evolutionary time? It is possible that memory errors are an inevitable by-product of our adaptive memories and that semantic false memories are specifically connected to our ability to learn rules and concepts and to classify objects by category memberships. Here we test this possibility using a standard experimental false memory paradigm and inter-individual variation in verbal categorisation ability. Indeed it turns out that the error scores are significantly negatively correlated, with those individuals scoring fewer errors on the categorisation test being more susceptible to false memory intrusions in a free recall test. A similar trend, though not significant, was observed between individual categorisation ability and false memory susceptibility in a word recognition task. Our results therefore indicate that false memories, to some extent, might be a by-product of our ability to learn rules, categories and concepts.

  14. False memory susceptibility is correlated with categorisation ability in humans [v2; ref status: indexed, http://f1000r.es/4k0

    Directory of Open Access Journals (Sweden)

    Kathryn Hunt

    2014-10-01

    Full Text Available Our memory is often surprisingly inaccurate, with errors ranging from misremembering minor details of events to generating illusory memories of entire episodes. The pervasiveness of such false memories generates a puzzle: in the face of selection pressure for accuracy of memory, how could such systematic failures have persisted over evolutionary time? It is possible that memory errors are an inevitable by-product of our adaptive memories and that semantic false memories are specifically connected to our ability to learn rules and concepts and to classify objects by category memberships. Here we test this possibility using a standard experimental false memory paradigm and inter-individual variation in verbal categorisation ability. Indeed it turns out that the error scores are significantly negatively correlated, with those individuals scoring fewer errors on the categorisation test being more susceptible to false memory intrusions in a free recall test. A similar trend, though not significant, was observed between individual categorisation ability and false memory susceptibility in a word recognition task. Our results therefore indicate that false memories, to some extent, might be a by-product of our ability to learn rules, categories and concepts.

  15. use of mutagens in the improvement of itaconic acid production by local isolate of aspergillus terreus ref from raw starchy materials and refused banana fruits

    International Nuclear Information System (INIS)

    Khalaf, S.A

    2004-01-01

    Itaconic acid (IA) production by local isolate o/Aspergillus terreus RBF from different acid hydrolyzed starchy materials such as corn starch, potato flour, sweet potato flour and market refused banana fruits extract (MRBFex) was investigated. Both production and yield were highest on corn starch with values of 12.9 g/l and 25.44%, respectively. MRBFex was explored as a good substrate for IA production with yield of '20.42%. The efficiency of IA production by this wild type strain was improved by ultraviolet, chemical and mixed mutagenic treatments. Three high IA yielding mutants, NA 2 , NAUV 2 4 and NASA 5 6 were obtained by gradient plating. One of these mutants (NAUV 2 4) was capable of producing about twice the yield of IA as the parent strain from acid hydrolyzed corn starch and/or MRBFex. Higher than 30 g/l of IA was produced by the mutant strain NAUV 2 4 in flask fermentation from medium containing of 120 g/l (as sugar) of MRBFex

  16. O último refúgio da língua geral no Brasil The last refuge of indigenous language in Brazil

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    Eduardo de Almeida Navarro

    2012-12-01

    Full Text Available Este artigo mostra a situação atual de uso da Língua Geral Amazônica, as causas de seu desaparecimento de grande parte do Norte do Brasil e as iniciativas atuais para sua revitalização.This paper focuses the present situation of Língua Geral Amazônica, the reasons for its extinction in most areas in Northern Brazil and the present efforts towards its revitalization.

  17. Critical care management of patients following transcatheter aortic valve replacement [v1; ref status: indexed, http://f1000r.es/nz

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    Jesse M Raiten

    2013-02-01

    Full Text Available Transcatheter aortic valve replacement (TAVR is rapidly gaining popularity as a technique to surgically manage aortic stenosis (AS in high risk patients. TAVR is significantly less invasive than the traditional approach to aortic valve replacement via median sternotomy. Patients undergoing TAVR often suffer from multiple comorbidities, and their postoperative course may be complicated by a unique set of complications that may become evident in the intensive care unit (ICU. In this article, we review the common complications of TAVR that may be observed in the ICU, and different strategies for their management.

  18. Matched molecular pair-based data sets for computer-aided medicinal chemistry [v1; ref status: indexed, http://f1000r.es/2w9

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    Ye Hu

    2014-02-01

    Full Text Available Matched molecular pairs (MMPs are widely used in medicinal chemistry to study changes in compound properties including biological activity, which are associated with well-defined structural modifications. Herein we describe up-to-date versions of three MMP-based data sets that have originated from in-house research projects. These data sets include activity cliffs, structure-activity relationship (SAR transfer series, and second generation MMPs based upon retrosynthetic rules. The data sets have in common that they have been derived from compounds included in the latest release of the ChEMBL database for which high-confidence activity data are available. Thus, the activity data associated with MMP-based activity cliffs, SAR transfer series, and retrosynthetic MMPs cover the entire spectrum of current pharmaceutical targets. Our data sets are made freely available to the scientific community.

  19. Active transmembrane drug transport in microgravity: a validation study using an ABC transporter model [v1; ref status: indexed, http://f1000r.es/41n

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    Sergi Vaquer

    2014-08-01

    Full Text Available Abstract Microgravity has been shown to influence the expression of ABC (ATP-Binding Cassette transporters in bacteria, fungi and mammals, but also to modify the activity of certain cellular components with structural and functional similarities to ABC transporters. Changes in activity of ABC transporters could lead to important metabolic disorders and undesired pharmacological effects during spaceflights. However, no current means exist to study the functionality of these transporters in microgravity. To this end, a Vesicular Transport Assay® (Solvo Biotechnology, Hungary was adapted to evaluate multi-drug resistance-associated protein 2 (MRP2 trans-membrane estradiol-17-β-glucuronide (E17βG transport activity, when activated by adenosine-tri-phosphate (ATP during parabolic flights. Simple diffusion, ATP-independent transport and benzbromarone inhibition were also evaluated. A high accuracy engineering system was designed to perform, monitor and synchronize all procedures. Samples were analysed using a validated high sensitivity drug detection protocol. Experiments were performed in microgravity during parabolic flights, and compared to 1g on ground results using identical equipment and procedures in all cases. Our results revealed that sufficient equipment accuracy and analytical sensitivity were reached to detect transport activity in both gravitational conditions. Additionally, transport activity levels of on ground samples were within commercial transport standards, proving the validity of the methods and equipment used. MRP2 net transport activity was significantly reduced in microgravity, so was signal detected in simple diffusion samples. Ultra-structural changes induced by gravitational stress upon vesicle membranes or transporters could explain the current results, although alternative explanations are possible. Further research is needed to provide a conclusive answer in this regard. Nevertheless, the present validated technology opens new and interesting research lines in biology and human physiology with the potential for significant benefits for both space and terrestrial medicine.

  20. Ten things to get right for marine conservation planning in the Coral Triangle [v2; ref status: indexed, http://f1000r.es/3ly

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    Rebecca Weeks

    2014-06-01

    Full Text Available Systematic conservation planning increasingly underpins the conservation and management of marine and coastal ecosystems worldwide. Amongst other benefits, conservation planning provides transparency in decision-making, efficiency in the use of limited resources, the ability to minimise conflict between diverse objectives, and to guide strategic expansion of local actions to maximise their cumulative impact. The Coral Triangle has long been recognised as a global marine conservation priority, and has been the subject of huge investment in conservation during the last five years through the Coral Triangle Initiative on Coral Reefs, Fisheries and Food Security. Yet conservation planning has had relatively little influence in this region. To explore why this is the case, we identify and discuss 10 challenges that must be resolved if conservation planning is to effectively inform management actions in the Coral Triangle. These are: making conservation planning accessible; integrating with other planning processes; building local capacity for conservation planning; institutionalising conservation planning within governments; integrating plans across governance levels; planning across governance boundaries; planning for multiple tools and objectives; understanding limitations of data; developing better measures of progress and effectiveness; and making a long term commitment. Most important is a conceptual shift from conservation planning undertaken as a project, to planning undertaken as a process, with dedicated financial and human resources committed to long-term engagement.

  1. 1-Octen-3-ol – the attractant that repels [v1; ref status: indexed, http://f1000r.es/5ic

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    Pingxi Xu

    2015-06-01

    Full Text Available Since the discovery in the early 1980s that 1-octen-3-ol, isolated from oxen breath, attracts tsetse fly, there has been growing interest in exploring the use of this semiochemical as a possible generic lure for trapping host-seeking mosquitoes. Intriguingly, traps baited with 1-octen-3-ol captured significantly more females of the malaria mosquito, Anopheles gambiae, and the yellow fever mosquito, Aedes aegypti, than control traps, but failed to attract the southern house mosquito, Culex quinquefasciatus. Additionally, it has been demonstrated that this attractant is detected with enantioselective odorant receptors (ORs expressed only in maxillary palps. On the basis of indoor behavioral assays it has even been suggested that 1-octen-3-ol might be a repellent to the southern house mosquito. Our approach was two-prong, i.e., to isolate 1-octen-3-ol-sensitive ORs expressed in maxillary palps and antennae of southern house female mosquito, and test the hypothesis that this semiochemical is a repellent. An OR with high transcript levels in maxillary palps, CquiOR118b, showed remarkable selectivity towards (R-1-octen-3-ol, whereas an OR expressed in antennae, CquiOR114b, showed higher preference for (S-1-octen-3-ol than its antipode. Repellency by a surface landing and feeding assay showed that not only racemic, but enantiopure (R- and (S-1-octen-3-ol are repellents at 1% dose thus suggesting the occurrence of other (S-1-octen-3-ol-sensitive OR(s. Female mosquitoes with ablated maxillary palps were repelled by 1-octen-3-ol, which implies that in addition to OR(s in the maxillary palps, antennal OR(s are essential for repellency activity.

  2. No psychological effect of color context in a low level vision task [v1; ref status: indexed, http://f1000r.es/202

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    Adam Pedley

    2013-11-01

    Full Text Available Background: A remarkable series of recent papers have shown that colour can influence performance in cognitive tasks. In particular, they suggest that viewing a participant number printed in red ink or other red ancillary stimulus elements improves performance in tasks requiring local processing and impedes performance in tasks requiring global processing whilst the reverse is true for the colour blue. The tasks in these experiments require high level cognitive processing such as analogy solving or remote association tests and the chromatic effect on local vs. global processing is presumed to involve widespread activation of the autonomic nervous system. If this is the case, we might expect to see similar effects on all local vs. global task comparisons. To test this hypothesis, we asked whether chromatic cues also influence performance in tasks involving low level visual feature integration. Methods: Subjects performed either local (contrast detection or global (form detection tasks on achromatic dynamic Glass pattern stimuli. Coloured instructions, target frames and fixation points were used to attempt to bias performance to different task types. Based on previous literature, we hypothesised that red cues would improve performance in the (local contrast detection task but would impede performance in the (global form detection task.  Results: A two-way, repeated measures, analysis of covariance (2×2 ANCOVA with gender as a covariate, revealed no influence of colour on either task, F(1,29 = 0.289, p = 0.595, partial η2 = 0.002. Additional analysis revealed no significant differences in only the first attempts of the tasks or in the improvement in performance between trials. Discussion: We conclude that motivational processes elicited by colour perception do not influence neuronal signal processing in the early visual system, in stark contrast to their putative effects on processing in higher areas.

  3. Prmt7 is dispensable in tissue culture models for adipogenic differentiation [v1; ref status: indexed, http://f1000r.es/2im

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    Yu-Jie Hu

    2013-12-01

    Full Text Available Protein arginine methylation is a common posttranslational modification that has been implicated in numerous biological processes including gene expression. The mammalian genome encodes nine protein arginine methyltransferases (Prmts that catalyze monomethylation, asymmetric dimethylation, and symmetric dimethylation on arginine residues. Protein arginine methyltransferase 7 (Prmt7 is categorized as a type II and type III enzyme that produces symmetric dimethylated arginine and monomethylated arginine, respectively. However, the biological role of Prmt7 is not well characterized. We previously showed that Prmt5, a type II Prmt that associates with Brg1-based SWI/SNF chromatin remodeling complex, is required for adipocyte differentiation. Since Prmt7 also associates with Brg1-based SWI/SNF complex and modifies core histones, we hypothesized that Prmt7 might play a role in transcriptional regulation of adipogenesis. In the present study, we determined that the expression of Prmt7 did not change throughout adipogenic differentiation of C3H10T1/2 mesenchymal cells. Knockdown or over-expression of Prmt7 had no effect on lipid accumulation or adipogenic gene expression in differentiating C3H10T1/2 cells or in C/EBPα-reprogrammed NIH3T3 fibroblasts. Based on these results, we conclude that Prmt7, unlike Prmt5, is dispensable for adipogenic differentiation in tissue culture models.

  4. CO2 elevation improves photosynthetic performance in progressive warming environment in white birch seedlings [v1; ref status: indexed, http://f1000r.es/up

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    Shouren Zhang

    2013-01-01

    Full Text Available White birch (Betula paperifera Mash seedlings were exposed to progressively warming in greenhouses under ambient and elevated CO2 concentrations for 5 months to explore boreal tree species’ potential capacity to acclimate to global climate warming and CO2 elevation. In situ foliar gas exchange, in vivo carboxylation characteristics and chlorophyll fluorescence were measured at temperatures of 26oC and 37oC. Elevated CO2 significantly increased net photosynthetic rate (Pn at both measurement temperatures, and Pn at 37oC was higher than that at 26oC under elevated CO2. Stomatal conductance (gs was lower at 37oC than at 26oC, while transpiration rate (E was higher at 37oC than that at 26oC. Elevated CO2 significantly increased instantaneous water-use efficiency (WUE at both 26oC and 37oC, but WUE was markedly enhanced at 37oC under elevated CO2. The effect of temperature on maximal carboxylation rate (Vcmax, PAR-saturated electron transport rate (Jmax and triose phosphate utilization (TPU varied with CO2, and the Vcmax and Jmax were significantly higher at 37oC than at 26oC under elevated CO2. However, there were no significant interactive effects of CO2 and temperature on TPU. The actual photochemical efficiency of PSII (DF/ Fm’, total photosynthetic linear electron transport rate through PSII (JT and the partitioning of JT to carboxylation (Jc were higher at 37oC than at 26oC under elevated CO2. Elevated CO2 significantly suppressed the partitioning of JT to oxygenation (Jo/JT. The data suggest that the CO2 elevation and progressive warming greatly enhanced photosynthesis in white birch seedlings in an interactive fashion.

  5. Internet-delivered eye movement desensitization and reprocessing (iEMDR: an open trial [v1; ref status: indexed, http://f1000r.es/8l

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    Jay Spence

    2013-03-01

    Full Text Available Recent research indicates internet-delivered cognitive behavioural therapy (iCBT can reduce symptoms of post traumatic stress disorder (PTSD. This study examined the efficacy of an internet-delivered treatment protocol that combined iCBT and internet-delivered eye movement desensitization and reprocessing (iEMDR, in an uncontrolled trial. Eleven of the 15 participants completed post-treatment questionnaires. Large effect sizes were found from pre-treatment to 3-month follow-up (d = 1.03 – 1.61 on clinician-assessed and self-reported measures of PTSD, anxiety and distress, with moderate effect sizes (d = 0.59 – 0.70 found on measures of depression and disability. At post-treatment, 55% of the participants no longer met criteria for PTSD and this was sustained at follow-up. Symptom worsening occurred in 3 of 15 (20% of the sample from pre- to post-treatment; however, these participants reported overall symptom improvement by follow-up. Future research directions for iEMDR are discussed.

  6. Thrombocytosis portends adverse prognostic significance in patients with stage II colorectal carcinoma [v2; ref status: indexed, http://f1000r.es/4k6

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    Tianhua Guo

    2014-10-01

    Full Text Available Thrombocytosis portends adverse prognostic significance in many types of cancers including ovarian and lung carcinoma. In this study, we determined the prevalence and prognostic significance of thrombocytosis (defined as platelet count in excess of 400 × 103/μl in patients with colorectal cancer. We performed a retrospective analysis of 310 consecutive patients diagnosed at our Institution between 2004 and 2013. The patients (48.7% male and 51.3% female had a mean age of 69.9 years (+/- 12.7 years at diagnosis. Thrombocytosis was found in a total of 25 patients, with a higher incidence in those with stage III and IV disease (14.4% of patients. Although the mean platelet count increased with the depth of tumor invasion (pT, its values remained within normal limits in the whole patient cohort. No patient with stage I cancer (n=57 had elevated platelet count at diagnosis. By contrast, five of the 78 patients (6.4% with stage II cancer showed thrombocytosis, and four of these patients showed early recurrence and/or metastatic disease, resulting in shortened survival (they died within one year after surgery. The incidence of thrombocytosis increased to 12.2% and 20.6%, respectively, in patients with stage III and IV disease. The overall survival rate of patients with thrombocytosis was lower than those without thrombocytosis in the stage II and III disease groups, but this difference disappeared in patients with stage IV cancer who did poorly regardless of their platelet count. We concluded that thrombocytosis at diagnosis indicates adverse clinical outcome in colorectal cancer patients with stage II or III disease. This observation is especially intriguing in stage II patients because the clinical management of these patients is controversial. If our data are confirmed in larger studies, stage II colon cancer patients with thrombocytosis may be considered for adjuvant chemotherapy.

  7. Case Report: Testicular failure possibly associated with chronic use of methylphenidate [v1; ref status: indexed, http://f1000r.es/48z

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    Ranjith Ramasamy

    2014-09-01

    Full Text Available Methylphenidate is a commonly prescribed treatment for attention deficit hyperactivity disorder (ADHD. However, little is known about its adverse effects on the male reproductive system. We report a 20-year-old male patient whose chief complaint was of delayed puberty. He spoke in a high-pitched voice and complained of lack of body hair, impaired libido, inadequate erectile function, chronic fatigue, and low energy. He had been treated with methylphenidate as an infant and had continued treatment for 17 years. On examination, the patient was lean and visibly lacked facial or body hair. He further explained that he had never been able to grow underarm or facial hair and that he was often mistakenly considered a young teenager rather than a 20-year-old. The patient’s genitalia were categorized as Tanner Stage 2. Laboratory studies confirmed low serum follicle-stimulating hormone (FSH, luteinizing hormone (LH, and testosterone levels. The patient was given exogenous testosterone supplementation with pellets and human chorionic gonadotropin to maintain testicular size. After 4 months his symptoms improved and he demonstrated signs of puberty. Our goal is to further elucidate the possible impact of methylphenidate on the male reproductive system.

  8. The effects of anaesthesia on the developing brain: a summary of the clinical evidence [v1; ref status: indexed, http://f1000r.es/16b

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    Clara KY Yu

    2013-08-01

    Full Text Available Introduction: There is data amassing in the literature regarding the potentially adverse effects of anaesthesia exposure on the developing human brain. The purpose of this article is to summarise current relevant data from clinical studies in this area. Methods: Articles from journals written in English were searched for using PubMed, Ovid and Medline. Keywords used included: brain (newborn, infant, child and neonate, neurodegeneration, apoptosis, toxicity, neurocognitive impairment (developmental impairment and learning disorders and anaesthesia (intravenous, inhalational and sedation. Results: From the initial search, 23 articles were identified as potentially relevant, with publication dates spanning from 1978 to 2012.  Twelve studies were deemed irrelevant to the research questions. The results of neurocognitive assessment from eight of the remaining eleven studies had showed some differences in the performances of children exposed to anaesthesia. The control population in these studies was highly variable. The age at which the subjects were exposed to anaesthesia ranged from prenatal to 4 years in the majority of studies with one including children aged up to 12 years when exposed. Discussion: Although there is clinical data suggesting a possible detrimental effect, the evidence is best considered preliminary and inconclusive at this stage. Many of the outcome measures were lacking in specificity and standardization in most cases. Parents should be counselled to not avoid necessary invasive procedures for fear of a currently ill-defined risk.  However, deferral of elective procedures beyond the first few years of life should be contemplated.

  9. HeatMapViewer: interactive display of 2D data in biology [v1; ref status: indexed, http://f1000r.es/2u6

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    Guy Yachdav

    2014-02-01

    Full Text Available Summary: The HeatMapViewer is a BioJS component that lays-out and renders two-dimensional (2D plots or heat maps that are ideally suited to visualize matrix formatted data in biology such as for the display of microarray experiments or the outcome of mutational studies and the study of SNP-like sequence variants. It can be easily integrated into documents and provides a powerful, interactive way to visualize heat maps in web applications. The software uses a scalable graphics technology that adapts the visualization component to any required resolution, a useful feature for a presentation with many different data-points. The component can be applied to present various biological data types. Here, we present two such cases – showing gene expression data and visualizing mutability landscape analysis. Availability: https://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7706.

  10. Congenital duplication of the urethra with urethral diverticulum: a case report [v1; ref status: indexed, http://f1000r.es/36h

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    Darshan H Shah

    2014-05-01

    Full Text Available Duplication of the urethra is a rare congenital anomaly. Urethral duplication with the presence of diverticulum is a rare combination and to the best of our knowledge has  not been previously reported. We report a case of a 16 month old male child with duplication of the urethra and diverticulum arising from the ventral urethra. We also cover the intricacies and challenges in the management of such a case. The opening of the narrowed accessory dorsal urethra at the verumontanum was cauterized and gradually the dorsal urethra became atrophied. The ventral urethral diverticulum was excised. This case is unique due to: The unusual presentation of swelling over the dorsum of the penis, together with duplication of the urethra with diverticulum. The use of cauterization as a treatment modality. Cauterization of the ventral urethra with a Bugbee electrode and diverticulectomy was performed. A glidewire helped in identifying the small opening of the dorsal urethra at the level of the verumontanum. The case also highlights the importance of endoscopic management of this clinical entity.

  11. Demonstration of natriuretic activity in urine of neurosurgical patients with renal salt wasting [v2; ref status: indexed, http://f1000r.es/1ax

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    Steven J Youmans

    2013-06-01

    Full Text Available We have utilized the persistent elevation of fractional excretion (FE of urate, > 10%, to differentiate cerebral/renal salt wasting (RSW from the syndrome of inappropriate antidiuretic hormone secretion (SIADH, in which a normalization of FEurate occurs after correction of hyponatremia.  Previous studies suggest as well  that an elevated FEurate with normonatremia, without pre-existing hyponatremia, is also consistent with RSW, including studies demonstrating induction of RSW in rats infused with plasma from normonatremic neurosurgical and Alzheimer’s disease patients.  The present studies were designed to test whether precipitates from the urine of normonatremic neurosurgical patients, with either normal or elevated FEurate, and patients with SIADH, display natriuretic activity.   Methods: Ammonium sulfate precipitates from the urine of 6 RSW and 5 non-RSW Control patients were dialyzed (10 kDa cutoff to remove the ammonium sulfate, lyophilized, and the reconstituted precipitate was tested for its effect on transcellular transport of 22Na across LLC-PK1 cells grown to confluency in transwells. Results: Precipitates from 5 of the 6 patients with elevated FEurate and normonatremia significantly inhibited the in vitro transcellular transport of 22Na above a concentration of 3 μg protein/ml, by 10-25%, versus to vehicle alone, and by 15-40% at concentrations of 5-20 μg/ml as compared to precipitates from 4 of the 5 non-RSW patients with either normal FEurate and normonatremia (2 patients or with SIADH (2 patients. Conclusion: These studies provide further evidence that an elevated FEurate with normonatremia is highly consistent with RSW.  Evidence in the urine of natriuretic activity suggests significant renal excretion of the natriuretic factor. The potentially large source of the natriuretic factor that this could afford, coupled with small analytical sample sizes required by the in-vitro bioassay used here, should facilitate future experimental analysis and allow the natriuretic factor to be investigated as a potential biomarker for RSW.

  12. Engineering food crops to grow in harsh environments [v1; ref status: indexed, http://f1000r.es/5f1

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    Damar López-Arredondo

    2015-09-01

    Full Text Available Achieving sustainable agriculture and producing enough food for the increasing global population will require effective strategies to cope with harsh environments such as water and nutrient stress, high temperatures and compacted soils with high impedance that drastically reduce crop yield. Recent advances in the understanding of the molecular, cellular and epigenetic mechanisms that orchestrate plant responses to abiotic stress will serve as the platform to engineer improved crop plants with better designed root system architecture and optimized metabolism to enhance water and nutrients uptake and use efficiency and/or soil penetration. In this review we discuss such advances and how the generated knowledge could be used to integrate effective strategies to engineer crops by gene transfer or genome editing technologies.

  13. Demonstration of natriuretic activity in urine of neurosurgical patients with renal salt wasting [v1; ref status: indexed, http://f1000r.es/nu

    Directory of Open Access Journals (Sweden)

    Steven J Youmans

    2013-05-01

    Full Text Available We have utilized the persistent elevation of fractional excretion (FE of urate, > 10%, to differentiate cerebral/renal salt wasting (RSW from the syndrome of inappropriate antidiuretic hormone secretion (SIADH, in which a normalization of FEurate occurs after correction of hyponatremia.  Previous studies suggest as well  that an elevated FEurate with normonatremia, without pre-existing hyponatremia, is also consistent with RSW, including studies demonstrating induction of RSW in rats infused with plasma from normonatremic neurosurgical and Alzheimer’s disease patients.  The present studies were designed to test whether precipitates from the urine of normonatremic neurosurgical patients, with either normal or elevated FEurate, and patients with SIADH, display natriuretic activity.   Methods: Ammonium sulfate precipitates from the urine of 6 RSW and 5 non-RSW Control patients were dialyzed (10 kDa cutoff to remove the ammonium sulfate, lyophilized, and the reconstituted precipitate was tested for its effect on transcellular transport of 22Na across LLC-PK1 cells grown to confluency in transwells. Results: Precipitates from 5 of the 6 patients with elevated FEurate and normonatremia significantly inhibited the in vitro transcellular transport of 22Na above a concentration of 3 μg protein/ml, by 10-25%, versus to vehicle alone, and by 15-40% at concentrations of 5-20 μg/ml as compared to precipitates from 4 of the 5 non-RSW patients with either normal FEurate and normonatremia (2 patients or with SIADH (2 patients. Conclusion: These studies provide further evidence that an elevated FEurate with normonatremia is highly consistent with RSW.  Evidence in the urine of natriuretic activity suggests significant renal excretion of the natriuretic factor. The potentially large source of the natriuretic factor that this could afford, coupled with small analytical sample sizes required by the in-vitro bioassay used here, should facilitate future experimental analysis and allow the natriuretic factor to be investigated as a potential biomarker for RSW.

  14. Authors are also reviewers: problems in assigning cause for missing negative studies [v1; ref status: indexed, http://f1000r.es/uo

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    Stephen Senn

    2013-01-01

    Full Text Available I compare two possible extreme hypotheses regarding submission of papers to journals: the Q hypothesis, whereby the decision to submit is based on quality of research; and the P hypothesis, whereby it is based on probability of acceptance. I give five reasons as to why the P hypothesis is more plausible and suggest that problems of missing data may previously have caused researchers to misinterpret the evidence on editorial bias.

  15. Misunderstanding publication bias: editors are not blameless after all [v1; ref status: indexed, http://f1000r.es/YvAwwD

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    Stephen Senn

    2012-12-01

    Full Text Available In analysing whether there is an editorial bias in favour of positive studies, researchers have made implicit assumptions that are implausible. In particular, to justify the conclusion that there is no bias because observed editorial acceptance rates do not favour positive studies, the assumption that the decision to submit an article is based solely on quality would be required. If, on the other hand, submission were based on perceived probability of acceptance, negative and positive studies would not differ in terms of acceptance rates, but in terms of quality. It is shown, using a simple graphical model, how similar underlying situations as regards the relationship between quality and probability of acceptance on the one hand and study outcome (positive or negative and probability of acceptance on the other could produce dramatically different results depending on the behaviour of authors. Furthermore, there is, in fact, some evidence that submitted negative studies are, on average, of higher quality than positive ones. This calls into question the standard interpretation of the studies examining editorial bias. It would appear that despite similar probabilities of acceptance for negative and positive studies, editors could be discriminating against negative studies.

  16. High-resolution view of compound promiscuity [v2; ref status: indexed, http://f1000r.es/1ig

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    Ye Hu

    2013-07-01

    Full Text Available Compound promiscuity is defined as the ability of a small molecule to specifically interact with multiple biological targets. So-defined promiscuity is relevant for drug discovery because it provides the molecular basis of polypharmacology, which is increasingly implicated in the therapeutic efficacy of drugs. Recent studies have analyzed different aspects of compound promiscuity on the basis of currently available activity data. In this commentary, we present take-home messages from these studies augmented with new results to generate a detailed picture of compound promiscuity that might serve as a reference for further discussions and research activities.

  17. Streptococcal taxonomy based on genome sequence analyses [v1; ref status: indexed, http://f1000r.es/o1

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    Cristiane C Thompson

    2013-03-01

    Full Text Available The identification of the clinically relevant viridans streptococci group, at species level, is still problematic. The aim of this study was to extract taxonomic information from the complete genome sequences of 67 streptococci, comprising 19 species, by means of genomic analyses, multilocus sequence analysis (MLSA, average amino acid identity (AAI, genomic signatures, genome-to-genome distances (GGD and codon usage bias. We then attempted to determine the usefulness of these genomic tools for species identification in streptococci. Our results showed that MLSA, AAI and GGD analyses are robust markers to identify streptococci at the species level, for instance, S. pneumoniae, S. mitis, and S. oralis. A Streptococcus species can be defined as a group of strains that share ≥ 95% DNA similarity in MLSA and AAI, and > 70% DNA identity in GGD. This approach allows an advanced understanding of bacterial diversity.

  18. Prediction of post-operative pain following arthroscopic subacromial decompression surgery: an observational study [v1; ref status: indexed, http://f1000r.es/9s

    Directory of Open Access Journals (Sweden)

    Anthony Davis

    2013-02-01

    Full Text Available Background: Arthroscopic shoulder surgery is increasingly performed as a day case procedure. Optimal post-operative pain relief remains a challenge due to considerable variations in the level of pain experienced between individuals. Our aim was to examine whether the preoperative electrical pain threshold was a strong predictor of elevated postoperative pain levels following arthroscopic subacromial decompression (ASD surgery. Methods: Forty consenting patients with American Society of Anesthesiologists (ASA grade 1-2 presenting for elective ASD surgery were recruited. Patients’ electrical pain thresholds were measured preoperatively using a PainMatcher® (Cefar Medical AB, Lund, Sweden device. Following surgery under general anaesthesia, the maximum pain experienced at rest and movement was recorded using a visual analogue scale until the end of postoperative day four. Results: In univariate analyses (t-test, the postoperative pain experienced (Area Under Curve was significantly greater in patients with a low pain threshold as compared with a high pain threshold at both rest (mean 12.5, S.E. 1.7 v mean 6.5, S.E.1.2. P=0.008 and on movement (mean 18.7, S.E. 1.5 v mean 14.1, S.E.1.4. P=0.031. In multivariate analyses, adjusting for additional extra analgesia, the pain experienced postoperatively was significantly greater in the low pain threshold group both at rest (mean difference 4.9, 95% CI 1.5 to 8.4, P=0.007 and on movement (mean difference 4.1, 95%CI 0.03 to 8.2, P=0.049. Conclusions: Preoperative pain threshold can predict postoperative pain level following ASD of the shoulder. Trial registration: Clinicaltrials.gov identifier: NCT01351363 Level of Evidence: II

  19. Alternative ideas to increase the percentage of filled seats in nephrology fellowships [v2; ref status: indexed, http://f1000r.es/2sa

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    Tejas Desai

    2014-01-01

    Full Text Available Interest in nephrology has been decreasing for the last decade. In this opinion piece, the author provides four unconventional, outside-the-box strategies to increase the percentage of filled nephrology training positions.

  20. Does vitamin D deficiency contribute to post-burn bone loss? [v1; ref status: indexed, http://f1000r.es/QLDkCs

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    Gordon L Klein

    2012-11-01

    Full Text Available Burn injury results in the acute loss of bone as well as the development of progressive vitamin D deficiency. Bone loss occurs acutely due to resorption, which is then followed by apoptosis of osteoblasts preventing repair of the bone loss. The acute resorption is due to a combination of the inflammatory response and the stress response to the burn injury. The resultant production of inflammatory cytokines and endogenous glucocorticoids initially stimulate the osteoblasts to produce RANK ligand, which stimulates marrow stem cell differentiation into osteoclasts. As the stress response persists for approximately one year post-burn the glucocorticoids produced by the body will cause osteoblast apoptosis and adynamic bone, impairing the ability of bone to recover its resorptive losses. The vitamin D deficiency is due to the failure to supplement the diet of burn patients with vitamin D on discharge from hospital and to failure of the skin to make normal quantities of vitamin D on sunlight exposure. Because the bone resorption can be prevented by the acute administration of bisphosphonates it is unlikely that vitamin D deficiency is responsible for the early-onset bone loss following burns. However, because a deficit in trabecular bone remains for at least two years post-burn, it is possible that vitamin D deficiency prevents the recovery of trabecular bone density over the long term.

  1. Recent scientific advances in leiomyoma (uterine fibroids research facilitates better understanding and management [v1; ref status: indexed, http://f1000r.es/54a

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    Darlene K. Taylor

    2015-07-01

    Full Text Available Uterine leiomyomas (fibroids are the most prevalent medical problem of the female reproductive tract, but there are few non-surgical treatment options. Although many advances in the understanding of the molecular components of these tumors have occurred over the past five years, an effective pharmaceutical approach remains elusive. Further, there is currently no clinical method to distinguish a benign uterine leiomyoma from a malignant leiomyosarcoma prior to treatment, a pressing need given concerns about the use of the power morcellator for minimally invasive surgery. This paper reviews current studies regarding the molecular biology of uterine fibroids, discusses non-surgical approaches and suggests new cutting-edge therapeutic and diagnostic approaches.

  2. Every scientist is a memory researcher: Suggestions for making research more memorable [v1; ref status: indexed, http://f1000r.es/500

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    Christopher R. Madan

    2015-01-01

    Full Text Available Independent of the actual results, some scientific articles are more memorable than others. As anyone who has written an article collaboratively knows, there are numerous ways a manuscript can be written to convey the same general ideas. To aid with this, many scientific writing books and editorials provide advice, often anecdotal, on how to make articles more memorable. Here I ground these suggestions with empirical support from memory research. Specifically, I suggest that researchers consider how to emphasize their work’s novelty, strive to describe their work using concrete, easy-to-understand terms, and use caution when attempting to evoke an emotional response in the reader. I also discuss considerations in title selections and conference presentations.

  3. Murine Tim-1 is excluded from the immunological synapse [v2; ref status: indexed, http://f1000r.es/QSgUx0

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    Jean Lin

    2012-10-01

    Full Text Available The interaction between T cells and APCs bearing cognate antigen results in the formation of an immunological synapse (IS. During this process, many receptors and signaling proteins segregate to regions proximal to the synapse. This protein movement is thought to influence T cell function. However, some proteins are transported away from the IS, which is controlled in part by ERM family proteins. Tim-1 is a transmembrane protein with co-stimulatory functions that is found on many immune cells, including T cells. However, the expression pattern of Tim-1 on T cells upon activation by APCs has not been explored. Interestingly, in this study we demonstrate that the majority of Tim-1 on activated T cells is excluded from the IS. Tim-1 predominantly resides outside of the IS, and structure/function studies indicate that the cytoplasmic tail influences Tim-1 polarization. Specifically, a putative ERM binding motif (KRK 244-246 in the Tim-1 cytoplasmic tail appears necessary for proper Tim-1 localization. Furthermore, mutation of the KRK motif results in enhanced early tyrosine phosphorylation downstream of TCR/CD28 stimulation upon ectopic expression of Tim-1. Paradoxically however, the KRK motif is necessary for Tim-1 co-stimulation of NFAT/AP-1 activation and co-stimulation of cytokine production. This work reveals unexpected complexity underlying Tim-1 localization and suggests potentially novel mechanisms by which Tim-1 modulates T cell activity.

  4. Shaping the Future of Research: a perspective from junior scientists [v2; ref status: indexed, http://f1000r.es/4yc

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    Gary S. McDowell

    2015-01-01

    Full Text Available The landscape of scientific research and funding is in flux as a result of tight budgets, evolving models of both publishing and evaluation, and questions about training and workforce stability. As future leaders, junior scientists are uniquely poised to shape the culture and practice of science in response to these challenges. A group of postdocs in the Boston area who are invested in improving the scientific endeavor, planned a symposium held on October 2nd and 3rd, 2014, as a way to join the discussion about the future of US biomedical research. Here we present a report of the proceedings of participant-driven workshops and the organizers’ synthesis of the outcomes.

  5. Nigrostriatal dynein changes in A53T alpha-synuclein transgenic mice [v1; ref status: indexed, http://f1000r.es/2wb

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    Yan Liu

    2014-03-01

    Full Text Available The accumulation of misfolded a-synuclein is mechanistically linked to neurodegeneration in Parkinson’s disease (PD and other alpha-synucleinopathies. However, how alpha-synuclein causes neurodegeneration is unresolved. Several studies have supported the involvement of dynein, the major motor for retrograde axonal transport in alpha-synuclein-dependent neurodegeneration, especially in the nigrostriatal system. Therefore, we examined the nigrostriatal dyneins in transgenic mice that overexpress human A53T alpha-synuclein and recapitulate key features of a PD-like neuronal synucleinopathy. Age-matched nontransgenic littermates were used as controls. The results demonstrated that the protein level of dynein was decreased in the striatum, whereas it was elevated in the substantia nigra. Double immunostaining results revealed that the reduction in dynein level was associated with aggregation of A53T a-synuclein in the striatum. Furthermore, we performed a quantitative analysis of motor behaviors in A53T alpha-synuclein transgenic mice and controls using a modified open field test. We demonstrated that the protein level of dynein in the striatum was significantly correlated with the motor behaviors. Together, our data indicate that dynein changes in the nigrostriatal system of A53T alpha-synuclein transgenic mice may contribute to their severe movement disorder.

  6. Novel Insights and Therapeutics in Multiple Sclerosis [v1; ref status: indexed, http://f1000r.es/59z

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    Catriona A. Wagner

    2015-08-01

    Full Text Available The last twelve years have witnessed the development of new therapies for relapsing-remitting multiple sclerosis that demonstrate increased efficacy relative to previous therapies. Many of these new drugs target the inflammatory phase of disease by manipulating different aspects of the immune system. While these new treatments are promising, the development of therapies for patients with progressive multiple sclerosis remains a significant challenge. We discuss the distinct mechanisms that may contribute to these two types of multiple sclerosis and the implications of these differences in the development of new therapeutic targets for this debilitating disease.

  7. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API [v1; ref status: indexed, http://f1000r.es/5ly

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    Keiichiro Ono

    2015-08-01

    Full Text Available As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated only manually via a point-and-click user interface. Consequently, Cytoscape-oriented tasks are laborious and often error prone, especially with multistep protocols involving many networks. In this paper, we present the new cyREST Cytoscape app and accompanying harmonization libraries. Together, they improve workflow reproducibility and researcher productivity by enabling popular languages (e.g., Python and R, JavaScript, and C# and tools (e.g., IPython/Jupyter Notebook and RStudio to directly define and query networks, and perform network analysis, layouts and renderings. We describe cyREST’s API and overall construction, and present Python- and R-based examples that illustrate how Cytoscape can be integrated into large scale data analysis pipelines. cyREST is available in the Cytoscape app store (http://apps.cytoscape.org where it has been downloaded over 1900 times since its release in late 2014.

  8. An object oriented implementation of the Yeadon human inertia model [v1; ref status: indexed, http://f1000r.es/4cr

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    Christopher Dembia

    2014-09-01

    Full Text Available We present an open source software implementation of a popular mathematical method developed by M.R. Yeadon for calculating the body and segment inertia parameters of a human body. The software is written in a high level open source language and provides three interfaces for manipulating the data and the model: a Python API, a command-line user interface, and a graphical user interface. Thus the software can fit into various data processing pipelines and requires only simple geometrical measures as input.

  9. Glycine-extended gastrin enhances somatostatin release from cultured rabbit fundic D-cells [v1; ref status: indexed, http://f1000r.es/8n

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    Ian LP Beales

    2013-02-01

    Full Text Available The role of the peptide hormone gastrin in stimulating gastric acid secretion is well established. Mature amidated gastrin is processed from larger peptide precursor forms. Increasingly these processing intermediates, such as glycine-extended gastrin (G-Gly and progastrin, have been shown to have biological activities of their own, often separate and complementary to gastrin. Although G-Gly is synthesized and secreted by gastric antral G-cells, the physiological functions of this putative mediator are unclear. Gastrin and cholecystokinin (CCK stimulate the secretion of somatostatin from gastric D-cells as part of the feedback control of gastric acid. In this study the effect of G-Gly and gastrin on the release of somatostatin from rabbit fundic D-cells was examined. D-cells were obtained by collagenase-EDTA digestion and elutriation and cultured for 48 hours. With a 2 hour exposure to the peptides, gastrin but not G-Gly stimulated somatostatin release. Treatment of D-cells for 24 hours with gastrin or G-Gly individually, significantly enhanced subsequent basal as well as CCK- and GLP-1-stimulated somatostatin release. Twenty four hours exposure to gastrin combined with G-Gly synergistically enhanced basal and agonist-stimulated somatostatin release and cellular somatostatin content. Gastrin and G-Gly may be important in the longer term regulation of D-cell function.

  10. AGA: Interactive pipeline for reproducible genomics analyses [v1; ref status: indexed, http://f1000r.es/4zc

    Directory of Open Access Journals (Sweden)

    Michael Considine

    2015-01-01

    Full Text Available Automated Genomics Analysis (AGA is an interactive program to analyze high-throughput genomic data sets on a variety of platforms. An easy to use, point and click, guided pipeline is implemented to combine, define, and compare datasets, and customize their outputs. In contrast to other automated programs, AGA enables flexible selection of sample groups for comparison from complex sample annotations. Batch correction techniques are also included to further enable the combination of datasets from diverse studies in this comparison. AGA also allows users to save plots, tables and data, and log files containing key portions of the R script run for reproducible analyses. The link between the interface and R supports collaborative research, enabling advanced R users to extend preliminary analyses generated from bioinformatics novices.

  11. Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors [v1; ref status: indexed, http://f1000r.es/z6

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    Thomas B Kepler

    2013-04-01

    Full Text Available One of the key phenomena in the adaptive immune response to infection and immunization is affinity maturation, during which antibody genes are mutated and selected, typically resulting in a substantial increase in binding affinity to the eliciting antigen. Advances in technology on several fronts have made it possible to clone large numbers of heavy-chain light-chain pairs from individual B cells and thereby identify whole sets of clonally related antibodies. These collections could provide the information necessary to reconstruct their own history - the sequence of changes introduced into the lineage during the development of the clone - and to study affinity maturation in detail. But the success of such a program depends entirely on accurately inferring the founding ancestor and the other unobserved intermediates. Given a set of clonally related immunoglobulin V-region genes, the method described here allows one to compute the posterior distribution over their possible ancestors, thereby giving a thorough accounting of the uncertainty inherent in the reconstruction. I demonstrate the application of this method on heavy-chain and light-chain clones, assess the reliability of the inference, and discuss the sources of uncertainty.

  12. Memory enhancement produced by post-training exposure to sucrose-conditioned cues [v1; ref status: indexed, http://f1000r.es/ur

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    Matthew R Holahan

    2013-01-01

    Full Text Available A number of aversive and appetitive unconditioned stimuli (such as shock and food are known to produce memory enhancement when they occur during the post-training period. Post-training exposure to conditioned aversive stimuli has also been shown to enhance memory consolidation processes. The present study shows for the first time that post-training exposure to conditioned stimuli previously paired with consumption of a sucrose solution also enhances memory consolidation. Male Long Evans rats were trained on a one-session conditioned cue preference (CCP task on a radial arm maze. Immediately or 2 hours after training, rats consumed a sucrose solution or were exposed to cues previously paired with consumption of sucrose or cues previously paired with water. Twenty-four hours later, the rats were tested for a CCP. Immediate, but not delayed, post-training consumption of sucrose enhanced memory for the CCP. Immediate, but not delayed, post-training exposure to cues previously paired with sucrose, but not with water, also enhanced CCP memory. The possibility that rewarding and aversive conditioned stimuli affect memory by a common physiological process is discussed.

  13. Portrayed emotions in the movie "Forrest Gump" [v1; ref status: indexed, http://f1000r.es/55o

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    Annika Labs

    2015-04-01

    Full Text Available Here we present a dataset with a description of portrayed emotions in the movie ”Forrest Gump”. A total of 12 observers independently annotated emotional episodes regarding their temporal location and duration. The nature of an emotion was characterized with basic attributes, such as arousal and valence, as well as explicit emotion category labels. In addition, annotations include a record of the perceptual evidence for the presence of an emotion. Two variants of the movie were annotated separately: 1 an audio-movie version of Forrest Gump that has been used as a stimulus for the acquisition of a large public functional brain imaging dataset, and 2 the original audio-visual movie. We present reliability and consistency estimates that suggest that both stimuli can be used to study visual and auditory emotion cue processing in real-life like situations. Raw annotations from all observers are publicly released in full in order to maximize their utility for a wide range of applications and possible future extensions. In addition, aggregate time series of inter-observer agreement with respect to particular attributes of portrayed emotions are provided to facilitate adoption of these data.

  14. Effect of storage levels of nitric oxide derivatives in blood components [v1; ref status: indexed, http://f1000r.es/WDkFtz

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    Melissa A Qazi

    2012-10-01

    Full Text Available Background: Potential deleterious effects of red blood cell (RBC transfusions, especially from blood kept at length, have been ascribed to biochemical changes during storage, including those of nitric oxide (NO metabolism. Study methods and design: In this study, NO metabolites, nitrite and nitrate, were quantified in RBCs and whole blood with time of storage. Whole blood (WB, leukoreduced (LR, and non-leukoreduced (NLR components were obtained from healthy volunteer donors and stored in polyvinyl chloride bags for 42 days. Nitrite and nitrate were measured using reductive gas-phase chemiluminescence. Results: Nitrite concentrations initially decreased rapidly from about 150nmol/L, but stabilized at about 44nmol/L in room air for up to 42 days. Nitrate concentrations remained stable during storage at about 35µmol/L. Cells from bags maintained in an argon chamber showed decreased nitrite levels compared to those maintained in room air. Inhibition of enzymes implicated in the NO cycle did not alter nitrite levels. Conclusion: As erythrocytes may contribute to the control of blood flow and oxygen delivery through reduction of nitrite to NO under hypoxic conditions, the present findings provide insight into possible effects of blood transfusion. These measurements may explain some adverse effects of RBC transfusion and suggest ways of optimizing the preservation of stored blood.

  15. setsApp: Set operations for Cytoscape Nodes and Edges [v1; ref status: indexed, http://f1000r.es/3ml

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    John H. Morris

    2014-07-01

    Full Text Available setsApp (http://apps.cytoscape.org/apps/setsapp is a relatively simple Cytoscape 3 app for users to handle groups of nodes and/or edges. It supports several important biological workflows and enables various set operations. setsApp provides basic tools to create sets of nodes or edges, import or export sets, and perform standard set operations (union, difference, intersection on those sets. The sets functionality is also exposed to users and app developers in the form of a set of commands that can be used for scripting purposes or integrated in other Cytoscape apps.

  16. setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges [v2; ref status: indexed, http://f1000r.es/5lz

    Directory of Open Access Journals (Sweden)

    John H. Morris

    2015-08-01

    Full Text Available setsApp (http://apps.cytoscape.org/apps/setsapp is a relatively simple Cytoscape 3 app for users to handle groups of nodes and/or edges. It supports several important biological workflows and enables various set operations. setsApp provides basic tools to create sets of nodes or edges, import or export sets, and perform standard set operations (union, difference, intersection on those sets. Automatic set partitioning and layout functions are also provided. The sets functionality is also exposed to users and app developers in the form of a set of commands that can be used for scripting purposes or integrated in other Cytoscape apps.

  17. CrossRef The Second Beam-Line and Experimental Area at n_TOF: A New Opportunity for Challenging Neutron Measurements at CERN

    CERN Document Server

    Colonna, Nicola; Chiaveri, Enrico

    2015-01-01

    Since 2001, a wealth of neutron capture and neutron-induced fission reactions has been measured at n_TOF, providing an important contribution to a wide variety of research fields. The experimental activity is driven mostly by two motivations: on the one hand, capture reactions are studied with the aim of improving current models of stellar nucleosynthesis of heavy elements. A review of the needs related to nuclear astrophysics and the contribution of the n_TOF program can be found in [1, 2].

  18. Learning intrinsic excitability in medium spiny neurons [v2; ref status: indexed, http://f1000r.es/30b

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    Gabriele Scheler

    2014-02-01

    Full Text Available We present an unsupervised, local activation-dependent learning rule for intrinsic plasticity (IP which affects the composition of ion channel conductances for single neurons in a use-dependent way. We use a single-compartment conductance-based model for medium spiny striatal neurons in order to show the effects of parameterization of individual ion channels on the neuronal membrane potential-curent relationship (activation function. We show that parameter changes within the physiological ranges are sufficient to create an ensemble of neurons with significantly different activation functions. We emphasize that the effects of intrinsic neuronal modulation on spiking behavior require a distributed mode of synaptic input and can be eliminated by strongly correlated input. We show how modulation and adaptivity in ion channel conductances can be utilized to store patterns without an additional contribution by synaptic plasticity (SP. The adaptation of the spike response may result in either "positive" or "negative" pattern learning. However, read-out of stored information depends on a distributed pattern of synaptic activity to let intrinsic modulation determine spike response. We briefly discuss the implications of this conditional memory on learning and addiction.

  19. JSim, an open-source modeling system for data analysis [v2; ref status: indexed, http://f1000r.es/39h

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    Erik Butterworth

    2014-05-01

    Full Text Available JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter sets, and for making comparisons among different models running simultaneously or separately. Interactive use is supported by a large collection of graphical user interfaces for model writing and compilation diagnostics, defining input functions, model runs, selection of algorithms solving ordinary and partial differential equations, run-time multidimensional graphics, parameter optimization (8 methods, sensitivity analysis, and Monte Carlo simulation for defining confidence ranges. JSim uses Mathematical Modeling Language (MML a declarative syntax specifying algebraic and differential equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc. are accessed through procedure calls. MML syntax is simple, basically defining the parameters and variables, then writing the equations in a straightforward, easily read and understood mathematical form. This makes JSim good for teaching modeling as well as for model analysis for research.   For high throughput applications, JSim can be run as a batch job.  JSim can automatically translate models from the repositories for Systems Biology Markup Language (SBML and CellML models. Stochastic modeling is supported. MML supports assigning physical units to constants and variables and automates checking dimensional balance as the first step in verification testing. Automatic unit scaling follows, e.g. seconds to minutes, if needed. The JSim Project File sets a standard for reproducible modeling analysis: it includes in one file everything for analyzing a set of experiments: the data, the models, the data fitting, and evaluation of parameter confidence ranges. JSim is open source; it and about 400 human readable open source physiological/biophysical models are available at http://www.physiome.org/jsim/.

  20. Factors that contribute to social media influence within an Internal Medicine Twitter learning community [v1; ref status: indexed, http://f1000r.es/3jd

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    Tejas Desai

    2014-05-01

    Full Text Available Medical societies, faculty, and trainees use Twitter to learn from and educate other social media users. These social media communities bring together individuals with various levels of experience. It is not known if experienced individuals are also the most influential members. We hypothesize that participants with the greatest experience would be the most influential members of a Twitter community. We analyzed the 2013 Association of Program Directors in Internal Medicine Twitter community. We measured the number of tweets authored by each participant and the number of amplified tweets (re-tweets. We developed a multivariate linear regression model to identify any relationship to social media influence, measured by the PageRank. Faculty (from academic institutions comprised 19% of the 132 participants in the learning community (p < 0.0001. Faculty authored 49% of all 867 tweets (p < 0.0001. Their tweets were the most likely to be amplified (52%, p < 0.01. Faculty had the greatest influence amongst all participants (mean 1.99, p < 0.0001. Being a faculty member had no predictive effect on influence (β = 0.068, p = 0.6. The only factors that predicted influence (higher PageRank were the number of tweets authored (p < 0.0001 and number of tweets amplified (p < 0.0001 The status of “faculty member” did not confer a greater influence. Any participant who was able to author the greatest number of tweets or have more of his/her tweets amplified could wield a greater influence on the participants, regardless of his/her authority.

  1. Pleural effusion as the initial extramedullary manifestation of Acute Myeloid Leukemia [v1; ref status: indexed, http://f1000r.es/PEKat0

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    José Nieves-Nieves

    2012-10-01

    Full Text Available Leukemias rarely debut by pleural involvement as the first manifestation of the hematologic malignancy. This complication is most commonly seen in solid tumors such as carcinomas of the breast, lung, gastrointestinal tract and lymphomas. We present a case of a 66 year old male who presented with a pleural leukemic infiltration of his undiagnosed Acute Myeloid Leukemia that was not a complication of the disease extension, but the acute presentation of the illness. Progressive shortness of breath for two weeks, cough, clear sputum and weight loss were the initial complaints. Serum dyscrasia suggested a hematologic abnormality. A chest x-ray performed demonstrated a buildup of fluid with layering in the left pleural cavity. Diagnostic thoracentesis suggested an exudative etiology with cytology remarkable for 62% leukemic myeloblast. The diagnosis was confirmed by bone marrow biopsy with expression of the antigens CD 34+ and CD13+, with unfavorable cytogenetic prognosis and a trisomy 21 chromosomal defect. Chemotherapy was initiated, though no remission achieved with induction chemotherapy. Complications and disease progression precludes in the patient’s death. Although rare, due to the unusual presentation of the disease, this case clearly demonstrates the importance of biochemical analysis and cytopathology specimens obtained in pleural fluid.

  2. Activity artifacts in drug discovery and different facets of compound promiscuity [v1; ref status: indexed, http://f1000r.es/4gz

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    Jürgen Bajorath

    2014-10-01

    Full Text Available Compounds with apparent activity in a variety of assays might disable target proteins or produce false assay signals in the absence of specific interactions. In some instances, such effects are easy to detect, in others they are not. Observed promiscuity of compounds might be due to such non-specific assay artifacts. By contrast, promiscuity might also result from specific interactions with multiple targets. In the latter case, promiscuous compounds can be attractive candidates for certain therapeutic applications. However, compounds with artificial activity readouts are often not recognized and are further progressed, which presents a substantial problem for drug discovery. In this context, the concept of PAINS (pan-assay interference compounds should be seriously considered, which makes it possible to eliminate flawed compounds from the discovery pipeline, even if their activities appear to be sound at a first glance.

  3. Aging and energetics’ ‘Top 40’ future research opportunities 2010-2013 [v1; ref status: indexed, http://f1000r.es/4ae

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    David B. Allison

    2014-09-01

    Full Text Available Background: As part of a coordinated effort to expand our research activity at the interface of Aging and Energetics a team of investigators at The University of Alabama at Birmingham systematically assayed and catalogued the top research priorities identified in leading publications in that domain, believing the result would be useful to the scientific community at large. Objective: To identify research priorities and opportunities in the domain of aging and energetics as advocated in the 40 most cited papers related to aging and energetics in the last 4 years. Design: The investigators conducted a search for papers on aging and energetics in Scopus, ranked the resulting papers by number of times they were cited, and selected the ten most-cited papers in each of the four years that include 2010 to 2013, inclusive. Results:   Ten research categories were identified from the 40 papers.  These included: (1 Calorie restriction (CR longevity response, (2 role of mTOR (mechanistic target of Rapamycin and related factors in lifespan extension, (3 nutrient effects beyond energy (especially resveratrol, omega-3 fatty acids, and selected amino acids, 4 autophagy and increased longevity and health, (5 aging-associated predictors of chronic disease, (6 use and effects of mesenchymal stem cells (MSCs, (7 telomeres relative to aging and energetics, (8 accretion and effects of body fat, (9 the aging heart,  and (10 mitochondria, reactive oxygen species, and cellular energetics. Conclusion: The field is rich with exciting opportunities to build upon our existing knowledge about the relations among aspects of aging and aspects of energetics and to better understand the mechanisms which connect them.

  4. Periprosthetic bone loss: diagnostic and therapeutic approaches [v2; ref status: indexed, http://f1000r.es/3pz

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    Loredana Cavalli

    2014-06-01

    Full Text Available Total joint replacement surgery is being performed on an increasingly large part of the population. Clinical longevity of implants depends on their osseointegration, which is influenced by the load, the characteristics of the implant and the bone-implant interface, as well as by the quality and quantity of the surrounding bone. Aseptic loosening due to periprosthetic osteolysis is the most frequent known cause of implant failure. Wear of prosthetic materials results in the formation of numerous particles of debris that cause a complex biological response. Dual-energy X-ray Absorptiometry (DXA is regarded as an accurate method to evaluate Bone Mineral Density (BMD around hip or knee prostheses. Further data may be provided by a new device, the Bone Microarchitecture Analysis (BMA, which combines bone microarchitecture quantification and ultra high resolution osteo-articular imaging. Pharmacological strategies have been developed to prevent bone mass loss and to extend implant survival. Numerous trials with bisphosphonates show a protective effect on periprosthetic bone mass, up to 72 months after arthroplasty. Strontium ranelate has been demonstrated to increase the osseointegration of titanium implants in treated animals with improvement of bone microarchitecture and bone biomaterial properties.

  5. Behavioural evidence for self-medication in bumblebees? [v2; ref status: indexed, http://f1000r.es/5ep

    OpenAIRE

    David Baracchi; Mark J. F. Brown; Lars Chittka

    2015-01-01

    The presence of antimicrobial secondary metabolites in nectar suggests that pollinators, which are threatened globally by emergent disease, may benefit from the consumption of nectars rich in these metabolites. We tested whether nicotine, a nectar secondary metabolite common in Solanaceae and Tilia species, is used by parasitized bumblebees as a source of self-medication, using a series of toxicological, microbiological and behavioural experiments. Caged bees infected with Crithidia bombi had...

  6. Behavioural evidence for self-medication in bumblebees? [v2; ref status: indexed, http://f1000r.es/5ep

    Directory of Open Access Journals (Sweden)

    David Baracchi

    2015-05-01

    Full Text Available The presence of antimicrobial secondary metabolites in nectar suggests that pollinators, which are threatened globally by emergent disease, may benefit from the consumption of nectars rich in these metabolites. We tested whether nicotine, a nectar secondary metabolite common in Solanaceae and Tilia species, is used by parasitized bumblebees as a source of self-medication, using a series of toxicological, microbiological and behavioural experiments. Caged bees infected with Crithidia bombi had a slight preference for sucrose solution laced with the alkaloid and behavioural tests showed that the parasite infection induced an increased consumption of nicotine during foraging activity, though nicotine had an appetite-reducing effect overall. When ingested, nicotine delayed the progression of a gut infection in bumblebees by a few days, but dietary nicotine did not clear the infection, and after 10 days the parasite load approached that of control bees. Moreover, when pathogens were exposed to the alkaloid prior to host ingestion, the protozoan’s viability was not directly affected, suggesting that anti-parasite effects were relatively weak. Nicotine consumption in a single dose did not impose any cost even in starved bees but the alkaloid had detrimental effects on healthy bees if consistently consumed for weeks. These toxic effects disappeared in infected bees, suggesting that detoxification costs might have been counterbalanced by the advantages in slowing the progression of the infection. Nicotine consumption did not affect bee lifespan but the reduction in the parasite load may have other likely unexplored subtle benefits both for individual bees and their colony.  Potential evidence for self-medication is discussed. The contention that secondary metabolites in nectar may be under selection from pollinators, or used by plants to enhance their own reproductive success, remains to be confirmed.

  7. Nelfinavir and other protease inhibitors in cancer: mechanisms involved in anticancer activity [v2; ref status: indexed, http://f1000r.es/536

    Directory of Open Access Journals (Sweden)

    Tomas Koltai

    2015-03-01

    Full Text Available Objective: To review the mechanisms of anti-cancer activity of nelfinavir and other protease inhibitors (PIs based on evidences reported in the published literature. Methods: We extensively reviewed the literature concerning nelfinavir (NFV as an off target anti-cancer drug and other PIs. A classification of PIs based on anti-cancer mode of action was proposed. Controversies regarding nelfinavir mode of action were also addressed. Conclusions: The two main mechanisms involved in anti-cancer activity are endoplasmic reticulum stress-unfolded protein response pathway and Akt inhibition. However there are many other effects, partially dependent and independent of those mentioned, that may be useful in cancer treatment, including MMP-9 and MMP-2 inhibition, down-regulation of CDK-2, VEGF, bFGF, NF-kB, STAT-3, HIF-1 alfa, IGF, EGFR, survivin, BCRP, androgen receptor, proteasome, fatty acid synthase (FAS, decrease in cellular ATP concentration and upregulation of TRAIL receptor DR5, Bax, increased radiosensitivity, and autophagy. The end result of all these effects is slower growth, decreased angiogenesis, decreased invasion and increased apoptosis, which means reduced proliferation and increased cancer cells death. PIs may be classified according to their anticancer activity at clinically achievable doses, in AKT inhibitors, ER stressors and Akt inhibitors/ER stressors. Beyond the phase I trials that have been recently completed, adequately powered and well-designed clinical trials are needed in the various cancer type settings, and specific trials where NFV is tested in association with other known anti-cancer pharmaceuticals should be sought, in order to find an appropriate place for NFV in cancer treatment. The analysis of controversies on the molecular mechanisms of NFV hints to the possibility that NFV works in a different way in tumor cells and in hepatocytes and adipocytes.

  8. SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes [v1; ref status: indexed, http://f1000r.es/445

    Directory of Open Access Journals (Sweden)

    Jennifer Wyffels

    2014-08-01

    Full Text Available Chondrichthyan fishes are a diverse class of gnathostomes that provide a valuable perspective on fundamental characteristics shared by all jawed and limbed vertebrates. Studies of phylogeny, species diversity, population structure, conservation, and physiology are accelerated by genomic, transcriptomic and protein sequence data. These data are widely available for many sarcopterygii (coelacanth, lungfish and tetrapods and actinoptergii (ray-finned fish including teleosts taxa, but limited for chondrichthyan fishes.  In this study, we summarize available data for chondrichthyes and describe resources for one of the largest projects to characterize one of these fish, Leucoraja erinacea, the little skate.  SkateBase (http://skatebase.org serves as the skate genome project portal linking data, research tools, and teaching resources.

  9. Traditional medicine: a rare cause of lead poisoning in Western countries [v1; ref status: indexed, http://f1000r.es/2c6

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    Halima Muller

    2013-11-01

    Full Text Available A 42-year-old man from Bhutan was admitted to the emergency department with a 5-day history of abdominal pain, nausea and vomiting. Enhanced abdominal CT scan was found negative, however laboratory tests showed hemolytic anemia and basophilic stippling which are often seen in lead and heavy metal poisoning. Additional tests revealed a high level of lead in blood and urine. The patient was administered a chelator treatment with rapid improvement of the symptoms. A detailed interview revealed that the patient had been taking daily Bhutanese traditional medicines to treat a Bell’s palsy from which he had been suffering for a few months. The analysis of these medicines confirmed the presence of a high level of lead.

  10. A flexible user-interface for audiovisual presentation and interactive control in neurobehavioral experiments [v1; ref status: indexed, http://f1000r.es/wt

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    Christopher T Noto

    2013-01-01

    Full Text Available A major problem facing behavioral neuroscientists is a lack of unified, vendor-distributed data acquisition systems that allow stimulus presentation and behavioral monitoring while recording neural activity. Numerous systems perform one of these tasks well independently, but to our knowledge, a useful package with a straightforward user interface does not exist. Here we describe the development of a flexible, script-based user interface that enables customization for real-time stimulus presentation, behavioral monitoring and data acquisition. The experimental design can also incorporate neural microstimulation paradigms. We used this interface to deliver multimodal, auditory and visual (images or video stimuli to a nonhuman primate and acquire single-unit data. Our design is cost-effective and works well with commercially available hardware and software. Our design incorporates a script, providing high-level control of data acquisition via a sequencer running on a digital signal processor to enable behaviorally triggered control of the presentation of visual and auditory stimuli. Our experiments were conducted in combination with eye-tracking hardware. The script, however, is designed to be broadly useful to neuroscientists who may want to deliver stimuli of different modalities using any animal model.

  11. Selection and validation of reference genes for quantitative gene expression studies in Erythroxylum coca [v1; ref status: indexed, http://f1000r.es/y1

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    Teresa Docimo

    2013-02-01

    Full Text Available Real-time quantitative PCR is a powerful technique for the investigation of comparative gene expression, but its accuracy and reliability depend on the reference genes used as internal standards. Only genes that show a high level of expression stability are suitable for use as reference genes, and these must be identified on a case-by-case basis. Erythroxylum coca produces and accumulates high amounts of the pharmacologically active tropane alkaloid cocaine (especially in the leaves, and is an emerging model for the investigation of tropane alkaloid biosynthesis. The identification of stable internal reference genes for this species is important for its development as a model species, and would enable comparative analysis of candidate biosynthetic genes in the different tissues of the coca plant. In this study, we evaluated the expression stability of nine candidate reference genes in E. coca (Ec6409, Ec10131, Ec11142, Actin, APT2, EF1α, TPB1, Pex4, Pp2aa3. The expression of these genes was measured in seven tissues (flowers, stems, roots and four developmental leaf stages and the stability of expression was assessed using three algorithms (geNorm, NormFinder and BestKeeper. From our results we conclude that Ec10131 and TPB1 are the most appropriate internal reference genes in leaves (where the majority of cocaine is produced, while Ec10131 and Ec6409 are the most suitable internal reference genes across all of the tissues tested.

  12. A common feature pharmacophore for FDA-approved drugs inhibiting the Ebola virus [v1; ref status: indexed, http://f1000r.es/4qh

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    Sean Ekins

    2014-11-01

    Full Text Available We are currently faced with a global infectious disease crisis which has been anticipated for decades. While many promising biotherapeutics are being tested, the search for a small molecule has yet to deliver an approved drug or therapeutic for the Ebola or similar filoviruses that cause haemorrhagic fever. Two recent high throughput screens published in 2013 did however identify several hits that progressed to animal studies that are FDA approved drugs used for other indications. The current computational analysis uses these molecules from two different structural classes to construct a common features pharmacophore. This ligand-based pharmacophore implicates a possible common target or mechanism that could be further explored. A recent structure based design project yielded nine co-crystal structures of pyrrolidinone inhibitors bound to the viral protein 35 (VP35. When receptor-ligand pharmacophores based on the analogs of these molecules and the protein structures were constructed, the molecular features partially overlapped with the common features of solely ligand-based pharmacophore models based on FDA approved drugs. These previously identified FDA approved drugs with activity against Ebola were therefore docked into this protein. The antimalarials chloroquine and amodiaquine docked favorably in VP35. We propose that these drugs identified to date as inhibitors of the Ebola virus may be targeting VP35. These computational models may provide preliminary insights into the molecular features that are responsible for their activity against Ebola virus in vitro and in vivo and we propose that this hypothesis could be readily tested.

  13. Environmental enrichment does not impact on tumor growth in mice [v1; ref status: indexed, http://f1000r.es/18c

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    Jennifer A Westwood

    2013-06-01

    Full Text Available The effect of environmental enrichment (EE on a variety of physiologic and disease processes has been studied in laboratory mice. During EE, a large group of mice are housed in larger cages than the standard cage and are given toys and equipment, enabling more social contact, and providing a greater surface area per mouse, and a more stimulating environment. Studies have been performed into the effect of EE on neurogenesis, brain injury, cognitive capacity, memory, learning, neuronal pathways, diseases such as Alzheimer’s, anxiety, social defeat, emotionality, depression, drug addiction, alopecia, and stereotypies. In the cancer field, three papers have reported effects on mice injected with tumors and housed in enriched environments compared with those housed in standard conditions. One paper reported a significant decrease in tumor growth in mice in EE housing. We attempted to replicate this finding in our animal facility, because the implications of repeating this finding would have profound implications for how we house all our mice in our studies on cancer. We were unable to reproduce the results in the paper in which B16F10 subcutaneous tumors of mice housed in EE conditions were smaller than those of mice housed in standard conditions. The differences in results could have been due to the different growth rate of the B16F10 cultures from the different laboratories, the microbiota of the mice housed in the two animal facilities, variations in noise and handling between the two facilities, food composition, the chemical composition of the cages or the detergents used for cleaning, or a variety of other reasons. EE alone does not appear to consistently result in decreased tumor growth, but other factors would appear to be able to counteract or inhibit the effects of EE on cancer progression.

  14. Food sovereignty: an alternative paradigm for poverty reduction and biodiversity conservation in Latin America [v1; ref status: indexed, http://f1000r.es/23s

    Directory of Open Access Journals (Sweden)

    M Jahi Chappell

    2013-11-01

    Full Text Available Strong feedback between global biodiversity loss and persistent, extreme rural poverty are major challenges in the face of concurrent food, energy, and environmental crises. This paper examines the role of industrial agricultural intensification and market integration as exogenous socio-ecological drivers of biodiversity loss and poverty traps in Latin America. We then analyze the potential of a food sovereignty framework, based on protecting the viability of a diverse agroecological matrix while supporting rural livelihoods and global food production. We review several successful examples of this approach, including ecological land reform in Brazil, agroforestry, milpa, and the uses of wild varieties in smallholder systems in Mexico and Central America. We highlight emergent research directions that will be necessary to assess the potential of the food sovereignty model to promote both biodiversity conservation and poverty reduction.

  15. Two fatal cases of melioidosis on the Thai-Myanmar border [v1; ref status: indexed, http://f1000r.es/2os

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    Cindy S. Chu

    2014-01-01

    Full Text Available Melioidosis is endemic in areas of Southeast Asia, however, there are no published reports from the Thai-Myanmar border.  We report the first two cases of fatal melioidosis in this region. This is of great public health importance and highlights the need to increase clinical awareness of melioidosis on the Thai-Myanmar border and to assess the true burden of disease in the area through improved case detection and Burkholderia pseudomallei prevalence studies.

  16. Two fatal cases of melioidosis on the Thai-Myanmar border [v2; ref status: indexed, http://f1000r.es/373

    Directory of Open Access Journals (Sweden)

    Cindy S. Chu

    2014-03-01

    Full Text Available Melioidosis is endemic in areas of Southeast Asia, however, there are no published reports from the Thai-Myanmar border. We report the first two documented cases of fatal melioidosis in this region. This is of great public health importance and highlights the need to both increase clinical awareness of melioidosis on the Thai-Myanmar border, and to assess the true burden of disease in the area through improved case detection and Burkholderia pseudomallei prevalence studies.

  17. Functional characterization of Candida albicans Hos2 histone deacetylase [v3; ref status: indexed, http://f1000r.es/3xh

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    G Karthikeyan

    2014-07-01

    Full Text Available Candida albicans is a mucosal commensal organism capable of causing superficial (oral and vaginal thrush infections in immune normal hosts, but is a major pathogen causing systemic and mucosal infections in immunocompromised individuals. Azoles have been very effective anti-fungal agents and the mainstay in treating opportunistic mold and yeast infections. Azole resistant strains have emerged compromising the utility of this class of drugs. It has been shown that azole resistance can be reversed by the co-administration of a histone deacetylase (HDAC inhibitor, suggesting that resistance is mediated by epigenetic mechanisms possibly involving Hos2, a fungal deacetylase. We report here the cloning and functional characterization of HOS2 (HighOsmolarity Sensitive, a gene coding for fungal histone deacetylase from C. albicans. Inhibition studies showed that Hos2 is susceptible to pan inhibitors such as trichostatin A (TSA and suberoylanilide hydroxamic acid (SAHA, but is not inhibited by class I inhibitors such as MS-275. This in vitro enzymatic assay, which is amenable to high throughput could be used for screening potent fungal Hos2 inhibitors that could be a potential anti-fungal adjuvant. Purified Hos2 protein consistently deacetylated tubulins, rather than histones from TSA-treated cells. Hos2 has been reported to be a putative NAD+ dependent histone deacetylase, a feature of sirtuins. We assayed for sirtuin activation with resveratrol and purified Hos2 protein and did not find any sirtuin activity.

  18. Astrocytes require insulin-like growth factor I to protect neurons against oxidative injury [v2; ref status: indexed, http://f1000r.es/38u

    Directory of Open Access Journals (Sweden)

    Laura Genis

    2014-04-01

    Full Text Available Oxidative stress is a proposed mechanism in brain aging, making the study of its regulatory processes an important aspect of current neurobiological research. In this regard, the role of the aging regulator insulin-like growth factor I (IGF-I in brain responses to oxidative stress remains elusive as both beneficial and detrimental actions have been ascribed to this growth factor. Because astrocytes protect neurons against oxidative injury, we explored whether IGF-I participates in astrocyte neuroprotection and found that blockade of the IGF-I receptor in astrocytes abrogated their rescuing effect on neurons. We found that IGF-I directly protects astrocytes against oxidative stress (H2O2. Indeed, in astrocytes but not in neurons, IGF-I decreases the pro-oxidant protein thioredoxin-interacting protein 1 and normalizes the levels of reactive oxygen species. Furthermore, IGF-I cooperates with trophic signals produced by astrocytes in response to H2O2 such as stem cell factor (SCF to protect neurons against oxidative insult. After stroke, a condition associated with brain aging where oxidative injury affects peri-infarcted regions, a simultaneous increase in SCF and IGF-I expression was found in the cortex, suggesting that a similar cooperative response takes place in vivo. Cell-specific modulation by IGF-I of brain responses to oxidative stress may contribute in clarifying the role of IGF-I in brain aging.

  19. Enhancement of COPD biological networks using a web-based collaboration interface [v2; ref status: indexed, http://f1000r.es/5ew

    Directory of Open Access Journals (Sweden)

    The sbv IMPROVER project team (in alphabetical order

    2015-05-01

    Full Text Available The construction and application of biological network models is an approach that offers a holistic way to understand biological processes involved in disease. Chronic obstructive pulmonary disease (COPD is a progressive inflammatory disease of the airways for which therapeutic options currently are limited after diagnosis, even in its earliest stage. COPD network models are important tools to better understand the biological components and processes underlying initial disease development. With the increasing amounts of literature that are now available, crowdsourcing approaches offer new forms of collaboration for researchers to review biological findings, which can be applied to the construction and verification of complex biological networks. We report the construction of 50 biological network models relevant to lung biology and early COPD using an integrative systems biology and collaborative crowd-verification approach. By combining traditional literature curation with a data-driven approach that predicts molecular activities from transcriptomics data, we constructed an initial COPD network model set based on a previously published non-diseased lung-relevant model set. The crowd was given the opportunity to enhance and refine the networks on a website (https://bionet.sbvimprover.com/ and to add mechanistic detail, as well as critically review existing evidence and evidence added by other users, so as to enhance the accuracy of the biological representation of the processes captured in the networks. Finally, scientists and experts in the field discussed and refined the networks during an in-person jamboree meeting. Here, we describe examples of the changes made to three of these networks: Neutrophil Signaling, Macrophage Signaling, and Th1-Th2 Signaling. We describe an innovative approach to biological network construction that combines literature and data mining and a crowdsourcing approach to generate a comprehensive set of COPD-relevant models that can be used to help understand the mechanisms related to lung pathobiology. Registered users of the website can freely browse and download the networks.

  20. Prism adaptation does not alter object-based attention in healthy participants [v1; ref status: indexed, http://f1000r.es/210

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    Janet H. Bultitude

    2013-11-01

    Full Text Available Hemispatial neglect (‘neglect’ is a disabling condition that can follow damage to the right side of the brain, in which patients show difficulty in responding to or orienting towards objects and events that occur on the left side of space. Symptoms of neglect can manifest in both space- and object-based frames of reference. Although patients can show a combination of these two forms of neglect, they are considered separable and have distinct neurological bases. In recent years considerable evidence has emerged to demonstrate that spatial symptoms of neglect can be reduced by an intervention called prism adaptation. Patients point towards objects viewed through prismatic lenses that shift the visual image to the right. Approximately five minutes of repeated pointing results in a leftward recalibration of pointing and improved performance on standard clinical tests for neglect. The understanding of prism adaptation has also been advanced through studies of healthy participants, in whom adaptation to leftward prismatic shifts results in temporary neglect-like performance. Here we examined the effect of prism adaptation on the performance of healthy participants who completed a computerised test of space- and object-based attention. Participants underwent adaptation to leftward- or rightward-shifting prisms, or performed neutral pointing according to a between-groups design. Significant pointing after-effects were found for both prism groups, indicating successful adaptation. In addition, the results of the computerised test revealed larger reaction-time costs associated with shifts of attention between two objects compared to shifts of attention within the same object, replicating previous work. However there were no differences in the performance of the three groups, indicating that prism adaptation did not influence space- or object-based attention for this task. When combined with existing literature, the results are consistent with the proposal that prism adaptation may only perturb cognitive functions for which normal baseline performance is already biased.

  1. Implementing a successful journal club in an anesthesiology residency program [v1; ref status: indexed, http://f1000r.es/xe

    Directory of Open Access Journals (Sweden)

    Nathaniel D Pitner

    2013-01-01

    Full Text Available Journal clubs are an integral element of residency training. We report the successful implementation of a monthly structured journal club in our anesthesia residency program. Based on resident surveys before and one year after its start, the journal club led to a significantly higher confidence in how to critically appraise literature and present a manuscript. The journal club also improved the residents' ability to search the literature and their statistical knowledge, skills that are essential in the practice of evidence-based medicine. We describe key features that may aid other training programs in organizing a stimulating an educational and sustainable journal club.

  2. An analysis on the entity annotations in biological corpora [v1; ref status: indexed, http://f1000r.es/2o0

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    Mariana Neves

    2014-04-01

    Full Text Available Collection of documents annotated with semantic entities and relationships are crucial resources to support development and evaluation of text mining solutions for the biomedical domain. Here I present an overview of 36 corpora and show an analysis on the semantic annotations they contain. Annotations for entity types were classified into six semantic groups and an overview on the semantic entities which can be found in each corpus is shown. Results show that while some semantic entities, such as genes, proteins and chemicals are consistently annotated in many collections, corpora available for diseases, variations and mutations are still few, in spite of their importance in the biological domain.

  3. CPIRD: A successful Thai programme to produce clinically competent medical graduates [v1; ref status: indexed, http://f1000r.es/5i3

    Directory of Open Access Journals (Sweden)

    Yanhua Yi

    2015-06-01

    Full Text Available The programme titled “Collaborative Project to Increase Production of Rural Doctors” (CPIRD is a rural medical education project launched in 1994 in Thailand. This study aimed to compare the academic performances in medical study over five years and the pass rates in national medical license examinations (MLE between students enrolled in CPIRD and two other tracks. Grade point average (GPA over five years and results of MLEs for four cohorts of students enrolled from 2003 to 2006 in Prince of Songkla University were collected from the registration department. A longitudinal analysis was used to compare the GPA over time for medical students enrolled in CPIRD and those from the national and direct regional tracks through generalized estimating equation (GEE models. The MLE pass rates were compared using chi-square and fisher's exact tests as appropriate. Female students dominated the CPIRD group. GPAs in the first three years in the CPIRD group were significantly lower than those of the other two groups, this disparity narrowed in the fourth and fifth years. For step one of the MLE (basic sciences, cohorts 2003 and 2006 of the CPIRD group had a significantly lower pass rate than the other two groups but there was no significant difference in cohort 2004 and cohort 2005. The CPIRD step two and three MLE pass rates were not significantly different from the national track in all cohorts and lower than the direct track only for step two in cohort 2003 and step three in cohort 2006. The step three pass rate of the CPIRD group in cohort 2004 was significantly higher than the other two tracks. Despite weaker competency in basic science, the CPIRD was successful in forming clinical competency.

  4. Implementation of a worksite educational program focused on promoting healthy eating habits [v2; ref status: indexed, http://f1000r.es/32x

    Directory of Open Access Journals (Sweden)

    Dimitra Tanagra

    2014-03-01

    Full Text Available Objective: To estimate the effectiveness of a short-term educational-counseling worksite program focused on lipid intake, by monitoring the possible change on nutrition knowledge and eating habits. Methods: an 8-week educational program based on the Health Belief Model was implemented in a honey packaging and sales company in Greece. 20 out of the 29 employees initially enrolled completed the program. Knowledge level and eating habits were evaluated prior and after the intervention by the “Nutrition Knowledge Questionnaire” and the “Food Habits Questionnaire”. ANOVA, Spearman rho test and paired Wilcoxon test were employed in statistical analysis. Results: Non smokers and those with higher educational level had healthier eating habits. Knowledge following the intervention was significantly improved concerning recommendations and basic food ingredients but as far as eating habits were concerned, scores were not improved significantly, while intake of fried food was increased. Conclusions and Implications: Short-term interventions may produce substantial improvement in knowledge but not necessarily modifications in unhealthy eating habits.

  5. Resources, challenges and way forward in rare mitochondrial diseases research [v1; ref status: indexed, http://f1000r.es/54x

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    Anshu Bhardwaj

    2015-03-01

    Full Text Available Over 300 million people are affected by about 7000 rare diseases globally. There are tremendous resource limitations and challenges in driving research and drug development for rare diseases. Hence, innovative approaches are needed to identify potential solutions. This review focuses on the resources developed over the past years for analysis of genome data towards understanding disease biology especially in the context of mitochondrial diseases, given that mitochondria are central to major cellular pathways and their dysfunction leads to a broad spectrum of diseases. Platforms for collaboration of research groups, clinicians and patients and the advantages of community collaborative efforts in addressing rare diseases are also discussed. The review also describes crowdsourcing and crowdfunding efforts in rare diseases research and how the upcoming initiatives for understanding disease biology including analyses of large number of genomes are also applicable to rare diseases.

  6. Resources, challenges and way forward in rare mitochondrial diseases research [v2; ref status: indexed, http://f1000r.es/5r6

    Directory of Open Access Journals (Sweden)

    Neeraj Kumar Rajput

    2015-08-01

    Full Text Available Over 300 million people are affected by about 7000 rare diseases globally. There are tremendous resource limitations and challenges in driving research and drug development for rare diseases. Hence, innovative approaches are needed to identify potential solutions. This review focuses on the resources developed over the past years for analysis of genome data towards understanding disease biology especially in the context of mitochondrial diseases, given that mitochondria are central to major cellular pathways and their dysfunction leads to a broad spectrum of diseases. Platforms for collaboration of research groups, clinicians and patients and the advantages of community collaborative efforts in addressing rare diseases are also discussed. The review also describes crowdsourcing and crowdfunding efforts in rare diseases research and how the upcoming initiatives for understanding disease biology including analyses of large number of genomes are also applicable to rare diseases.

  7. A brief review of recent Charcot-Marie-Tooth research and priorities [v1; ref status: indexed, http://f1000r.es/53g

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    Sean Ekins

    2015-02-01

    Full Text Available This brief review of current research progress on Charcot-Marie-Tooth (CMT disease is a summary of discussions initiated at the Hereditary Neuropathy Foundation (HNF scientific advisory board meeting on November 7, 2014. It covers recent published and unpublished in vitro and in vivo research. We discuss recent promising preclinical work for CMT1A, the development of new biomarkers, the characterization of different animal models, and the analysis of the frequency of gene mutations in patients with CMT. We also describe how progress in related fields may benefit CMT therapeutic development, including the potential of gene therapy and stem cell research. We also discuss the potential to assess and improve the quality of life of CMT patients. This summary of CMT research identifies some of the gaps which may have an impact on upcoming clinical trials. We provide some priorities for CMT research and areas which HNF can support. The goal of this review is to inform the scientific community about ongoing research and to avoid unnecessary overlap, while also highlighting areas ripe for further investigation. The general collaborative approach we have taken may be useful for other rare neurological diseases.

  8. Cytoplasmic nanojunctions between lysosomes and sarcoplasmic reticulum are required for specific calcium signaling [v1; ref status: indexed, http://f1000r.es/32q

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    Nicola Fameli

    2014-04-01

    Full Text Available Herein we demonstrate how nanojunctions between lysosomes and sarcoplasmic reticulum (L-SR junctions serve to couple lysosomal activation to regenerative, ryanodine receptor-mediated cellular Ca2+ waves. In pulmonary artery smooth muscle cells (PASMCs it has been proposed that nicotinic acid adenine dinucleotide phosphate (NAADP triggers increases in cytoplasmic Ca2+ via L-SR junctions, in a manner that requires initial Ca2+ release from lysosomes and subsequent Ca2+-induced Ca2+ release (CICR via ryanodine receptor (RyR subtype 3 on the SR membrane proximal to lysosomes. L-SR junction membrane separation has been estimated to be < 400 nm and thus beyond the resolution of light microscopy, which has restricted detailed investigations of the junctional coupling process. The present study utilizes standard and tomographic transmission electron microscopy to provide a thorough ultrastructural characterization of the L-SR junctions in PASMCs. We show that L-SR nanojunctions are prominent features within these cells and estimate that the junctional membrane separation and extension are about 15 nm and 300 nm, respectively. Furthermore, we develop a quantitative model of the L-SR junction using these measurements, prior kinetic and specific Ca2+ signal information as input data. Simulations of NAADP-dependent junctional Ca2+ transients demonstrate that the magnitude of these signals can breach the threshold for CICR via RyR3. By correlation analysis of live cell Ca2+ signals and simulated Ca2+ transients within L-SR junctions, we estimate that “trigger zones” comprising 60–100 junctions are required to confer a signal of similar magnitude. This is compatible with the 110 lysosomes/cell estimated from our ultrastructural observations. Most importantly, our model shows that increasing the L-SR junctional width above 50 nm lowers the magnitude of junctional [Ca2+] such that there is a failure to breach the threshold for CICR via RyR3. L-SR junctions are therefore a pre-requisite for efficient Ca2+signal coupling and may contribute to cellular function in health and disease.

  9. A letter to the Master Clinician [v1; ref status: indexed, http://f1000r.es/2m0

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    Kenar D. Jhaveri

    2014-01-01

    Full Text Available In this commentary, the author writes a letter to the Master Clinician about his concerns regarding the teaching responsibilities of current faculty members during ward rounds. This short essay highlights the transition that has been noticed in medical training in the last decade.

  10. A letter to the Master Clinician [v1; ref status: indexed, http://f1000r.es/2m0

    OpenAIRE

    Kenar D. Jhaveri

    2014-01-01

    In this commentary, the author writes a letter to the Master Clinician about his concerns regarding the teaching responsibilities of current faculty members during ward rounds. This short essay highlights the transition that has been noticed in medical training in the last decade.

  11. CAPHIGAS Project: Design of a Novel WGS-Adsorbent-Membrane Hybrid System for the Simultaneous Capture of CO{sub 2} and Production of H2 (Ref.: Ene2009-08002); Proyecto CAPHIGAS: Diseno de un Sistema Hibrido WGS-Adsorbente-Membrana para la Captura de CO{sub 2} con Produccion de H{sub 2} (Ref: Ene2009-08002)

    Energy Technology Data Exchange (ETDEWEB)

    Marano, M.; Barreiro, M. M.; Sanchez, J. M.

    2014-02-01

    This report describes the general objective, tasks and main results and conclusions drawn within CAPHIGAS Project, Plan Nacional de I+D+I 2008-2011, financed by the Spanish Ministry of Science and Innovation and carried out by the Valorization of Fuels and Wastes Group of Ciemat. The general objective of the project was the design and development of a novel hybrid system for the simultaneous removal of CO{sub 2} and production of H{sub 2} using a WGS catalyst-adsorbent membrane configuration. The novel system proposed has provided new insight into the adsorption and reaction processes and has allowed an optimization of the operating conditions to take advantage of the synergies between both processes. In this report main future activities are also reported. (Author)

  12. Multi-Index Monte Carlo and stochastic collocation methods for random PDEs

    KAUST Repository

    Nobile, Fabio

    2016-01-09

    In this talk we consider the problem of computing statistics of the solution of a partial differential equation with random data, where the random coefficient is parametrized by means of a finite or countable sequence of terms in a suitable expansion. We describe and analyze a Multi-Index Monte Carlo (MIMC) and a Multi-Index Stochastic Collocation method (MISC). the former is both a stochastic version of the combination technique introduced by Zenger, Griebel and collaborators and an extension of the Multilevel Monte Carlo (MLMC) method first described by Heinrich and Giles. Instead of using firstorder differences as in MLMC, MIMC uses mixed differences to reduce the variance of the hierarchical differences dramatically. This in turn yields new and improved complexity results, which are natural generalizations of Giles s MLMC analysis, and which increase the domain of problem parameters for which we achieve the optimal convergence, O(TOL-2). On the same vein, MISC is a deterministic combination technique based on mixed differences of spatial approximations and quadratures over the space of random data. Provided enough mixed regularity, MISC can achieve better complexity than MIMC. Moreover, we show that in the optimal case the convergence rate of MISC is only dictated by the convergence of the deterministic solver applied to a one-dimensional spatial problem. We propose optimization procedures to select the most effective mixed differences to include in MIMC and MISC. Such optimization is a crucial step that allows us to make MIMC and MISC computationally effective. We finally show the effectiveness of MIMC and MISC with some computational tests, including tests with a infinite countable number of random parameters.

  13. Multi-Index Stochastic Collocation for random PDEs

    KAUST Repository

    Haji Ali, Abdul Lateef

    2016-03-28

    In this work we introduce the Multi-Index Stochastic Collocation method (MISC) for computing statistics of the solution of a PDE with random data. MISC is a combination technique based on mixed differences of spatial approximations and quadratures over the space of random data. We propose an optimization procedure to select the most effective mixed differences to include in the MISC estimator: such optimization is a crucial step and allows us to build a method that, provided with sufficient solution regularity, is potentially more effective than other multi-level collocation methods already available in literature. We then provide a complexity analysis that assumes decay rates of product type for such mixed differences, showing that in the optimal case the convergence rate of MISC is only dictated by the convergence of the deterministic solver applied to a one dimensional problem. We show the effectiveness of MISC with some computational tests, comparing it with other related methods available in the literature, such as the Multi-Index and Multilevel Monte Carlo, Multilevel Stochastic Collocation, Quasi Optimal Stochastic Collocation and Sparse Composite Collocation methods.

  14. A Review on Anodic Aluminum Oxide Methods for Fabrication of Nanostructures for Organic Solar Cells

    DEFF Research Database (Denmark)

    Goszczak, Arkadiusz Jaroslaw; Cielecki, Pawel Piotr

    2018-01-01

    , low fabrication cost and easy control over its nano-scale morphology, make AAO patterning methods an intriguing candidate for nanopatterning. Hence, in this work, we present a review on the fabrication techniques and on nanostructures from Anodic Aluminum Oxide (AAO) for OSC applications....... The versatility of such patterning technique is shown by pointing out the possibility of using an AAO template for the fabrication of nanowires by wetting, nanodots by evaporation, nanostructures by imprinting resists, organic layers and much more....

  15. Photoconductivity of Germanium Nanowire Arrays Incorporated in Anodic Aluminum Oxide

    International Nuclear Information System (INIS)

    Polyakov, B; Prikulis, J; Grigorjeva, L; Millers, D; Daly, B; Holmes, J D; Erts, D

    2007-01-01

    Photoconductivity of germanium nanowire arrays of 50 and 100 nm diameter incorporated into Anodic Aluminum Oxide (AAO) membranes illuminated with visible light is investigated. Photocurrent response to excitation radiation with time constants faster than 10 -4 s were governed by absorption of incident light by nanowires, while photokinetics with time constants of the order of 10 -3 s originates from the photoluminescence of the AAO matrix. Possible applications of nanowire arrays inside AAO as photoresistors are discussed

  16. Ordered arrays of Ni magnetic nanowires: Synthesis and investigation

    Science.gov (United States)

    Napolskii, K. S.; Eliseev, A. A.; Yesin, N. V.; Lukashin, A. V.; Tretyakov, Yu. D.; Grigorieva, N. A.; Grigoriev, S. V.; Eckerlebe, H.

    2007-03-01

    The present study is focused on the synthesis and investigation of anodic aluminum oxide (AAO) films and magnetic nanocomposites Ni/AAO obtained by Ni electrodeposition into porous matrix. AAO membranes and magnetic nanocomposites were investigated by HRSEM, EDX microanalysis, XRD, nitrogen capillary adsorption method, SQUID magnetometry, and polarized small-angle neutron scattering (SANS). The influence of synthesis conditions and form factor effect on the magnetic properties of nanowire arrays is reported.

  17. Nano structured porous anodized aluminium oxide by using C2H2O4 for electronic applications: Study of the cell potential effects on formation of porous alumina

    International Nuclear Information System (INIS)

    Nur Hafiza Mohd Najib; Derman, M.N.M.; Nuzaihan, M.N.; Nazwa, T.; Azniza, A.

    2011-01-01

    In this research, a nano porous anodized aluminium oxide AAO thin film was successfully grown onto oxide layer on silicon substrate. The anodization of Si/ SiO 2 / Al substrate was conducted in a vigorous stirring oxalic acid bath solution. The rate of growth, morphology and also the kinetic study of the AAO thin film were investigated. The resulting array, pores structure and pores density of AAO strongly depends on an applied voltage of the anodizing process. (author)

  18. International Society of Refractive Surgery of the American Academy of Ophthalmology

    Science.gov (United States)

    Meetings Meetings Overview Meetings Calendar International Meetings ISRS at AAO Refractive Surgery Subspecialty Day, ISRS Annual Meeting Meetings Blog ISRS Member Lunch Multimedia Library Resources Community Photos ...

  19. Advancing methods for reliably assessing motivational interviewing fidelity using the motivational interviewing skills code.

    Science.gov (United States)

    Lord, Sarah Peregrine; Can, Doğan; Yi, Michael; Marin, Rebeca; Dunn, Christopher W; Imel, Zac E; Georgiou, Panayiotis; Narayanan, Shrikanth; Steyvers, Mark; Atkins, David C

    2015-02-01

    The current paper presents novel methods for collecting MISC data and accurately assessing reliability of behavior codes at the level of the utterance. The MISC 2.1 was used to rate MI interviews from five randomized trials targeting alcohol and drug use. Sessions were coded at the utterance-level. Utterance-based coding reliability was estimated using three methods and compared to traditional reliability estimates of session tallies. Session-level reliability was generally higher compared to reliability using utterance-based codes, suggesting that typical methods for MISC reliability may be biased. These novel methods in MI fidelity data collection and reliability assessment provided rich data for therapist feedback and further analyses. Beyond implications for fidelity coding, utterance-level coding schemes may elucidate important elements in the counselor-client interaction that could inform theories of change and the practice of MI. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Factors influencing the development of early- or late-onset ...

    African Journals Online (AJOL)

    Background. Neurodegenerative disorders such as Parkinsonfs disease (PD) contribute significantly to global disease burden. PD can be categorised into early-onset PD (EOPD) with an age at onset (AAO) of .50 years and late-onset PD (LOPD) with an AAO of >50 years. Aims. To identify factors influencing EOPD and ...

  1. Synthesis and magnetic properties of multilayer Ni/Cu and NiFe/Cu ...

    Indian Academy of Sciences (India)

    have been fabricated by pulsed electrodeposition into nanoporous alumina membrane. The diameter of wires can be ... First silver of 5000 Å thickness was thermally evaporated onto one side of AAO to serve as back ... ter the nanowires were formed, the silver electrode was removed by 6 M HNO3, and then the AAO was ...

  2. Density functional theory investigations on the binding modes of amidoximes with uranyl ions.

    Science.gov (United States)

    Yang, Chuting; Pei, Shuqi; Chen, Baihua; Ye, Lina; Yu, Haizhu; Hu, Sheng

    2016-02-21

    Density functional theory (DFT) calculations have been carried out to examine the relative facilities of different coordination modes of aromatic amidoximes (AOs) with UO2(NO3)2. Various η(1)-, η(2)- and chelated κ(2)-coordination modes of the possible neutral AO, tautomerized neutral (TAO, with the hydroxylic hydrogen transferring to the oximic nitrogen atom) and anionic amidoxime (AAO, formed by the deprotonation of AO) were examined. The results indicate that η(1)-O of the TAO and η(1)-O/η(2)-NO of AAO are the most plausible coordination modes. Three types of uranyl complexes, i.e. UO2(NO3)2(TAO)(AAO), UO2(NO3)2(AAO)2 and UO2(EtOH)2(AAO)2 are the predominant binding structures. The good consistency between the calculation results and the experimental observations verifies the proposed conclusions.

  3. An image-based, dual fluorescence reporter assay to evaluate the efficacy of shRNA for gene silencing at the single-cell level [v1; ref status: indexed, http://f1000r.es/2tt

    Directory of Open Access Journals (Sweden)

    Shin-ichiro Kojima

    2014-02-01

    Full Text Available RNA interference (RNAi is widely used to suppress gene expression in a specific manner. The efficacy of RNAi is mainly dependent on the sequence of small interfering RNA (siRNA in relation to the target mRNA. Although several algorithms have been developed for the design of siRNA, it is still difficult to choose a really effective siRNA from among multiple candidates. In this article, we report the development of an image-based, quantitative, ratiometric fluorescence reporter assay to evaluate the efficacy of RNAi at the single-cell level. Two fluorescence reporter constructs are used. One expresses the candidate small hairpin RNA (shRNA together with an enhanced green fluorescent protein (EGFP; the other expresses a 19-nt target sequence inserted into a cassette expressing a red fluorescent protein (either DsRed or mCherry. Effectiveness of the candidate shRNA is evaluated as the extent to which it knocks down expression of the red fluorescent protein. Thus, the red-to-green fluorescence intensity ratio (appropriately normalized to controls is used as the read-out for quantifying the siRNA efficacy at the individual cell level. We tested this dual fluorescence assay and compared predictions to actual endogenous knockdown levels for three different genes (vimentin, lamin A/C and Arp3 and twenty different shRNAs. For each of the genes, our assay successfully predicted the target sequences for effective RNAi. To further facilitate testing of RNAi efficacy, we developed a negative selection marker (ccdB method for construction of shRNA and red fluorescent reporter plasmids that allowed us to purify these plasmids directly from transformed bacteria without the need for colony selection and DNA sequencing verification.

  4. An image-based, dual fluorescence reporter assay to evaluate the efficacy of shRNA for gene silencing at the single-cell level [v2; ref status: indexed, http://f1000r.es/39j

    Directory of Open Access Journals (Sweden)

    Shin-ichiro Kojima

    2014-05-01

    Full Text Available RNA interference (RNAi is widely used to suppress gene expression in a specific manner. The efficacy of RNAi is mainly dependent on the sequence of small interfering RNA (siRNA in relation to the target mRNA. Although several algorithms have been developed for the design of siRNA, it is still difficult to choose a really effective siRNA from among multiple candidates. In this article, we report the development of an image-based, quantitative, ratiometric fluorescence reporter assay to evaluate the efficacy of RNAi at the single-cell level. Two fluorescence reporter constructs are used. One expresses the candidate small hairpin RNA (shRNA together with an enhanced green fluorescent protein (EGFP; the other expresses a 19-nt target sequence inserted into a cassette expressing a red fluorescent protein (either DsRed or mCherry. Effectiveness of the candidate shRNA is evaluated as the extent to which it knocks down expression of the red fluorescent protein. Thus, the red-to-green fluorescence intensity ratio (appropriately normalized to controls is used as the read-out for quantifying the siRNA efficacy at the individual cell level. We tested this dual fluorescence assay and compared predictions to actual endogenous knockdown levels for three different genes (vimentin, lamin A/C and Arp3 and twenty different shRNAs. For each of the genes, our assay successfully predicted the target sequences for effective RNAi. To further facilitate testing of RNAi efficacy, we developed a negative selection marker (ccdB method for construction of shRNA and red fluorescent reporter plasmids that allowed us to purify these plasmids directly from transformed bacteria without the need for colony selection and DNA sequencing verification.

  5. Mutation detection in cholestatic patients using microarray resequencing of ATP8B1 and ABCB11 [v2; ref status: indexed, http://f1000r.es/yv

    Directory of Open Access Journals (Sweden)

    Kirsten E McKay

    2013-03-01

    Full Text Available Background: Neonatal cholestasis is a common presentation of childhood liver diseases and can be a feature of various conditions including disorders of bile acid biogenesis and transport, various inborn errors of metabolism and perinatal infections. Some inherited metabolic diseases can be easily screened using biochemical assays, however many can only be accurately diagnosed by DNA sequencing. Fluorescent capillary Sanger sequencing (FS is the gold standard method used by clinical laboratories for genetic diagnosis of many inherited conditions; however, it does have limitations. Recently microarray resequencing (MR has been introduced into research and clinical practice as an alternative method for genetic diagnosis of heterogeneous conditions. In this report we compared the accuracy of mutation detection for MR with FS in a group of patients with ‘low-normal’ gamma glutamyl transpeptidase (gGT cholestasis without known molecular diagnoses. Methods: 29 patient DNA samples were tested for mutations in the ATP8B1 and ABCB11 genes using both FS and MR. Other known causes of “low gGT cholestasis” such as ARC syndrome and bile acid biosynthesis disorders were excluded. Results: Mutations were identified in 13/29 samples. In 3/29 samples FS and MR gave discordant results: MR had a false positive rate of 3.4% and a false negative rate of 7%. Conclusions: The major advantage of MR over FS is that multiple genes can be screened in one experiment, allowing rapid and cost-effective diagnoses.  However, we have demonstrated that MR technology is limited in sensitivity. We therefore recommend that MR be used as an initial evaluation, with FS deployed when genetic and clinical or histopathological findings are discordant.

  6. Thermoregulation strategies in ants in comparison to other social insects, with a focus on Formica rufa [v1; ref status: indexed, http://f1000r.es/2fv

    Directory of Open Access Journals (Sweden)

    Štěpánka Kadochová

    2013-12-01

    Full Text Available Temperature influences every aspect of ant biology, especially metabolic rate, growth and development. Maintenance of high inner nest temperature increases the rate of sexual brood development and thereby increases the colony fitness. Insect societies can achieve better thermoregulation than solitary insects due to the former’s ability to build large and elaborated nests and display complex behaviour. In ants and termites the upper part of the nest, the mound, often works as a solar collector and can also have an efficient ventilation system. Two thermoregulatory strategies could be applied. Firstly the ants use an increased thermal gradient available in the mound for brood relocation. Nurse workers move the brood according to the thermal gradients to ensure the ideal conditions for development. A precise perception of temperature and evolution of temperature preferences are needed to make the correct choices. A second thermoregulatory strategy used by mound nesting ants is keeping a high temperature inside large nests. The unique thermal and insulation properties of the nest material help to maintain stable conditions, which is the case of the Wood ant genus Formica. Ants can regulate thermal loss by moving nest aggregation and alternating nest ventilation. Metabolic heat produced by ant workers or associated micro organisms is an important additional source of heat which helps to maintain thermal homeostasis in the nest.

  7. Exploring the membrane topology of prohormone convertase 1 in AtT20 Cells: in situ analysis by immunofluorescence microscopy [v1; ref status: indexed, http://f1000r.es/QFfyFd

    Directory of Open Access Journals (Sweden)

    Niamh X Cawley

    2012-08-01

    Full Text Available Prohormone convertase 1 (PC1 was previously characterized as a partially transmembrane protein in purified chromaffin granules of bovine adrenal medulla1. This was challenged with experiments on transfected PC1 in COS1 cells, a non-endocrine cell line2. To address this issue, we undertook to analyze its extraction properties in vitro and its immunocytochemical localization in situ in AtT20 cells, an endocrine cell line that expresses PC1. Most of the 87 kDa form of PC1 was resistant to carbonate extraction suggesting that it had properties of a transmembrane protein. Under semi-permeabilized conditions whereby only the plasma membrane was permeabilized, the carboxy-terminus of PC1 was specifically immunostained whereas the amino-terminus was not. These results indicate that the amino-terminus of PC1 was within the lumen of the Golgi and granules, and some of the C-terminus was exposed to the cytosol. Thus, endogenous PC1 can assume a transmembrane orientation in situ in AtT20 cells.

  8. Ecological implications of reduced pollen supply in the alpine: a case study using a dominant cushion plant species [v2; ref status: indexed, http://f1000r.es/3xc

    Directory of Open Access Journals (Sweden)

    Anya Reid

    2014-08-01

    Full Text Available The reproductive assurance hypothesis states that self-incompatible female plants must produce twice the number of seeds relative to their self-compatible hermaphroditic counterparts to persist in gynodioecious populations. This is a viable life-history strategy, provided that pollination rates are sufficiently high. However, reduced pollination rates in alpine plants are likely due to climate induced plant-pollinator mismatches and general declines in pollinators. Using a gynodioecious population of the dominant plant Silene acaulis (Caryophyllaceae, we tested the reproductive assurance hypothesis and also the stress gradient hypothesis with a series of pollinator exclusion trials and extensive measurements of subsequent reproductive output (gender ratio, plant size, percent fruit-set, fruit weight, seeds per fruit, total seeds, seed weight, and seed germination. The reproductive assurance hypothesis was supported with female plants being more sensitive to and less likely to be viable under reductions in pollination rates. These findings are the first to show that the stress gradient hypothesis is also supported under a gradient of pollen supply instead of environmental limitations. Beneficiary abundance was negatively correlated to percent fruit-set under current pollen supply, but became positive under reduced pollen supply suggesting that there are important plant-plant-pollinator interactions related to reproduction in these alpine plant species.

  9. TNF-alpha neutralizing antibody blocks thermal sensitivity induced by compound 48/80-provoked mast cell degranulation [v2; ref status: indexed, http://f1000r.es/1w5

    Directory of Open Access Journals (Sweden)

    Devavani Chatterjea

    2013-09-01

    Full Text Available Background: Neuro-inflammatory circuits in the tissue regulate the complex pathophysiology of pain. Protective nociceptive pain serves as an early warning system against noxious environmental stimuli. Tissue-resident mast cells orchestrate the increased thermal sensitivity following injection of basic secretagogue compound 48/80 in the hind paw tissues of ND4 mice. Here we investigated the effects of pre-treatment with TNF-α neutralizing antibody on compound 48/80-provoked thermal hyperalgesia. Methods: We treated ND4 Swiss male mice with intravenous anti-TNF-α antibody or vehicle 30 minutes prior to bilateral, intra-plantar compound 48/80 administration and measured changes in the timing of hind paw withdrawal observed subsequent to mice being placed on a 51oC hotplate. We also assessed changes in tissue swelling, TNF-α gene expression and protein abundance, mast cell degranulation, and neutrophil influx in the hind paw tissue. Findings: We found that TNF-α neutralization significantly blocked thermal hyperalgesia, and reduced early tissue swelling. TNF-α neutralization had no significant effect on mast cell degranulation or neutrophil influx into the tissue, however. Moreover, no changes in TNF-α protein or mRNA levels were detected within 3 hours of administration of compound 48/80. Interpretation:  The neutralizing antibodies likely target pre-formed TNF-α including that stored in the granules of tissue-resident mast cells. Pre-formed TNF-α, released upon degranulation, has immediate effects on nociceptive signaling prior to the induction of neutrophil influx. These early effects on nociceptors are abrogated by TNF-α blockade, resulting in compromised nociceptive withdrawal responses to acute, harmful environmental stimuli.

  10. TNF-alpha neutralizing antibody blocks thermal sensitivity induced by compound 48/80-provoked mast cell degranulation [v1; ref status: indexed, http://f1000r.es/1mq

    Directory of Open Access Journals (Sweden)

    Devavani Chatterjea

    2013-08-01

    Full Text Available Background:  Neuro-inflammatory circuits in the tissue regulate the complex pathophysiology of pain.  Protective nociceptive pain serves as an early warning system against noxious environmental stimuli.  Tissue-resident mast cells orchestrate the increased thermal sensitivity following injection of basic secretagogue compound 48/80 in the hind paw tissues of ND4 mice.  Here we investigated the effects of pre-treatment with TNF-α neutralizing antibody on compound 48/80-provoked thermal hyperalgesia.  Methods:  We treated ND4 Swiss male mice with intravenous anti-TNF-α antibody or vehicle 30 minutes prior to bilateral, intra-plantar compound 48/80 administration and measured changes in the timing of hind paw withdrawal observed subsequent to mice being placed on a 51oC hotplate.  We also assessed changes in tissue swelling, TNF-α gene expression and protein abundance, mast cell degranulation, and neutrophil influx in the hind paw tissue.  Findings:  We found that TNF-α neutralization significantly blocked thermal hyperalgesia, and reduced early tissue swelling. TNF-α neutralization had no significant effect on mast cell degranulation or neutrophil influx into the tissue, however.  Moreover, no changes in TNF-α protein or mRNA levels were detected within 3 hours of administration of compound 48/80.  Interpretation:  The neutralizing antibodies likely target pre-formed TNF-α including that stored in the granules of tissue-resident mast cells. Pre-formed TNF-α, released upon degranulation, has immediate effects on nociceptive signaling prior to the induction of neutrophil influx.  These direct effects on nociceptors are abrogated by TNF-α blockade resulting in compromised nociceptive withdrawal responses to acute, harmful environmental stimuli.

  11. Ant-App-DB: a smart solution for monitoring arthropods activities, experimental data management and solar calculations without GPS in behavioral field studies [v2; ref status: indexed, http://f1000r.es/59a

    Directory of Open Access Journals (Sweden)

    Zeeshan Ahmed

    2015-04-01

    Full Text Available Field studies on arthropod ecology and behaviour require simple and robust monitoring tools, preferably with direct access to an integrated database. We have developed and here present a database tool allowing smart-phone based monitoring of arthropods. This smart phone application provides an easy solution to collect, manage and process the data in the field which has been a very difficult task for field biologists using traditional methods. To monitor our example species, the desert ant Cataglyphis fortis, we considered behavior, nest search runs, feeding habits and path segmentations including detailed information on solar position and Azimuth calculation, ant orientation and time of day. For this we established a user friendly database system integrating the Ant-App-DB with a smart phone and tablet application, combining experimental data manipulation with data management and providing solar position and timing estimations without any GPS or GIS system. Moreover, the new desktop application Dataplus allows efficient data extraction and conversion from smart phone application to personal computers, for further ecological data analysis and sharing. All features, software code and database as well as Dataplus application are made available completely free of charge and sufficiently generic to be easily adapted to other field monitoring studies on arthropods or other migratory organisms. The software applications Ant-App-DB and Dataplus described here are developed using the Android SDK, Java, XML, C# and SQLite Database.

  12. Ant-App-DB: a smart solution for monitoring arthropods activities, experimental data management and solar calculations without GPS in behavioral field studies [v3; ref status: indexed, http://f1000r.es/5dm

    Directory of Open Access Journals (Sweden)

    Zeeshan Ahmed

    2015-05-01

    Full Text Available Field studies on arthropod ecology and behaviour require simple and robust monitoring tools, preferably with direct access to an integrated database. We have developed and here present a database tool allowing smart-phone based monitoring of arthropods. This smart phone application provides an easy solution to collect, manage and process the data in the field which has been a very difficult task for field biologists using traditional methods. To monitor our example species, the desert ant Cataglyphis fortis, we considered behavior, nest search runs, feeding habits and path segmentations including detailed information on solar position and azimuth calculation, ant orientation and time of day. For this we established a user friendly database system integrating the Ant-App-DB with a smart phone and tablet application, combining experimental data manipulation with data management and providing solar position and timing estimations without any GPS or GIS system. Moreover, the new desktop application Dataplus allows efficient data extraction and conversion from smart phone application to personal computers, for further ecological data analysis and sharing. All features, software code and database as well as Dataplus application are made available completely free of charge and sufficiently generic to be easily adapted to other field monitoring studies on arthropods or other migratory organisms. The software applications Ant-App-DB and Dataplus described here are developed using the Android SDK, Java, XML, C# and SQLite Database.

  13. Pandemic 2009 Influenza A (H1N1 virus infection in cancer and hematopoietic stem cell transplant recipients; a multicenter observational study. [v1; ref status: indexed, http://f1000r.es/4bi

    Directory of Open Access Journals (Sweden)

    Maria Cecilia Dignani

    2014-09-01

    Full Text Available Background: During March 2009 a novel Influenza A virus emerged in Mexico. We describe the clinical picture of the pandemic Influenza A (H1N1 Influenza in cancer patients during the 2009 influenza season. Methods: Twelve centers participated in a multicenter retrospective observational study of cancer patients with confirmed infection with the 2009 H1N1 Influenza A virus (influenza-like illness or pneumonia plus positive PCR for the 2009 H1N1 Influenza A virus  in respiratory secretions. Clinical data were obtained by retrospective chart review and analyzed.  Results: From May to August 2009, data of 65 patients were collected. Median age was 51 years, 57 % of the patients were female. Most patients (47 had onco-hematological cancers and 18 had solid tumors. Cancer treatment mainly consisted of chemotherapy (46, or stem cell transplantation (SCT (16. Only 19 of 64 patients had received the 2009 seasonal Influenza vaccine. Clinical presentation included pneumonia (43 and upper respiratory tract infection (22. Forty five of 58 ambulatory patients were admitted. Mechanical ventilation was required in 12 patients (18%. Treatment included oseltamivir monotherapy or in combination with amantadine for a median of 7 days. The global 30-day mortality rate was 18%. All 12 deaths were among the non-vaccinated patients. No deaths were observed among the 19 vaccinated patients. Oxygen saturation <96% at presentation was a predictor of mortality (OR 19.5; 95%CI: 2.28 to 165.9. Conclusions: In our cancer patient population, the pandemic 2009 Influenza A (H1N1 virus was associated with high incidence of pneumonia (66%, and 30-day mortality (18.5%. Saturation <96% was significantly associated with death. No deaths were observed among vaccinated patients.

  14. Promoting self-management through adherence among heart failure patients discharged from rural hospitals: a study protocol [v1; ref status: indexed, http://f1000r.es/4y8

    Directory of Open Access Journals (Sweden)

    Lufei Young

    2014-12-01

    Full Text Available Background Heart failure is one of the most prevalent chronic conditions in adults, leading to prolonged morbidity, repeated hospitalizations, and placing tremendous economic burden on the healthcare system. Heart failure patients discharged from rural hospitals, or primarily critical access hospitals, have higher 30-day readmission and mortality rates compared to patients discharged from urban hospitals. Self-management improves heart failure patients’ health outcomes and reduces re-hospitalizations, but adherence to self-management guidelines is low. We propose a home based post-acute care service managed by advanced practice nurses to enhance patient activation and lead to the improvement of self-management adherence in heart failure patients discharged from rural hospitals. Objective This article describes the study design and research methods used to implement and evaluate the intervention. Method Our intervention is a 12-week patient activation (Patient AcTivated Care at Home [PATCH] to improve self-management adherence. Patients were randomized into two parallel groups (12-week PATCH intervention + usual care vs. usual care only to evaluate the effectiveness of this intervention. Outcomes were measured at baseline, 3 and 6 months. Discussion This study aimed to examine the effectiveness of a rural theory based, advance practice nurse led, activation enhancing intervention on the self-management adherence in heart failure patients residing in rural areas. Our expectation is to facilitate adherence to self-management behaviors in heart failure patients following discharge from rural hospitals and decrease complications and hospital readmissions, leading to the reduction of economic burden.  Clinical Trial Registration Information: ClinicalTrials.gov; https://register.clinicaltrials.gov/ NCT01964053

  15. Comparison of phenothrin mousse, phenothrin lotion, and wet-combing for treatment of head louse infestation in the UK: a pragmatic randomised, controlled, assessor blind trial [v1; ref status: indexed, http://f1000r.es/1px

    Directory of Open Access Journals (Sweden)

    Ian F. Burgess

    2014-07-01

    Full Text Available In this investigation of effectiveness of an alternative pediculicide dosage form, we recruited 228 children and 50 adult participants from Bedfordshire, UK, to a randomised, controlled, assessor blind trial comparing two insecticide products with mechanical removal of lice as a control group.  Participants using insecticide were treated with either the investigative 0.5% phenothrin mousse, for 30 minutes, or 0.2% phenothrin lotion, for 2 hours as the reference product.  Both treatments were applied only once, followed by shampoo washing.  Those treated by wet-combing with conditioner were combed 4 times over 12 days.  Parents/carers carried out the treatments to mimic normal consumer use.  The outcome measure was the absence of lice, 14 days after treatment for the insecticides, and up to 14 days after completion of combing.  Intention to treat analysis of the outcomes for 275 participants showed success for phenothrin mousse in 21/105 (20.0%, in 23/107 (21.5% for phenothrin lotion, and in 12/63 (19.1% for wet-combing.  People receiving mousse were 1.07 (95% CI, 0.63 to 1.81 times more likely to still have lice after treatment compared with those treated with lotion. The group of participants who received the wet combing treatment were 1.13 (95% CI, 0.61 to 2.11 times more likely to still have lice after the treatment.  None of the treatments was significantly (p < 0.05 more effective than any other. This study was carried out in an area where moderate resistance to phenothrin was demonstrated after the study by using a bioassay.  Analysis of post treatment assessments found that failure of insecticides to kill louse eggs had influenced the outcome.

  16. Problematizing Digital Research Evaluation using DOIs in Practice-Based Arts, Humanities and Social Science Research [v1; ref status: indexed, http://f1000r.es/5dy

    Directory of Open Access Journals (Sweden)

    Muriel Swijghuisen Reigersberg

    2015-07-01

    Full Text Available This paper explores emerging practices in research data management in the arts, humanities and social sciences (AHSS. It will do so vis-à-vis current citation conventions and impact measurement for research in AHSS. Case study findings on research data inventoried at Goldsmiths’, University of London will be presented. Goldsmiths is a UK research-intensive higher education institution which specialises in arts, humanities and social science research. The paper’s aim is to raise awareness of the subject-specific needs of AHSS scholars to help inform the design of future digital tools for impact analysis in AHSS. Firstly, I shall explore the definition of research data and how it is currently understood by AHSS researchers. I will show why many researchers choose not to engage with digital dissemination techniques and ORCID. This discussion must necessarily include the idea that practice-based and applied AHSS research are processes which are not easily captured in numerical ‘sets’ and cannot be labelled electronically without giving careful consideration to what a group or data item ‘represents’ as part of the academic enquiry, and therefore how it should be cited and analysed as part of any impact assessment. Then, the paper will explore: the role of the monograph and arts catalogue in AHSS scholarship; how citation practices and digital impact measurement in AHSS currently operate in relation to authorship and how digital identifiers may hypothetically impact on metrics, intellectual property (IP, copyright and research integrity issues in AHSS. I will also show that, if we are to be truly interdisciplinary, as research funders and strategic thinkers say we should, it is necessary to revise the way we think about digital research dissemination. This will involve breaking down the boundaries between AHSS and other types of research.

  17. Eco-physiological adaptation of dominant tree species at two contrasting karst habitats in southwestern China [v2; ref status: indexed, http://f1000r.es/2d9

    Directory of Open Access Journals (Sweden)

    Shouren Zhang

    2013-11-01

    Full Text Available The purpose of this study was to investigate the eco-physiological adaptation of indigenous woody species to their habitats in karst areas of southwestern China. Two contrasting forest habitats were studied: a degraded habitat in Daxiagu and a well-developed habitat in Tianlongshan, and the eco-physiological characteristics of the trees were measured for three growth seasons. Photosynthetic rate (Pn, stomatal conductance (gs, and transpiration rate (Tr of the tree species in Daxiagu were 2-3 times higher than those in Tianlongshan under ambient conditions. However, this habitat effect was not significant when measurements were taken under controlled conditions. Under controlled conditions, Pn, gs, and Tr of the deciduous species were markedly higher than those for the evergreen species. Habitat had no significant effect on water use efficiency (WUE or photochemical characteristics of PSII. The stomatal sensitivity of woody species in the degraded habitat was much higher than that in the well-developed habitat. Similarly, the leaf total nitrogen (N and phosphorus (P contents expressed on the basis of either dry mass or leaf area were also much higher in Daxiagu than they were in Tianlongshan. The mass-based leaf total N content of deciduous species was much higher than that of evergreen species, while leaf area-based total N and P contents of evergreens were significantly higher than those of deciduous species. The photosynthetic nitrogen- and phosphorus-use efficiencies (PNUE and PPUE of deciduous species were much higher than those of evergreens. Further, the PPUE of the woody species in Tianlongshan was much higher than that  of the woody species in Daxiagu. The results from three growth seasons imply that the tree species were able to adapt well to their growth habitats. Furthermore, it seems that so-called “temporary drought stress” may not occur, or may not be severe for most woody plants in karst areas of southwestern China.

  18. IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities [v2; ref status: indexed, http://f1000r.es/13y

    Directory of Open Access Journals (Sweden)

    Natalja Kurbatova

    2013-05-01

    Full Text Available IsoCleft Finder is a web-based tool for the detection of local geometric and chemical similarities between potential small-molecule binding cavities and a non-redundant dataset of ligand-bound known small-molecule binding-sites. The non-redundant dataset developed as part of this study is composed of 7339 entries representing unique Pfam/PDB-ligand (hetero group code combinations with known levels of cognate ligand similarity. The query cavity can be uploaded by the user or detected automatically by the system using existing PDB entries as well as user-provided structures in PDB format. In all cases, the user can refine the definition of the cavity interactively via a browser-based Jmol 3D molecular visualization interface. Furthermore, users can restrict the search to a subset of the dataset using a cognate-similarity threshold. Local structural similarities are detected using the IsoCleft software and ranked according to two criteria (number of atoms in common and Tanimoto score of local structural similarity and the associated Z-score and p-value measures of statistical significance. The results, including predicted ligands, target proteins, similarity scores, number of atoms in common, etc., are shown in a powerful interactive graphical interface. This interface permits the visualization of target ligands superimposed on the query cavity and additionally provides a table of pairwise ligand topological similarities. Similarities between top scoring ligands serve as an additional tool to judge the quality of the results obtained. We present several examples where IsoCleft Finder provides useful functional information. IsoCleft Finder results are complementary to existing approaches for the prediction of protein function from structure, rational drug design and x-ray crystallography. IsoCleft Finder can be found at: http://bcb.med.usherbrooke.ca/isocleftfinder.

  19. Cocaine self-administration in mice with forebrain knock-down of trpc5 ion channels [v1; ref status: indexed, http://f1000r.es/pb

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    Matthew B Pomrenze

    2013-02-01

    Full Text Available Canonical transient receptor potential (TRPC channels are a family of non-selective cation channels that play a crucial role in modulating neuronal excitability due to their involvement in intracellular Ca2+ regulation and dendritic growth. TRPC5 channels a are one of the two most prevalent TRPC channels in the adult rodent brain; b are densely expressed in deep layer pyramidal neurons of the prefrontal cortex (PFC; and c modulate neuronal persistent activity necessary for working memory and attention. In order to evaluate the causal role of TRPC5 in motivation/reward-related behaviors, conditional forebrain TRPC5 knock-down (trpc5-KD mice were generated and trained to nose-poke for intravenous cocaine. Here we present a data set containing the first 6 days of saline or cocaine self-administration in wild type (WT and trpc5-KD mice. In addition, we also present a data set showing the dose-response to cocaine after both groups had achieved similar levels of cocaine self-administration. Compared to WT mice, trpc5-KD mice exhibited an apparent increase in self-administration on the first day of cocaine testing without prior operant training. There were no apparent differences between WT and trpc5-KD mice for saline responding on the first day of training. Both groups showed similar dose-response sensitivity to cocaine after several days of achieving similar levels of cocaine intake.

  20. Case Report: Mammary and rectal metastases from an ovarian cancer: report of two cases and review of literature [v2; ref status: indexed, http://f1000r.es/4wh

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    Mounia Amzerin

    2014-12-01

    Full Text Available In this paper we report two interesting cases of metastatic ovarian cancer. The first case is a patient who developed rectal and breast metastases mimicking an inflammatory breast cancer. In the second case, subclinical breast and axillary lymph node metastases were revealed by PET/CT. Metastases in the breast originating from solid tumors are extremely rare. The ovarian primitive is the fourth most common origin. The occurrence of breast metastasis is associated with an advanced disease and a poor prognosis. Their incidence is increasing since they are found more often due to better imaging techniques and to better treatment that, accordingly, improve patients’ survival. Thus, unusual sites of metastases are more and more reported. Indeed, some authors reported the occurrence of colorectal metastases from ovarian cancer. However, they remain much less frequent.

  1. CrossRef Antiproton Flux, Antiproton-to-Proton Flux Ratio, and Properties of Elementary Particle Fluxes in Primary Cosmic Rays Measured with the Alpha Magnetic Spectrometer on the International Space Station

    CERN Document Server

    Aguilar, M; Alpat, B; Ambrosi, G; Arruda, L; Attig, N; Aupetit, S; Azzarello, P; Bachlechner, A; Barao, F; Barrau, A; Barrin, L; Bartoloni, A; Basara, L; Başeǧmez-du Pree, S; Battarbee, M; Battiston, R; Bazo, J; Becker, U; Behlmann, M; Beischer, B; Berdugo, J; Bertucci, B; Bindi, V; Boella, G; de Boer, W; Bollweg, K; Bonnivard, V; Borgia, B; Boschini, M  J; Bourquin, M; Bueno, E  F; Burger, J; Cadoux, F; Cai, X  D; Capell, M; Caroff, S; Casaus, J; Castellini, G; Cernuda, I; Cervelli, F; Chae, M  J; Chang, Y  H; Chen, A  I; Chen, G  M; Chen, H  S; Cheng, L; Chou, H  Y; Choumilov, E; Choutko, V; Chung, C  H; Clark, C; Clavero, R; Coignet, G; Consolandi, C; Contin, A; Corti, C; Coste, B; Creus, W; Crispoltoni, M; Cui, Z; Dai, Y  M; Delgado, C; Della Torre, S; Demirköz, M  B; Derome, L; Di Falco, S; Dimiccoli, F; Díaz, C; von Doetinchem, P; Dong, F; Donnini, F; Duranti, M; D'Urso, D; Egorov, A; Eline, A; Eronen, T; Feng, J; Fiandrini, E; Finch, E; Fisher, P; Formato, V; Galaktionov, Y; Gallucci, G; García, B; García-López, R  J; Gargiulo, C; Gast, H; Gebauer, I; Gervasi, M; Ghelfi, A; Giovacchini, F; Goglov, P; Gómez-Coral, D  M; Gong, J; Goy, C; Grabski, V; Grandi, D; Graziani, M; Guerri, I; Guo, K  H; Habiby, M; Haino, S; Han, K  C; He, Z  H; Heil, M; Hoffman, J; Hsieh, T  H; Huang, H; Huang, Z  C; Huh, C; Incagli, M; Ionica, M; Jang, W  Y; Jinchi, H; Kang, S  C; Kanishev, K; Kim, G  N; Kim, K  S; Kirn, Th; Konak, C; Kounina, O; Kounine, A; Koutsenko, V; Krafczyk, M  S; La Vacca, G; Laudi, E; Laurenti, G; Lazzizzera, I; Lebedev, A; Lee, H  T; Lee, S  C; Leluc, C; Li, H  S; Li, J  Q; Li, Q; Li, T  X; Li, W; Li, Z  H; Li, Z  Y; Lim, S; Lin, C  H; Lipari, P; Lippert, T; Liu, D; Liu, Hu; Lu, S  Q; Lu, Y  S; Luebelsmeyer, K; Luo, F; Luo, J  Z; Lv, S  S; Majka, R; Mañá, C; Marín, J; Martin, T; Martínez, G; Masi, N; Maurin, D; Menchaca-Rocha, A; Meng, Q; Mo, D  C; Morescalchi, L; Mott, P; Nelson, T; Ni, J  Q; Nikonov, N; Nozzoli, F; Nunes, P; Oliva, A; Orcinha, M; Palmonari, F; Palomares, C; Paniccia, M; Pauluzzi, M; Pensotti, S; Pereira, R; Picot-Clemente, N; Pilo, F; Pizzolotto, C; Plyaskin, V; Pohl, M; Poireau, V; Putze, A; Quadrani, L; Qi, X  M; Qin, X; Qu, Z  Y; Räihä, T; Rancoita, P  G; Rapin, D; Ricol, J  S; Rodríguez, I; Rosier-Lees, S; Rozhkov, A; Rozza, D; Sagdeev, R; Sandweiss, J; Saouter, P; Schael, S; Schmidt, S  M; Schulz von Dratzig, A; Schwering, G; Seo, E  S; Shan, B  S; Shi, J  Y; Siedenburg, T; Son, D; Song, J  W; Sun, W  H; Tacconi, M; Tang, X  W; Tang, Z  C; Tao, L; Tescaro, D; Ting, Samuel C  C; Ting, S  M; Tomassetti, N; Torsti, J; Türkoğlu, C; Urban, T; Vagelli, V; Valente, E; Vannini, C; Valtonen, E; Vázquez Acosta, M; Vecchi, M; Velasco, M; Vialle, J  P; Vitale, V; Vitillo, S; Wang, L  Q; Wang, N  H; Wang, Q  L; Wang, X; Wang, X  Q; Wang, Z  X; Wei, C  C; Weng, Z  L; Whitman, K; Wienkenhöver, J; Willenbrock, M; Wu, H; Wu, X; Xia, X; Xiong, R  Q; Xu, W; Yan, Q; Yang, J; Yang, M; Yang, Y; Yi, H; Yu, Y  J; Yu, Z  Q; Zeissler, S; Zhang, C; Zhang, J; Zhang, J  H; Zhang, S  D; Zhang, S  W; Zhang, Z; Zheng, Z  M; Zhu, Z  Q; Zhuang, H  L; Zhukov, V; Zichichi, A; Zimmermann, N; Zuccon, P

    2016-01-01

    A precision measurement by AMS of the antiproton flux and the antiproton-to-proton flux ratio in primary cosmic rays in the absolute rigidity range from 1 to 450 GV is presented based on 3.49×105 antiproton events and 2.42×109 proton events. The fluxes and flux ratios of charged elementary particles in cosmic rays are also presented. In the absolute rigidity range ∼60 to ∼500  GV, the antiproton p¯, proton p, and positron e+ fluxes are found to have nearly identical rigidity dependence and the electron e− flux exhibits a different rigidity dependence. Below 60 GV, the (p¯/p), (p¯/e+), and (p/e+) flux ratios each reaches a maximum. From ∼60 to ∼500  GV, the (p¯/p), (p¯/e+), and (p/e+) flux ratios show no rigidity dependence. These are new observations of the properties of elementary particles in the cosmos.

  2. edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens [v2; ref status: indexed, http://f1000r.es/4kw

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    Zhiyin Dai

    2014-10-01

    Full Text Available Pooled library sequencing screens that perturb gene function in a high-throughput manner are becoming increasingly popular in functional genomics research. Irrespective of the mechanism by which loss of function is achieved, via either RNA interference using short hairpin RNAs (shRNAs or genetic mutation using single guide RNAs (sgRNAs with the CRISPR-Cas9 system, there is a need to establish optimal analysis tools to handle such data. Our open-source processing pipeline in edgeR provides a complete analysis solution for screen data, that begins with the raw sequence reads and ends with a ranked list of candidate genes for downstream biological validation. We first summarize the raw data contained in a fastq file into a matrix of counts (samples in the columns, genes in the rows with options for allowing mismatches and small shifts in sequence position. Diagnostic plots, normalization and differential representation analysis can then be performed using established methods to prioritize results in a statistically rigorous way, with the choice of either the classic exact testing methodology or generalized linear modeling that can handle complex experimental designs. A detailed users’ guide that demonstrates how to analyze screen data in edgeR along with a point-and-click implementation of this workflow in Galaxy are also provided. The edgeR package is freely available from http://www.bioconductor.org.

  3. Virtual screen for repurposing approved and experimental drugs for candidate inhibitors of EBOLA virus infection [v1; ref status: indexed, http://f1000r.es/51s

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    Veljko Veljkovic

    2015-02-01

    Full Text Available The ongoing Ebola virus epidemic has presented numerous challenges with respect to control and treatment because there are no approved drugs or vaccines for the Ebola virus disease (EVD. Herein is proposed simple theoretical criterion for fast virtual screening of molecular libraries for candidate inhibitors of Ebola virus infection. We performed a repurposing screen of 6438 drugs from DrugBank using this criterion and selected 267 approved and 382 experimental drugs as candidates for treatment of EVD including 15 anti-malarial drugs and 32 antibiotics. An open source Web server allowing screening of molecular libraries for candidate drugs for treatment of EVD was also established.

  4. In silico analysis suggests repurposing of ibuprofen for prevention and treatment of EBOLA virus disease [v1; ref status: indexed, http://f1000r.es/5bs

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    Veljko Veljkovic

    2015-05-01

    Full Text Available The large 2014/2015 Ebola virus outbreak in West Africa points out the urgent need to develop new preventive and therapeutic approaches that are effective against Ebola viruses and  can be rapidly utilized. Recently, a simple theoretical criterion for the virtual screening of molecular libraries for candidate inhibitors of Ebola virus infection was proposed. Using this method the ‘drug space’ was screened and 267 approved and 382 experimental drugs as candidates for treatment of the Ebola virus disease (EVD have been selected. Detailed analysis of these drugs revealed the non-steroidal anti-inflammatory drug ibuprofen as an inexpensive, widely accessible and minimally toxic candidate for prevention and treatment of EVD. Furthermore, the molecular mechanism underlying this possible protective effect of ibuprofen against EVD is suggested in this article.

  5. The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold [v2; ref status: indexed, http://f1000r.es/1nx

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    Daniel J Rigden

    2013-08-01

    Full Text Available We report the crystal structure solution of the Intracellular Protease Inhibitor (IPI protein from Bacillus subtilis, which has been reported to be an inhibitor of the intracellular subtilisin Isp1 from the same organism. The structure of IPI is a variant of the all-beta, immunoglobulin (Ig fold. It is possible that IPI is important for protein-protein interactions, of which inhibition of Isp1 is one. The intracellular nature of ISP is questioned, because an alternative ATG codon in the ipi gene would produce a protein with an N-terminal extension containing a signal peptide. It is possible that alternative initiation exists, producing either an intracellular inhibitor or a secreted form that may be associated with the cell surface.  Homologues of the IPI protein from other species are multi-domain proteins, containing signal peptides and domains also associated with the bacterial cell-surface. The cysteine peptidase inhibitors chagasin and amoebiasin also have Ig-like folds, but their topology differs significantly from that of IPI, and they share no recent common ancestor. A model of IPI docked to Isp1 shows similarities to other subtilisin:inhibitor complexes, particularly where the inhibitor interacts with the peptidase active site.

  6. Homologous electron transport components fail to increase fatty acid hydroxylation in transgenic Arabidopsis thaliana [v2; ref status: indexed, http://f1000r.es/2a3

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    Laura L. Wayne

    2013-11-01

    Full Text Available Ricinoleic acid, a hydroxylated fatty acid (HFA present in castor (Ricinus communis seeds, is an important industrial commodity used in products ranging from inks and paints to polymers and fuels. However, due to the deadly toxin ricin and allergens also present in castor, it would be advantageous to produce ricinoleic acid in a different agricultural crop. Unfortunately, repeated efforts at heterologous expression of the castor fatty acid hydroxylase (RcFAH12 in the model plant Arabidopsis thaliana have produced only 17-19% HFA in the seed triacylglycerols (TAG, whereas castor seeds accumulate up to 90% ricinoleic acid in the endosperm TAG. RcFAH12 requires an electron supply from NADH:cytochrome b5 reductase (CBR1 and cytochrome b5 (Cb5 to synthesize ricinoleic acid. Previously, our laboratory found a mutation in the Arabidopsis CBR1 gene, cbr1-1, that caused an 85% decrease in HFA levels in the RcFAH12 Arabidopsis line. These results raise the possibility that electron supply to the heterologous RcFAH12 may limit the production of HFA. Therefore, we hypothesized that by heterologously expressing RcCb5, the reductant supply to RcFAH12 would be improved and lead to increased HFA accumulation in Arabidopsis seeds. Contrary to this proposal, heterologous expression of the top three RcCb5 candidates did not increase HFA accumulation. Furthermore, coexpression of RcCBR1 and RcCb5 in RcFAH12 Arabidopsis also did not increase in HFA levels compared to the parental lines. These results demonstrate that the Arabidopsis electron transfer system is supplying sufficient reductant to RcFAH12 and that there must be other bottlenecks limiting the accumulation of HFA.

  7. Thermoregulation strategies in ants in comparison to other social insects, with a focus on red wood ants (Formica rufa group [v2; ref status: indexed, http://f1000r.es/35p

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    Štěpánka Kadochová

    2014-03-01

    Full Text Available Temperature influences every aspect of ant biology, especially metabolic rate, growth and development. Maintenance of high inner nest temperature increases the rate of sexual brood development and thereby increases the colony fitness. Insect societies can achieve better thermoregulation than solitary insects due to the former’s ability to build large and elaborated nests and display complex behaviour. In ants and termites the upper part of the nest, the mound, often works as a solar collector and can also have an efficient ventilation system. Two thermoregulatory strategies could be applied. Firstly the ants use an increased thermal gradient available in the mound for brood relocation. Nurse workers move the brood according to the thermal gradients to ensure the ideal conditions for development. A precise perception of temperature and evolution of temperature preferences are needed to make the correct choices. A second thermoregulatory strategy used by mound nesting ants is keeping a high temperature inside large nests. The unique thermal and insulation properties of the nest material help to maintain stable conditions, which is the case of the Wood ant genus Formica. Ants can regulate thermal loss by moving nest aggregation and alternating nest ventilation. Metabolic heat produced by ant workers or associated micro organisms is an important additional source of heat which helps to maintain thermal homeostasis in the nest.

  8. Prevalence of antibiotic-resistant E. coli in retail chicken: comparing conventional, organic, kosher, and raised without antibiotics [v2; ref status: indexed, http://f1000r.es/1pu

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    Jack M Millman

    2013-09-01

    Full Text Available Retail poultry products are known sources of antibiotic-resistant Escherichia coli, a major human health concern. Consumers have a range of choices for poultry, including conventional, organic, kosher, and raised without antibiotics (RWA – designations that are perceived to indicate differences in quality and safety. However, whether these categories vary in the frequency of contamination with antibiotic-resistant E. coli is unknown. We examined the occurrence of antibiotic-resistant E. coli on raw chicken marketed as conventional, organic, kosher and RWA. From April – June 2012, we purchased 213 samples of raw chicken from 15 locations in the New York City metropolitan area. We screened E. coli isolates from each sample for resistance to 12 common antibiotics. Although the organic and RWA labels restrict the use of antibiotics, the frequency of antibiotic-resistant E. coli tended to be only slightly lower for RWA, and organic chicken was statistically indistinguishable from conventional products that have no restrictions. Kosher chicken had the highest frequency of antibiotic-resistant E. coli, nearly twice that of conventional products, a result that belies the historical roots of kosher as a means to ensure food safety. These results indicate that production methods influence the frequency of antibiotic-resistant E. coli on poultry products available to consumers. Future research to identify the specific practices that cause the high frequency of antibiotic-resistant E. coli in kosher chicken could promote efforts to reduce consumer exposure to this potential pathogen.

  9. PPI layouts: BioJS components for the display of Protein-Protein Interactions [v1; ref status: indexed, http://f1000r.es/2u5

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    Gustavo A. Salazar

    2014-02-01

    Full Text Available Summary: We present two web-based components for the display of Protein-Protein Interaction networks using different self-organizing layout methods: force-directed and circular. These components conform to the BioJS standard and can be rendered in an HTML5-compliant browser without the need for third-party plugins. We provide examples of interaction networks and how the components can be used to visualize them, and refer to a more complex tool that uses these components. Availability: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7753

  10. A rare aggravation of severe mucositis post chemotherapy in a child with acute lymphoblastic leukemia [v1; ref status: indexed, http://f1000r.es/1tf

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    Adlette Inati

    2013-09-01

    Full Text Available Oral mucositis is a debilitating manifestation in children undergoing chemotherapy and radiotherapy. Children with mucositis should be properly managed in order to prevent further exacerbation and adverse complications. We hereby present the first report of a severe chemotherapy-induced mucositis, plausibly aggravated by improper dental hygiene leading to shedding of the ventral part of the tongue in a child with pre-B acute lymphoblastic leukemia (ALL. The patient steadily and gradually recovered her oral maneuvers and ability to speak several months later. Her tongue underwent hypertrophy as a compensatory mechanism. We recommend that critical and regular assessment of the oral mucosa and proper dental care and oral hygiene be emphasized in all pediatric patients receiving chemotherapy. Families of affected children need to be educated about the benefits and modes of optimal oral hygiene for their children and the need to seek immediate care for mouth pain and or lesions. Optimal treatment for mucositis needs to be instituted without delay in this high risk pediatric population. Such a preventive and therapeutic approach may prevent associated life threatening oral and systemic complications, promote rapid and complete mucosal healing, alleviate pain and improve quality of life in children with cancer.

  11. Characterization of a SAM-dependent fluorinase from a latent biosynthetic pathway for fluoroacetate and 4-fluorothreonine formation in Nocardia brasiliensis [v1; ref status: indexed, http://f1000r.es/2tz

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    Yaya Wang

    2014-02-01

    Full Text Available Fluorination has been widely used in chemical synthesis, but is rare in nature. The only known biological fluorination scope is represented by the fl pathway from Streptomyces cattleya that produces fluoroacetate (FAc and 4-fluorothreonine (4-FT. Here we report the identification of a novel pathway for FAc and 4-FT biosynthesis from the actinomycetoma-causing pathogen Nocardia brasiliensis ATCC 700358. The new pathway shares overall conservation with the fl pathway in S. cattleya. Biochemical characterization of the conserved domains revealed a novel fluorinase NobA that can biosynthesize 5’-fluoro-5’-deoxyadenosine (5’-FDA from inorganic fluoride and S-adenosyl-l-methionine (SAM. The NobA shows similar halide specificity and characteristics to the fluorination enzyme FlA of the fl pathway. Kinetic parameters for fluoride (Km 4153 μM, kcat 0.073 min-1 and SAM (Km 416 μM, kcat 0.139 min-1 have been determined, revealing that NobA is slightly (2.3 fold slower than FlA. Upon sequence comparison, we finally identified a distinct loop region in the fluorinases that probably accounts for the disparity of fluorination activity.

  12. Deletion of ENTPD3 does not impair nucleotide hydrolysis in primary somatosensory neurons or spinal cord [v1; ref status: indexed, http://f1000r.es/3rm

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    Eric McCoy

    2014-07-01

    Full Text Available Ectonucleotidases are membrane-bound or secreted proteins that hydrolyze extracellular nucleotides.  Recently, we identified three ectonucleotidases that hydrolyze extracellular adenosine 5’-monophosphate (AMP to adenosine in primary somatosensory neurons.  Currently, it is unclear which ectonucleotidases hydrolyze ATP and ADP in these neurons.  Ectonucleoside triphosphate diphosphohydrolases (ENTPDs comprise a class of enzymes that dephosphorylate extracellular ATP and ADP.  Here, we found that ENTPD3 (also known as NTPDase3 or CD39L3 was located in nociceptive and non-nociceptive neurons of the dorsal root ganglion (DRG, in the dorsal horn of the spinal cord, and in free nerve endings in the skin.  To determine if ENTPD3 contributes directly to ATP and ADP hydrolysis in these tissues, we generated and characterized an Entpd3 knockout mouse.  This mouse lacks ENTPD3 protein in all tissues examined, including the DRG, spinal cord, skin, and bladder.  However, DRG and spinal cord tissues from Entpd3-/- mice showed no reduction in histochemical staining when ATP, ADP, AMP, or UTP were used as substrates.  Additionally, using fast-scan cyclic voltammetry (FSCV, adenosine production was not impaired in the dorsal spinal cord of Entpd3-/- mice when the substrate ADP was applied.  Further, Entpd3-/- mice did not differ in nociceptive behaviors when compared to wild-type mice, although Entpd3-/- mice showed a modest reduction in β-alanine-mediated itch.  Taken together, our data indicate that deletion of Entpd3 does not impair ATP or ADP hydrolysis in primary somatosensory neurons or in dorsal spinal cord.  Moreover, our data suggest there could be multiple ectonucleotidases that act redundantly to hydrolyze nucleotides in these regions of the nervous system.

  13. Deletion of ENTPD3 does not impair nucleotide hydrolysis in primary somatosensory neurons or spinal cord [v2; ref status: indexed, http://f1000r.es/4dl

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    Eric McCoy

    2014-09-01

    Full Text Available Ectonucleotidases are membrane-bound or secreted proteins that hydrolyze extracellular nucleotides.  Recently, we identified three ectonucleotidases that hydrolyze extracellular adenosine 5’-monophosphate (AMP to adenosine in primary somatosensory neurons.  Currently, it is unclear which ectonucleotidases hydrolyze ATP and ADP in these neurons.  Ectonucleoside triphosphate diphosphohydrolases (ENTPDs comprise a class of enzymes that dephosphorylate extracellular ATP and ADP.  Here, we found that ENTPD3 (also known as NTPDase3 or CD39L3 was located in nociceptive and non-nociceptive neurons of the dorsal root ganglion (DRG, in the dorsal horn of the spinal cord, and in free nerve endings in the skin.  To determine if ENTPD3 contributes directly to ATP and ADP hydrolysis in these tissues, we generated and characterized an Entpd3 knockout mouse.  This mouse lacks ENTPD3 protein in all tissues examined, including the DRG, spinal cord, skin, and bladder.  However, DRG and spinal cord tissues from Entpd3-/- mice showed no reduction in histochemical staining when ATP, ADP, AMP, or UTP were used as substrates.  Additionally, using fast-scan cyclic voltammetry (FSCV, adenosine production was not impaired in the dorsal spinal cord of Entpd3-/- mice when the substrate ADP was applied.  Further, Entpd3-/- mice did not differ in nociceptive behaviors when compared to wild-type mice, although Entpd3-/- mice showed a modest reduction in β-alanine-mediated itch.  Taken together, our data indicate that deletion of Entpd3 does not impair ATP or ADP hydrolysis in primary somatosensory neurons or in dorsal spinal cord.  Moreover, our data suggest there could be multiple ectonucleotidases that act redundantly to hydrolyze nucleotides in these regions of the nervous system.

  14. Directed evolution induces tributyrin hydrolysis in a virulence factor of Xylella fastidiosa using a duplicated gene as a template [v1; ref status: indexed, http://f1000r.es/48i

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    Hossein Gouran

    2014-09-01

    Full Text Available Duplication of genes is one of the preferred ways for natural selection to add advantageous functionality to the genome without having to reinvent the wheel with respect to catalytic efficiency and protein stability. The duplicated secretory virulence factors of Xylella fastidiosa (LesA, LesB and LesC, implicated in Pierce's disease of grape and citrus variegated chlorosis of citrus species, epitomizes the positive selection pressures exerted on advantageous genes in such pathogens. A deeper insight into the evolution of these lipases/esterases is essential to develop resistance mechanisms in transgenic plants. Directed evolution, an attempt to accelerate the evolutionary steps in the laboratory, is inherently simple when targeted for loss of function. A bigger challenge is to specify mutations that endow a new function, such as a lost functionality in a duplicated gene. Previously, we have proposed a method for enumerating candidates for mutations intended to transfer the functionality of one protein into another related protein based on the spatial and electrostatic properties of the active site residues (DECAAF. In the current work, we present in vivo validation of DECAAF by inducing tributyrin hydrolysis in LesB based on the active site similarity to LesA. The structures of these proteins have been modeled using RaptorX based on the closely related LipA protein from Xanthomonas oryzae. These mutations replicate the spatial and electrostatic conformation of LesA in the modeled structure of the mutant LesB as well, providing in silico validation before proceeding to the laborious in vivo work. Such focused mutations allows one to dissect the relevance of the duplicated genes in finer detail as compared to gene knockouts, since they do not interfere with other moonlighting functions, protein expression levels or protein-protein interaction.

  15. Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes [v2; ref status: indexed, http://f1000r.es/2x3

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    Ted Kalbfleisch

    2014-02-01

    Full Text Available Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease.  High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals.  Comparisons between these species have provided unique insights into mammalian gene function.  However, the number of species with reference genomes is small compared to those needed for studying molecular evolutionary relationships in the tree of life.  For example, among the even-toed ungulates there are approximately 300 species whose phylogenetic relationships have been calculated in the 10k trees project.  Only six of these have reference genomes:  cattle, swine, sheep, goat, water buffalo, and bison.  Although reference sequences will eventually be developed for additional hoof stock, the resources in terms of time, money, infrastructure and expertise required to develop a quality reference genome may be unattainable for most species for at least another decade.  In this work we mapped 35 Gb of next generation sequence data of a Katahdin sheep to its own species’ reference genome (Ovis aries Oar3.1 and to that of a species that diverged 15 to 30 million years ago (Bos taurus UMD3.1.  In total, 56% of reads covered 76% of UMD3.1 to an average depth of 6.8 reads per site, 83 million variants were identified, of which 78 million were homozygous and likely represent interspecies nucleotide differences. Excluding repeat regions and sex chromosomes, nearly 3.7 million heterozygous sites were identified in this animal vs. bovine UMD3.1, representing polymorphisms occurring in sheep.  Of these, 41% could be readily mapped to orthologous positions in ovine Oar3.1 with 80% corroborated as heterozygous.  These variant sites, identified via interspecies mapping could be used for comparative genomics, disease association studies, and ultimately to understand mammalian gene function.

  16. A review of creatine supplementation in age-related diseases: more than a supplement for athletes [v1; ref status: indexed, http://f1000r.es/4ak

    Directory of Open Access Journals (Sweden)

    Rachel N. Smith

    2014-09-01

    Full Text Available Creatine is an endogenous compound synthesized from arginine, glycine and methionine. This dietary supplement can be acquired from food sources such as meat and fish, along with athlete supplement powders. Since the majority of creatine is stored in skeletal muscle, dietary creatine supplementation has traditionally been important for athletes and bodybuilders to increase the power, strength, and mass of the skeletal muscle. However, new uses for creatine have emerged suggesting that it may be important in preventing or delaying the onset of neurodegenerative diseases associated with aging. On average, 30% of muscle mass is lost by age 80, while muscular weakness remains a vital cause for loss of independence in the elderly population. In light of these new roles of creatine, the dietary supplement’s usage has been studied to determine its efficacy in treating congestive heart failure, gyrate atrophy, insulin insensitivity, cancer, and high cholesterol. In relation to the brain, creatine has been shown to have antioxidant properties, reduce mental fatigue, protect the brain from neurotoxicity, and improve facets/components of neurological disorders like depression and bipolar disorder. The combination of these benefits has made creatine a leading candidate in the fight against age-related diseases, such as Parkinson’s disease, Huntington’s disease, amyotrophic lateral sclerosis, long-term memory impairments associated with the progression of Alzheimer’s disease, and stroke. In this review, we explore the normal mechanisms by which creatine is produced and its necessary physiology, while paying special attention to the importance of creatine supplementation in improving diseases and disorders associated with brain aging and outlining the clinical trials involving creatine to treat these diseases.

  17. Kyasanur forest disease virus: viremia and challenge studies in monkeys with evidence of cross-protection by Langat virus infection [v1; ref status: indexed, http://f1000r.es/UiWGcy

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    Keerti V Shah

    2012-12-01

    Full Text Available Kyasanur Forest Disease Virus (KFDV, discovered in 1957, is a member of the tick-borne encephalitis virus (TBEV complex. Diseases caused by members of the TBEV complex occur in many parts of the world. KFDV produces a hemorrhagic fever in humans in South India and fatal illnesses in both species of monkeys in the area, the black faced langur (Presbytis entellus and the bonnet macaque (Macaca radiata. Experimental infection of the langur and the bonnet macaque with early mouse passage KFDV strain P9605 resulted in a viremia of up to 11 days duration, peak viremia titers as high as 109, and death in 82 = 100% of the animals. Prolonged passage of the KFDV strain P9605 in monkey kidney tissue culture resulted in a markedly reduced virulence of the virus for both species; peak viremia titers in monkeys decreased by 2.5 to 4.0 log LD 50 (p= 0.001, and the mortality decreased to 10% (p= 0.001. In challenge experiments, monkeys previously infected with tissue-culture-adapted KFDV, or with the related Langat virus from Malaysia, were fully protected against virulent KFDV. These studies in non-human primates lend support to the idea that a live virus vaccine from a member of the TBEV complex may be broadly protective against infections by other members of the TBEV complex.

  18. Casanovas are liars: behavioral syndromes, sperm competition risk, and the evolution of deceptive male mating behavior in live-bearing fishes [v2; ref status: indexed, http://f1000r.es/1ko

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    David Bierbach

    2013-08-01

    Full Text Available Male reproductive biology can by characterized through competition over mates as well as mate choice. Multiple mating and male mate choice copying, especially in internally fertilizing species, set the stage for increased sperm competition, i.e., sperm of two or more males can compete for fertilization of the female’s ova. In the internally fertilizing fish Poecilia mexicana, males respond to the presence of rivals with reduced expression of mating preferences (audience effect, thereby lowering the risk of by-standing rivals copying their mate choice. Also, males interact initially more with a non-preferred female when observed by a rival, which has been interpreted in previous studies as a strategy to mislead rivals, again reducing sperm competition risk (SCR. Nevertheless, species might differ consistently in their expression of aggressive and reproductive behaviors, possibly due to varying levels of SCR. In the current study, we present a unique data set comprising ten poeciliid species (in two cases including multiple populations and ask whether species can be characterized through consistent differences in the expression of aggression, sexual activity and changes in mate choice under increased SCR. We found consistent species-specific differences in aggressive behavior, sexual activity as well as in the level of misleading behavior, while decreased preference expression under increased SCR was a general feature of all but one species examined. Furthermore, mean sexual activity correlated positively with the occurrence of potentially misleading behavior. An alternative explanation for audience effects would be that males attempt to avoid aggressive encounters, which would predict stronger audience effects in more aggressive species. We demonstrate a positive correlation between mean aggressiveness and sexual activity (suggesting a hormonal link as a mechanistic explanation, but did not detect a correlation between aggressiveness and audience effects. Suites of correlated behavioral tendencies are termed behavioral syndromes, and our present study provides correlational evidence for the evolutionary significance of SCR in shaping a behavioral syndrome at the species level across poeciliid taxa.

  19. A mutation in negative regulator of basal resistance WRKY17 of Arabidopsis increases susceptibility to Agrobacterium-mediated transient genetic transformation [v2; ref status: indexed, http://f1000r.es/ya

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    Benoît Lacroix

    2013-02-01

    Full Text Available Agrobacterium is a phytopathogenic bacterium that induces crown gall disease in many plant species by transferring and integrating a segment of its own DNA (T-DNA into its host genome. Whereas Agrobacterium usually does not trigger an extensive defense response in its host plants, it induces the expression of several defense-related genes and activates plant stress reactions. In the complex interplay between Agrobacterium and its host plant, Agrobacterium has evolved to take advantage of these plant defense pathways for its own purpose of advancement of the infection process. For example, Agrobacterium utilizes the host stress response transcriptional regulator VIP1 to facilitate nuclear import and proteasomal uncoating of its T-DNA during genetic transformation of the host cell. In Arabidopsis, the VIP1 gene expression is repressed by WRKY17, a negative regulator of basal resistance to Pseudomonas. Thus, we examined whether WRKY17 is also involved in plant susceptibility to genetic transformation by Agrobacterium. Using reverse genetics, we showed that a wrky17 mutant displays higher expression of the VIP1 gene in roots, but not in shoots. In a root infection assay, the wrky17 mutant plants were hyper-susceptible to Agrobacterium compared to wild type plants. WRKY17, therefore, may act as a positive regulator of Arabidopsis resistance to Agrobacterium. This notion is important for understanding the complex regulation of Agrobacterium-mediated transient genetic transformation; thus, although this paper reports a relatively small set of data that we do not plan to pursue further in our lab, we believe it might be useful for the broad community of plant pathologists and plant biotechnologists.

  20. A mutation in negative regulator of basal resistance WRKY17 of Arabidopsis increases susceptibility to Agrobacterium-mediated genetic transformation [v1; ref status: indexed, http://f1000r.es/no

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    Benoît Lacroix

    2013-02-01

    Full Text Available Agrobacterium is a phytopathogenic bacterium that induces crown gall disease in many plant species by transferring and integrating a segment of its own DNA (T-DNA into its host genome. Whereas Agrobacterium usually does not trigger an extensive defense response in its host plants, it induces the expression of several defense-related genes and activates plant stress reactions. In the complex interplay between Agrobacterium and its host plant, Agrobacterium has evolved to take advantage of these plant defense pathways for its own purpose of advancement of the infection process. For example, Agrobacterium utilizes the host stress response transcriptional regulator VIP1 to facilitate nuclear import and proteasomal uncoating of its T-DNA during genetic transformation of the host cell. In Arabidopsis, the VIP1 gene expression is repressed by WRKY17, a negative regulator of basal resistance to Pseudomonas. Thus, we examined whether WRKY17 is also involved in plant susceptibility to genetic transformation by Agrobacterium. Using reverse genetics, we showed that a wrky17 mutant displays higher expression of the VIP1 gene in roots, but not in shoots. In a root infection assay, the wrky17 mutant plants were hyper-susceptible to Agrobacterium compared to wild type plants. WRKY17, therefore, may act as a positive regulator of Arabidopsis resistance to Agrobacterium. This notion is important for understanding the complex regulation of Agrobacterium-mediated genetic transformation; thus, although this paper reports a relatively small set of data that we do not plan to pursue further in our lab, we believe it might be useful for the broad community of plant pathologists and plant biotechnologists.

  1. Tissue-resident Sca1+ PDGFRα+ mesenchymal progenitors are the cellular source of fibrofatty infiltration in arrhythmogenic cardiomyopathy [v1; ref status: indexed, http://f1000r.es/17s

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    Ben Paylor

    2013-06-01

    Full Text Available Arrhythmogenic cardiomyopathy (AC is a disease of the heart involving myocardial dystrophy leading to fibrofatty scarring of the myocardium and is associated with an increased risk of both ventricular arrhythmias and sudden cardiac death. It often affects the right ventricle but may also involve the left. Although there has been significant progress in understanding the role of underlying desmosomal genetic defects in AC, there is still a lack of data regarding the cellular processes involved in its progression. The development of cardiac fibrofatty scarring is known to be a principal pathological process associated with ventricular arrhythmias, and it is vital that we elucidate the role of various cell populations involved in the disease if targeted therapeutics are to be developed. The known role of mesenchymal progenitor cells in the reparative process of both the heart and skeletal muscle has provided inspiration for the identification of the cellular basis of fibrofatty infiltration in AC. Here we hypothesize that reparative processes triggered by myocardial degeneration lead to the differentiation of tissue-resident Sca1+ PDGFRα+ mesenchymal progenitors into adipocytes and fibroblasts, which compose the fibrofatty lesions characteristic of AC.

  2. NIH Portfolio Allocation, Lemmings, and the Silent Spring: A Time-Capsule Commentary & Its Update [v1; ref status: indexed, http://f1000r.es/MNYl6Z

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    Mark Boothby

    2012-07-01

    Full Text Available With the release of the US President’s proposed budget for the Federal Fiscal year (FY 2013, to start October 1, 2012, we’ve spun yet again into the mad vortex of an appropriation season. Fundamental re-thinks of how biological and medical research are prioritized and funded are urgently needed, but sadly appear to be unlikely unless the research and advocacy communities push harder and in a more unified manner. Early in the Obama presidency and the NIH Directorship of Dr Francis Collins, the FASEB Office of Public Affairs performed an analysis of trends in funding of R01 and other Research Project Grants and shared that with the Director and his office. Using the FASEB analysis, whose numbers drew on NIH data, an independent commentary (below was submitted to (but not published in Science. With the analysis a few years old, this older viewpoint is followed by updates that touch on how the trends have fared since early 2010 and comment on other aspects of the ongoing cull in biomedical research. In particular, data on some of the growth areas that continue to prosper at the expense of the ever-declining direct support for R01 science are discussed.

  3. Characteristics of American coals in relation to their conversion into clean energy fuels. Quarterly technical progress report, January--March 1976. [2 appendices; 19 refs. Dryflo separation tests data

    Energy Technology Data Exchange (ETDEWEB)

    Spackman, W.; Davis, A.; Walker, P. L.; Lovell, H. L.; Essenhigh, R. H.; Vastola, F. J.; Given, P. H.

    1976-05-01

    Responses to the questionnaire, which was distributed to determine the extent to which the nation's coal seams have been sampled and characterized, are being received. Early comparisons indicate a mathematical relationship between average random reflectance (Rapid Scan) and the mean-maximum reflectance as obtained by standard reflectance analysis. Results obtained so far show support of a diffusion dominance mechanism in the oxidation region of a combustion pot and a chemical kinetic mechanism in the gasification region. Values of reaction rates in coke beds have been calculated from experiments with a fixed bed shaft gasifier. Devolatilization of a North Dakota lignite in a laminar flow reactor and subsequent treatment of the resulting char has shown that weight loss is strongly dependent upon the isothermal decomposition time. Although gasification rates increase with increase in partial pressure of oxygen, the mechanism for gasification of a given char is independent of partial pressure of oxygen. Study of the reactivity of ion-exchanged lignite chars to steam shows that increased heat treatment decreases reactivity and ion exchange increases reactivity. Use of the DSC technique to study the thermal effects involved during chemisorption of oxygen on Saran carbon has yielded information on the activation energy (EA) of the reaction. Work on the infinite parallel plane char combustion computer model has determined that low volatile chars and coals can be suitable fuels if adequate available internal surface area is present.

  4. Systematic assessment of benefits and risks: study protocol for a multi-criteria decision analysis using the Analytic Hierarchy Process for comparative effectiveness research [v1; ref status: indexed, http://f1000r.es/1fk

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    Nisa M Maruthur

    2013-07-01

    Full Text Available Background: Regulatory decision-making involves assessment of risks and benefits of medications at the time of approval or when relevant safety concerns arise with a medication. The Analytic Hierarchy Process (AHP facilitates decision-making in complex situations involving tradeoffs by considering risks and benefits of alternatives. The AHP allows a more structured method of synthesizing and understanding evidence in the context of importance assigned to outcomes. Our objective is to evaluate the use of an AHP in a simulated committee setting selecting oral medications for type 2 diabetes.  Methods: This study protocol describes the AHP in five sequential steps using a small group of diabetes experts representing various clinical disciplines. The first step will involve defining the goal of the decision and developing the AHP model. In the next step, we will collect information about how well alternatives are expected to fulfill the decision criteria. In the third step, we will compare the ability of the alternatives to fulfill the criteria and judge the importance of eight criteria relative to the decision goal of the optimal medication choice for type 2 diabetes. We will use pairwise comparisons to sequentially compare the pairs of alternative options regarding their ability to fulfill the criteria. In the fourth step, the scales created in the third step will be combined to create a summary score indicating how well the alternatives met the decision goal. The resulting scores will be expressed as percentages and will indicate the alternative medications' relative abilities to fulfill the decision goal. The fifth step will consist of sensitivity analyses to explore the effects of changing the estimates. We will also conduct a cognitive interview and process evaluation.  Discussion: Multi-criteria decision analysis using the AHP will aid, support and enhance the ability of decision makers to make evidence-based informed decisions consistent with their values and preferences.

  5. ANGDelMut – a web-based tool for predicting and analyzing functional loss mechanisms of amyotrophic lateral sclerosis-associated angiogenin mutations [v2; ref status: indexed, http://f1000r.es/2mc

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    Aditya K Padhi

    2013-12-01

    Full Text Available ANGDelMut is a web-based tool for predicting the functional consequences of missense mutations in the angiogenin (ANG protein, which is associated with amyotrophic lateral sclerosis (ALS. Missense mutations in ANG result in loss of either ribonucleolytic activity or nuclear translocation activity or both of these functions, and in turn cause ALS. However, no web-based tools are available to predict whether a newly identified ANG mutation will possibly lead to ALS. More importantly, no web-implemented method is currently available to predict the mechanisms of loss-of-function(s of ANG mutants. In light of this observation, we developed the ANGDelMut web-based tool, which predicts whether an ANG mutation is deleterious or benign. The user selects certain attributes from the input panel, which serves as a query to infer whether a mutant will exhibit loss of ribonucleolytic activity or nuclear translocation activity or whether the overall stability will be affected. The output states whether the mutation is deleterious or benign, and if it is deleterious, gives the possible mechanism(s of loss-of-function. This web-based tool, freely available at http://bioschool.iitd.ernet.in/DelMut/, is the first of its kind to provide a platform for researchers and clinicians, to infer the functional consequences of ANG mutations and correlate their possible association with ALS ahead of experimental findings.

  6. Novel somatic single nucleotide variants within the RNA binding protein hnRNP A1 in multiple sclerosis patients [v1; ref status: indexed, http://f1000r.es/3nv

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    Sangmin Lee

    2014-06-01

    Full Text Available Some somatic single nucleotide variants (SNVs are thought to be pathogenic, leading to neurological disease. We hypothesized that heterogeneous nuclear ribonuclear protein A1 (hnRNP A1, an autoantigen associated with multiple sclerosis (MS would contain SNVs. MS patients develop antibodies to hnRNP A1293-304, an epitope within the M9 domain (AA268-305 of hnRNP A1. M9 is hnRNP A1’s nucleocytoplasmic transport domain, which binds transportin-1 (TPNO-1 and allows for hnRNP A1’s transport into and out of the nucleus. Genomic DNA sequencing of M9 revealed nine novel SNVs that resulted in an amino acid substitution in MS patients that were not present in controls. SNVs occurred within the TPNO-1 binding domain (hnRNP A1268-289 and the MS IgG epitope (hnRNP A1293-304, within M9.  In contrast to the nuclear localization of wild type (WT hnRNP A1, mutant hnRNP A1 mis-localized to the cytoplasm, co-localized with stress granules and caused cellular apoptosis. Whilst WT hnRNP A1 bound TPNO-1, mutant hnRNP A1 showed reduced TPNO-1 binding. These data suggest SNVs in hnRNP A1 might contribute to pathogenesis of MS.

  7. The Perinatal Adverse events and Special Trends in Cognitive Trajectory (PLASTICITY - pre-protocol for a prospective longitudinal follow-up cohort study [v1; ref status: indexed, http://f1000r.es/qe

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    Laura Hokkanen

    2013-02-01

    Full Text Available Prospective follow-up studies on long term effects of pre- and perinatal adverse conditions in adulthood are rare. We will continue to follow the prospective cohort of initially 1196 subjects with predefined at-delivery risk factors out of 22,359 consecutive deliveries during 1971-74 at a single maternity hospital. The risk cohort and 93 controls have been followed up with a comprehensive clinical program at 5, 9, and 16 years of age and by questionnaire at the age of 30 years. Major medical events known to affect the development and growth of the brain, or cognitive functions and personality have been documented. Here we present a pre-protocol for the project, which we will call PLASTICITY, whose aim is to follow consenting subjects and controls into mid-adulthood and beyond, and to explore how the neonatal risk factors modulate neurodevelopmental and neurodegenerative processes such as learning disabilities, ADHD, aging, early onset mild cognitive impairment and even dementia. Our first focus is on the neurological and cognitive outcomes at age 40 years, using detailed neurological, neuropsychological, neuroimaging, genetic, blood chemistry and registry based methods. Results will be expected to offer information on the risk of neurological, psychiatric, metabolic and other medical consequences as well as the need for health and social services at the brink of middle age, when new degenerative phenomena are known to emerge. The evaluation at age 40 years will serve as a baseline for later aging studies. We welcome all comments and suggestions, which we will apply in finalizing details and inviting collaboration.

  8. Novel somatic single nucleotide variants within the RNA binding protein hnRNP A1 in multiple sclerosis patients [v2; ref status: indexed, http://f1000r.es/4dh

    Directory of Open Access Journals (Sweden)

    Sangmin Lee

    2014-09-01

    Full Text Available Some somatic single nucleotide variants (SNVs are thought to be pathogenic, leading to neurological disease. We hypothesized that heterogeneous nuclear ribonuclear protein A1 (hnRNP A1, an autoantigen associated with multiple sclerosis (MS would contain SNVs. MS patients develop antibodies to hnRNP A1293-304, an epitope within the M9 domain (AA268-305 of hnRNP A1. M9 is hnRNP A1’s nucleocytoplasmic transport domain, which binds transportin-1 (TPNO-1 and allows for hnRNP A1’s transport into and out of the nucleus. Genomic DNA sequencing of M9 revealed nine novel SNVs that resulted in an amino acid substitution in MS patients that were not present in controls. SNVs occurred within the TPNO-1 binding domain (hnRNP A1268-289 and the MS IgG epitope (hnRNP A1293-304, within M9.  In contrast to the nuclear localization of wild type (WT hnRNP A1, mutant hnRNP A1 mis-localized to the cytoplasm, co-localized with stress granules and caused cellular apoptosis. Whilst WT hnRNP A1 bound TPNO-1, mutant hnRNP A1 showed reduced TPNO-1 binding. These data suggest SNVs in hnRNP A1 might contribute to pathogenesis of MS.

  9. ANGDelMut – a web-based tool for predicting and analyzing functional loss mechanisms of amyotrophic lateral sclerosis-associated angiogenin mutations [v3; ref status: indexed, http://f1000r.es/2yt

    Directory of Open Access Journals (Sweden)

    Aditya K Padhi

    2014-02-01

    Full Text Available ANGDelMut is a web-based tool for predicting the functional consequences of missense mutations in the angiogenin (ANG protein, which is associated with amyotrophic lateral sclerosis (ALS. Missense mutations in ANG result in loss of either ribonucleolytic activity or nuclear translocation activity or both of these functions, and in turn cause ALS. However, no web-based tools are available to predict whether a newly identified ANG mutation will possibly lead to ALS. More importantly, no web-implemented method is currently available to predict the mechanisms of loss-of-function(s of ANG mutants. In light of this observation, we developed the ANGDelMut web-based tool, which predicts whether an ANG mutation is deleterious or benign. The user selects certain attributes from the input panel, which serves as a query to infer whether a mutant will exhibit loss of ribonucleolytic activity or nuclear translocation activity or whether the overall stability will be affected. The output states whether the mutation is deleterious or benign, and if it is deleterious, gives the possible mechanism(s of loss-of-function. This web-based tool, freely available at http://bioschool.iitd.ernet.in/DelMut/, is the first of its kind to provide a platform for researchers and clinicians, to infer the functional consequences of ANG mutations and correlate their possible association with ALS ahead of experimental findings.

  10. The role of globalization in drug development and access to orphan drugs: orphan drug legislation in the US/EU and in Latin America [v1; ref status: indexed, http://f1000r.es/3ix

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    Renée J.G. Arnold

    2015-02-01

    Full Text Available Compared to a decade ago, nearly three times as many drugs for rare diseases are slated for development. This article addresses the market access issues associated with orphan drug status in Europe and the United States in contrast to the legislation in five Latin American (LA countries that have made strides in this regard--Mexico, Brazil, Colombia, Chile and Argentina. Based on the success of orphan drug legislation in the EU and US, LA countries should strive to adopt similar strategies with regard to rare diseases and drug development. With the implementation of new targeted regulations, reimbursement strategies, and drug approvals, accessibility to treatment will be improved for people afflicted with rare diseases in these developing countries.

  11. Case Report: retained gutta-percha as a cause for persistent maxillary sinusitis and pain [v2; ref status: indexed, http://f1000r.es/3c6

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    Benjamin L. Hodnett

    2014-04-01

    Full Text Available Dental sources of infection can produce acute and chronic maxillary sinusitis. In some cases, the source of the infection may be related to the presence of endodontic materials in the oral cavity. In this article, we report a case of retained gutta-percha in the maxillary sinus resulting in chronic sinusitis.

  12. Transgenic supplementation of SIRT1 fails to alleviate acute loss of nigrostriatal dopamine neurons and gliosis in a mouse model of MPTP-induced parkinsonism [v1; ref status: indexed, http://f1000r.es/5a9

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    Yasuko Kitao

    2015-05-01

    Full Text Available Background Dopamine (DA neuron-selective uptake and toxicity of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP causes parkinsonism in humans. Loss of DA neurons via mitochondrial damage and oxidative stress is reproduced by systemic injection of MPTP in animals, which serves as models of parkinsonism and Parkinson’s disease (PD. This study aimed to test whether pan-neural supplementation of the longevity-related, pleiotropic deacetylase SIRT1, which confers partial tolerance to at least three models of stroke and neurodegeneration, could also alleviate MPTP-induced acute pathological changes in nigrostriatal DA neurons and neighboring glia. Results We employed a line of prion promoter-driven Sirt1-transgenic (Sirt1Tg mice that chronically overexpress murine SIRT1 in the brain and spinal cord. Sirt1Tg and wild-type (WT male littermates (3‒4 months old were subjected to intraperitoneal injection of MPTP. Acute histopathological changes in the midbrain and striatum (caudoputamen were assessed with serial coronal sections triply labeled for tyrosine hydroxylase (TH, glial fibrillary acidic protein (GFAP, and nuclear DNA. In the substantia nigra pars compacta (SNpc of the midbrain, the number of TH-positive neurons and the reactive gliosis were comparable between the Sirt1Tg and WT littermates. In the striatum, the relative fluorescence intensity of TH-positive nerve terminals and the level of gliosis did not differ by the genotypes. Conclusions Sirt1Tg and WT littermate mice exhibited comparable acute histopathological reactions to the systemic injection of MPTP, loss of TH-positive neurons and reactive gliosis. Thus, the genetic supplementation of SIRT1 does not confer histologically recognizable protection on nigrostriatal DA neurons against acute toxicity of MPTP.

  13. Benefit packages for chronic disease outpatients in the New Rural Cooperative Medical Scheme in 32 Chinese counties [v1; ref status: indexed, http://f1000r.es/z2

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    Chuangzhou Xu

    2013-06-01

    Full Text Available Introduction: Chronic disease has become a major problem affecting the health of the Chinese population. In response to this situation, the New Rural Cooperative Medical Scheme (NRCMS has begun to provide health cover for outpatients with chronic disease expenses, made possible by the increased risk pool of previous years. We compare the differences between Benefit Packages for Chronic Diseases Outpatients (BPCDO in order to produce a reference for policy makers. Methods: Information on the various BPCDO was located by searching the official NRCMS website in Chinese, using certain criteria to select the ideal BPCDO. Population coverage, service coverage and cost of coverage were chosen to form the analytical framework for this paper. The diseases were classified according to the World Health Organisation's (WHO International Classification of Diseases (ICD-10. Results: To avoid “moral hazard”, complex processes have been created. This has resulted in chronic disease patients finding it very difficult to become beneficiaries. Forty-one types of chronic diseases were listed in 32 different BPCDO. We found that different counties have different co-payment rates, deductible lines, ceilings, coverage of drugs and tests, appointed hospitals and reimbursement frequencies. Conclusion: High mortality diseases and diseases with a heavier cost burden should be the priority on the list of reimbursement. The BPCDO scheme should be introduced urgently at the national level. It should include twenty-one types of disease and eight essential factors.

  14. Correlating data from different sensors to increase the positive predictive value of alarms: an empiric assessment [v1; ref status: indexed, http://f1000r.es/RKkXdB

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    Yuval Bitan

    2012-11-01

    Full Text Available Objectives: Alarm fatigue from high false alarm rate is a well described phenomenon in the intensive care unit (ICU. Progress to further reduce false alarms must employ a new strategy. Highly sensitive alarms invariably have a very high false alarm rate. Clinically useful alarms have a high Positive-Predictive Value. Our goal is to demonstrate one approach to suppressing false alarms using an algorithm that correlates information across sensors and replicates the ways that human evaluators discriminate artifact from real signal. Methods: After obtaining IRB approval and waiver of informed consent, a set of definitions, (hypovolemia, left ventricular shock, tamponade, hemodynamically significant ventricular tachycardia, and hemodynamically significant supraventricular tachycardia, were installed in the monitors in a 10 bed cardiothoracic ICU and evaluated over an 85 day study period. The logic of the algorithms was intended to replicate the logic of practitioners, and correlated information across sensors in a way similar to that used by practitioners. The performance of the alarms was evaluated via a daily interview with the ICU attending and review of the tracings recorded over the previous 24 hours in the monitor. True alarms and false alarms were identified by an expert clinician, and the performance of the algorithms evaluated using the standard definitions of sensitivity, specificity, positive predictive value, and negative predictive value. Results: Between 1 and 221 instances of defined events occurred over the duration of the study, and the positive predictive value of the definitions varied between 4.1% and 84%. Conclusions: Correlation of information across alarms can suppress artifact, increase the positive predictive value of alarms, and can employ more sophisticated definitions of alarm events than present single-sensor based systems.

  15. Observation of a unique case of metastatic basal cell carcinoma found by radiographic evaluation in a patient with oculocutaneous albinism [v1; ref status: indexed, http://f1000r.es/2lw

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    Mickaila Johnston

    2014-01-01

    Full Text Available Background: Basal cell carcinoma is one of the more common cancers worldwide; 2.8 million are diagnosed annually in the USA.  However, the rate at which it metastasizes is considered very low, between 0.0028 and 0.5%.  For those rare cases in which metastases occur, approximately one third metastasize to the lung.  Case: Presented is a 62-year-old Caucasian male with oculocutaneous albinism and a history of basal cell carcinomas occurring in multiple anatomic sites, most recently at the bilateral forearm and back.  Surveillance PET/CT imaging led to the discovery of no less than 30 lung nodules which were consistent with basal cell carcinoma on biopsy.  Histological features were remarkably similar in both the primary tumor and in the metastases. Conclusion:  An unusual case of a non-head and neck primary basal cell carcinoma metastatic to the lung was discovered on surveillance PET/CT imaging, in a patient with oculocutaneous albinism.

  16. Nephron filtration rate and proximal tubular fluid reabsorption in the Akita mouse model of type I diabetes mellitus [v1; ref status: indexed, http://f1000r.es/yw

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    Jurgen Schnermann

    2013-03-01

    Full Text Available An increase of glomerular filtration rate (hyperfiltration is an early functional change associated with type I or type II diabetes mellitus in patients and animal models. The causes underlying glomerular hyperfiltration are not entirely clear. There is evidence from studies in the streptozotocin model of diabetes in rats that an increase of proximal tubular reabsorption results in the withdrawal of a vasoconstrictor input exerted by the tubuloglomerular feedback (TGF mechanism. In the present study, we have used micropuncture to assess single nephron function in wild type (WT mice and in two strains of type I diabetic Ins2+/- mice in either a C57Bl/6 (Akita or an A1AR-/- background (Akita/A1AR-/- in which TGF is non-functional. Kidney glomerular filtration rate (GFR of anesthetized mice was increased by 25% in Akita mice and by 52% in Akita/A1AR-/-, but did not differ between genotypes when corrected for kidney weight. Single nephron GFR (SNGFR measured by end-proximal fluid collections averaged 11.8 ± 1 nl/min (n=17, 13.05 ± 1.1 nl/min (n=23; p=0.27, and 15.4 ± 0.84 nl/min (n=26; p=0.009 compared to WT; p=0.09 compared to Akita in WT, Akita, and Akita/A1AR-/- mice respectively. Proximal tubular fluid reabsorption was not different between WT and diabetic mice and correlated with SNGFR in all genotypes. We conclude that glomerular hyperfiltration is a primary event in the Akita model of type I diabetes, perhaps driven by an increased filtering surface area, and that it is ameliorated by TGF to the extent that this regulatory system is functional.

  17. Variation in candidate genes CLOCK and ADCYAP1 does not consistently predict differences in migratory behavior in the songbird genus Junco [v1; ref status: indexed, http://f1000r.es/11p

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    Mark P Peterson

    2013-04-01

    Full Text Available Recent studies exploring the molecular genetic basis for migratory variation in animals have identified polymorphisms in two genes (CLOCK and ADCYAP1 that are linked to circadian rhythms and correlate with migratory propensity and phenology among individuals and populations. Results from these initial studies are mixed, however, and additional data are needed to assess the generality and diversity of the molecular mechanisms that regulate the biology of migration. We sequenced CLOCK and ADCYAP1 in 15 populations across the two species of the avian genus Junco, a North American lineage in which multiple recently diverged subspecies and populations range from sedentary to long-distance migrants. We found no consistent associations between allele length and migratory status across the genus for either CLOCK or ADCYAP1. However, within two subspecies groups, populations that migrate longer distances have longer CLOCK alleles on average. Additionally, there was a positive relationship between ADCYAP1 allele length and migratory restlessness (zugunruhe among individuals within one of two captive populations studied—a result similar to those reported previously within captive blackcaps (Sylvia atricapilla. We conclude that, while both ADCYAP1 and CLOCK may correlate with migratory propensity within or among certain populations or species, previously identified relationships between migratory behavior and sequence variants cannot be easily generalized across taxa.

  18. Journal ratings as predictors of articles quality in Arts, Humanities and Social Sciences: an analysis based on the Italian Research Evaluation Exercise [v1; ref status: indexed, http://f1000r.es/5d3

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    Andrea Bonaccorsi

    2015-07-01

    Full Text Available The aim of this paper is to understand whether the probability of receiving positive peer reviews is influenced by having published in an independently assessed, high-ranking journal: we eventually interpret a positive relationship among peer evaluation and journal ranking as evidence that journal ratings are good predictors of article quality. The analysis is based on a large dataset of over 11,500 research articles published in Italy in the period 2004-2010 in the areas of architecture, arts and humanities, history and philosophy, law, sociology and political sciences. These articles received a score by a large number of externally appointed referees in the context of the Italian research assessment exercise (VQR; similarly, journal scores were assigned in a panel-based independent assessment, which involved all academic journals in which Italian scholars have published, carried out under a different procedure. The score of an article is compared with that of the journal it is published in: more specifically, we first estimate an ordered probit model, assessing the probability for a paper of receiving a higher score, the higher the score of the journal; in a second step, we concentrate on the top papers, evaluating the probability of a paper receiving an excellent score having been published in a top-rated journal. In doing so, we control for a number of characteristics of the paper and its author, including the language of publication, the scientific field and its size, the age of the author and the academic status. We add to the literature on journal classification by providing for the first time a large scale test of the robustness of expert-based classification.

  19. Exercise-induced arterial hypertension - an independent factor for hypertrophy and a ticking clock for cardiac fatigue or atrial fibrillation in athletes? [v1; ref status: indexed, http://f1000r.es/3b4

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    Roman Leischik

    2014-05-01

    Full Text Available Background: Exercise-induced arterial hypertension (EIAH leads to myocardial hypertrophy and is associated with a poor prognosis. EIAH might be related to the “cardiac fatigue” caused by endurance training. The goal of this study was to examine whether there is any relationship between EIAH and left ventricular hypertrophy in Ironman-triathletes. Methods: We used echocardiography and spiroergometry to determine the left ventricular mass (LVM, the aerobic/anaerobic thresholds and the steady-state blood pressure of 51 healthy male triathletes. The main inclusion criterion was the participation in at least one middle or long distance triathlon. Results: When comparing triathletes with LVM 220g there was a significant difference between blood pressure values (BP at the anaerobic threshold (185.2± 21.5 mmHg vs. 198.8 ±22.3 mmHg, p=0.037. The spiroergometric results were: maximum oxygen uptake (relative VO2max 57.3 ±7.5ml/min/kg vs. 59.8±9.5ml/min/kg (p=ns. Cut-point analysis for the relationship of BP >170 mmHg at the aerobic threshold and the probability of LVM >220g showed a sensitivity of 95.8%, a specificity of 33.3%, with a positive predictive value of 56.8 %, a good negative predictive value of 90%. The probability of LVM >220g increased with higher BP during exercise (OR: 1.027, 95% CI 1.002-1.052, p= 0.034 or with higher training volume (OR: 1.23, 95% CI 1.04 -1.47, p = 0.019. Echocardiography showed predominantly concentric remodelling, followed by concentric hypertrophy. Conclusion: Significant left ventricular hypertrophy with LVM >220g is associated with higher arterial blood pressure at the aerobic or anaerobic threshold. The endurance athletes with EIAH may require a therapeutic intervention to at least prevent extensive stiffening of the heart muscle and exercise-induced cardiac fatigue.

  20. Case Report: Mammary and rectal metastases from an ovarian cancer: report of two cases and review of literature [v1; ref status: indexed, http://f1000r.es/27k

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    Mounia Amzerin

    2014-10-01

    Full Text Available In this paper we report two interesting cases of metastatic ovarian cancer. The first case is a patient who developed rectal and breast metastases mimicking an inflammatory breast cancer. In the second case, subclinical breast and axillary lymph node metastases were revealed by PET/CT. Metastases in the breast originating from solid tumors are extremely rare. The ovarian primitive is the fourth most common origin. The occurrence of breast metastasis is associated with an advanced disease and a poor prognosis. Their incidence is increasing since they are found more often due to better imaging techniques and to better treatment that, accordingly, improve patients’ survival. Thus, unusual sites of metastases are more and more reported. Indeed, some authors reported the occurrence of colorectal metastases from ovarian cancer. However, they remain much less frequent.

  1. Prostitution use has non sexual functions - case report of a depressed psychiatric out-patient [v2; ref status: indexed, http://f1000r.es/16c

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    Fátima Gysin

    2013-05-01

    Full Text Available Case: A shy, depressed 30 year old male discussed his frequent ego-syntonic indoor prostitution consumption in small peer groups. Several distinctive non-sexual functions of this paid sex habit were identified. Design and method: The patient had 40 hourly psychiatric sessions in the private practice setting over 14 months. The Arizona Sexual Experience Scale was applied to compare the subjective appraisal of both paid sex and sex in a relationship. The informal Social Atom elucidates social preferences and the Operationalized Psychodynamic Diagnostic-procedure was applied to describe a dominant relationship pattern. Results: The paid sex consumption functioned as a proud male life style choice to reinforce the patients fragile identity. The effect on self esteem was a release similar to his favorite past-time of kick-boxing. With paid sex asserted as a group ritual, it was practiced even with frequent erectile dysfunction and when sex with a stable romantic partner was more enjoyable and satisfying. The therapeutic attitude of the female psychiatrist, with her own ethical values, is put in to context with two opposing theories about prostitution: the ‘Sex-Work-model’ and the ‘Oppression-model’. The therapist’s reaction to the patients’ information was seen as a starting point to understanding the intrapsychic function of paid sex as a coping mechanism against depressive feelings. Conclusions: Exploring and understanding prostitution consumption patterns in young men can benefit the treatment of psychiatric disorders in the private practice setting. It is the psychiatrists task to investigate the patients hidden motives behind paid sex use to help patients achieve a greater inner and relational freedom.

  2. Depth-dependent mortality of reef corals following a severe bleaching event: implications for thermal refuges and population recovery [v3; ref status: indexed, http://f1000r.es/2zg

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    Tom C. L. Bridge

    2014-02-01

    Full Text Available Coral bleaching caused by rising sea temperature is a primary cause of coral reef degradation. However, bleaching patterns often show significant spatial variability, therefore identifying locations where local conditions may provide thermal refuges is a high conservation priority. Coral bleaching mortality often diminishes with increasing depth, but clear depth zonation of coral communities and putative limited overlap in species composition between deep and shallow reef habitats has led to the conclusion that deeper reef habitats will provide limited refuge from bleaching for most species. Here, we show that coral mortality following a severe bleaching event diminished sharply with depth. Bleaching-induced mortality of Acropora was approximately 90% at 0-2m, 60% at 3-4 m, yet at 6-8m there was negligible mortality. Importantly, at least two-thirds of the shallow-water (2-3 m Acropora assemblage had a depth range that straddled the transition from high to low mortality. Cold-water upwelling may have contributed to the lower mortality observed in all but the shallowest depths. Our results demonstrate that, in this instance, depth provided a refuge for individuals from a high proportion of species in this Acropora-dominated assemblage. The persistence of deeper populations may provide a critical source of propagules to assist recovery of adjacent shallow-water reefs.

  3. Depth-dependent mortality of reef corals following a severe bleaching event: implications for thermal refuges and population recovery [v2; ref status: indexed, http://f1000r.es/26m

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    Tom C. L. Bridge

    2013-10-01

    Full Text Available Coral bleaching caused by rising sea temperature is a primary cause of coral reef degradation. However, bleaching patterns often show significant spatial variability, therefore identifying locations where local conditions may provide thermal refuges is a high conservation priority. Coral bleaching mortality often diminishes with increasing depth, but clear depth zonation of coral communities and putative limited overlap in species composition between deep and shallow reef habitats has led to the conclusion that deeper reef habitats will provide limited refuge from bleaching for most species. Here, we show that coral mortality following a severe bleaching event diminished sharply with depth. Bleaching-induced mortality of Acropora was approximately 90% at 0-2m, 60% at 3-4 m, yet at 6-8m there was negligible mortality. Importantly, at least two-thirds of the shallow-water (2-3 m Acropora assemblage had a depth range that straddled the transition from high to low mortality. Cold-water upwelling may have contributed to the lower mortality observed in all but the shallowest depths. Our results demonstrate that, in this instance, depth provided a refuge for individuals from a high proportion of species in this Acropora-dominated assemblage. The persistence of deeper populations may provide a critical source of propagules to assist recovery of adjacent shallow-water reefs.

  4. Non-contact radiofrequency-induced reduction of subcutaneous abdominal fat correlates with initial cardiovascular autonomic balance and fat tissue hormones: safety analysis [v1; ref status: indexed, http://f1000r.es/4pj

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    Jiri Pumprla

    2015-02-01

    Full Text Available Background and objective: The non-invasive reduction of subcutaneous abdominal fat became popular in the last decade. Radiofrequency (RF, non-contact, selective-field device Vanquish® has been developed to selectively induce deep fat tissue heating to reduce waist circumference. Our analysis evaluates immediate and sustained effects of this treatment on cardiovascular autonomic function and on selected metabolic parameters. Study design/patients and methods: A retrospective proof-of-concept analysis of RF treatment effects was conducted in 20 individuals with metabolic syndrome, to reduce the subcutaneous abdominal fat. Four 30-minutes treatment sessions (manufacturer´s standard protocol were performed in 1-week intervals. Vital signs, ECG, lab screening, body composition, subcutaneous fat thickness and spectral analysis of heart rate variability (HRV have been examined before, after the 1st and 4th treatment, and at follow-up visits 1 month and 3 months after the treatment. Results: The RF treatment led to a significant reduction of abdominal circumference after the 4th session (p0.59, p<0.04. Conclusions: Our analysis shows that the selective-field RF treatment is safe and efficient for reduction of subcutaneous abdominal fat. While the treatment increases the immediate sympathetic response of the body to deep tissue heating, no sustained change in autonomic function could be recorded at 1 month follow-up. The observed correlation between initial VLF spectral power and waist circumference reduction at follow-up, as well as the association of initial adiponectin values and immediate autonomic response to the treatment might be instrumental for decisions on body contouring strategies.

  5. Interaction of growth hormone receptor/binding protein gene disruption and caloric restriction for insulin sensitivity and attenuated aging [v2; ref status: indexed, http://f1000r.es/5a7

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    Oge Arum

    2015-04-01

    Full Text Available The correlation of physiological sensitivity to insulin (vis-à-vis glycemic regulation and longevity is extensively established, creating a justifiable gerontological interest on whether insulin sensitivity is causative, or even predictive, of some or all phenotypes of slowed senescence (including longevity. The growth hormone receptor/ binding protein gene-disrupted (GHR-KO mouse is the most extensively investigated insulin-sensitive, attenuated aging model. It was reported that, in a manner divergent from similar mutants, GHR-KO mice fail to respond to caloric restriction (CR by altering their insulin sensitivity. We hypothesized that maximized insulin responsiveness is what causes GHR-KO mice to exhibit a suppressed survivorship response to dietary (including caloric restriction; and attempted to refute this hypothesis by assessing the effects of CR on GHR-KO mice for varied slow-aging-associated phenotypes. In contrast to previous reports, we found GHR-KO mice on CR to be less responsive than their ad libitum (A.L. counterparts to the hypoglycemia-inducing effects of insulin. Further, CR had negligible effects on the metabolism or cognition of GHR-KO mice. Therefore, our data suggest that the effects of CR on the insulin sensitivity of GHR-KO mice do not concur with the effects of CR on the aging of GHR-KO mice.

  6. Interaction of growth hormone receptor/binding protein gene disruption and caloric restriction for insulin sensitivity and attenuated aging [v1; ref status: indexed, http://f1000r.es/4fk

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    Oge Arum

    2014-10-01

    Full Text Available The correlation of physiological sensitivity to insulin (vis-à-vis glycemic regulation and longevity is extensively established, creating a justifiable gerontological interest on whether insulin sensitivity is causative, or even predictive, of some or all phenotypes of slowed senescence (including longevity. The growth hormone receptor/ binding protein gene-disrupted (GHR-KO mouse is the most extensively investigated insulin-sensitive, attenuated aging model. It was reported that, in a manner divergent from similar mutants, GHR-KO mice fail to respond to caloric restriction (CR by altering their insulin sensitivity. We hypothesized that maximized insulin responsiveness is what causes GHR-KO mice to exhibit a suppressed survivorship response to dietary (including caloric restriction; and attempted to refute this hypothesis by assessing the effects of CR on GHR-KO mice for varied slow-aging-associated phenotypes. In contrast to previous reports, we found GHR-KO mice on CR to be less responsive than their ad libitum (A.L. counterparts to the hypoglycemia-inducing effects of insulin. Further, CR had negligible effects on the metabolism or cognition of GHR-KO mice. Therefore, our data suggest that the effects of CR on the insulin sensitivity of GHR-KO mice do not concur with the effects of CR on the aging of GHR-KO mice.

  7. The net return from animal activity in agro-ecosystems: trading off benefits from ecosystem services against costs from crop damage [v2; ref status: indexed, http://f1000r.es/3c4

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    Gary W Luck

    2014-04-01

    Full Text Available Animals provide benefits to agriculture through the provision of ecosystem services, but also inflict costs such as damaging crops. These benefits and costs are mostly examined independently, rather than comparing the trade-offs of animal activity in the same system and quantifying the net return from beneficial minus detrimental activities. Here, I examine the net return associated with the activity of seed-eating birds in almond orchards by quantifying the economic costs and benefits of bird consumption of almonds. Pre-harvest, the consumption of harvestable almonds by birds cost growers AUD$57.50 ha-1 when averaged across the entire plantation. Post-harvest, the same bird species provide an ecosystem service by removing mummified nuts from trees that growers otherwise need to remove to reduce threats from fungal infection or insect pest infestations. The value of this ecosystem service ranged from AUD$82.50 ha-1–$332.50 ha-1 based on the replacement costs of mechanical or manual removal of mummified nuts, respectively. Hence, bird consumption of almonds yielded a positive net return of AUD$25–$275 ha-1 averaged across the entire plantation. However, bird activity varied spatially resulting in positive net returns occurring primarily at the edges of crops where activity was higher, compared to negative net returns in crop interiors. Moreover, partial mummy nut removal by birds meant that bird activity may only reduce costs to growers rather than replace these costs completely. Similar cost-benefit trade-offs exist across nature, and quantifying net returns can better inform land management decisions such as when to control pests or promote ecosystem service provision.

  8. Rapamycin-insensitive mTORC1 activity controls eIF4E:4E-BP1 binding [v1; ref status: indexed, http://f1000r.es/NM6hpo

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    Mark Livingstone

    2012-07-01

    Full Text Available The recent development of mammalian target of rapamycin (mTOR kinase domain inhibitors and genetic dissection of rapamycin-sensitive and -insensitive mTOR protein complexes (mTORC1 and mTORC2 have revealed that phosphorylation of the mTOR substrate 4E-BP1 on amino acids Thr37 and/or Thr46 represents a rapamycin-insensitive activity of mTORC1. Despite numerous previous reports utilizing serine (Ser-to-alanine (Ala and threonine (Thr-to-Ala phosphorylation site mutants of 4E-BP1 to assess which post-translational modification(s directly regulate binding to eIF4E, an ambiguous understanding persists. This manuscript demonstrates that the initial, rapamycin-insensitive phosphorylation event at Thr46 is sufficient to prevent eIF4E:4E-BP1 binding. This finding is relevant, particularly as mTOR kinase domain inhibitors continue to be assessed for clinical efficacy, since it clarifies a difference between the action of these second-generation mTOR inhibitors and those of rapamycin analogues.

  9. Case Report: Rare occurrence of Pseudomonas aeruginosa osteomyelitis of the right clavicle in a patient with IgA nephropathy [v1; ref status: indexed, http://f1000r.es/37r

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    Aishwarya Damodaran

    2014-11-01

    Full Text Available We describe the case of a 47 year old patient with proven primary IgA nephropathy who presented with osteomyelitis of the medial end of the right clavicle. The patient was not on immunosuppressive medications. He underwent aspiration curettage and CT scan of the clavicle which yielded pus that grew Pseudomonas aeruginosa. Following treatment with appropriate antibiotic therapy the patient presented a complete recovery of the lesion with no loss of renal function. This case highlights the importance of positive cultures in the choice of the appropriate therapy in an extremely rare case of an immunocompetent patient with osteomyelitis of the clavicle.

  10. Detection of Burkholderia pseudomallei in Sputum using Selective Enrichment Broth and Ashdown’s Medium at Kampong Cham Provincial Hospital, Cambodia [v1; ref status: indexed, http://f1000r.es/4w7

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    Somary Nhem

    2014-12-01

    Full Text Available Melioidosis infection, caused by Burkholderia pseudomallei, is increasingly reported in Cambodia. We hypothesized that implementation of an enhanced sputum testing protocol in a provincial hospital diagnostic microbiology laboratory would increase detection of B. pseudomallei. We tested 241 sputum specimens that were deemed acceptable for culture, comparing culture in selective enrichment broth followed by sub-culture on Ashdown’s medium to standard culture methods. Two specimens (0.8% were positive for B. pseudomallei using the enhanced protocol whereas one specimen (0.4% was positive using standard methods. These findings demonstrate that B. pseudomallei is rarely detected in sputum at this hospital. The low frequency of B. pseudomallei in sputum specimens precludes drawing any conclusions about the relative benefits of an enhanced sputum testing protocol at this site. Promoting clinician awareness of the infection and encouraging utilization of diagnostic microbiology services are likely to be important factors in facilitating identification of melioidosis.

  11. Visualizing and quantifying movement from pre-recorded videos: The spectral time-lapse (STL algorithm [v1; ref status: indexed, http://f1000r.es/2qo

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    Christopher R Madan

    2014-01-01

    Full Text Available When studying animal behaviour within an open environment, movement-related data are often important for behavioural analyses. Therefore, simple and efficient techniques are needed to present and analyze the data of such movements. However, it is challenging to present both spatial and temporal information of movements within a two-dimensional image representation. To address this challenge, we developed the spectral time-lapse (STL algorithm that re-codes an animal’s position at every time point with a time-specific color, and overlays it with a reference frame of the video, to produce a summary image. We additionally incorporated automated motion tracking, such that the animal’s position can be extracted and summary statistics such as path length and duration can be calculated, as well as instantaneous velocity and acceleration. Here we describe the STL algorithm and offer a freely available MATLAB toolbox that implements the algorithm and allows for a large degree of end-user control and flexibility.

  12. Student perception about working in rural United States/Canada after graduation: a study in an offshore Caribbean medical school [v1; ref status: indexed, http://f1000r.es/4vz

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    P Ravi Shankar

    2014-12-01

    Full Text Available Introduction: Rural residents of the United States (US and Canada face problems in accessing healthcare. International medical graduates (IMGs play an important role in delivering rural healthcare. IMGs from Caribbean medical schools have the highest proportion of physicians in primary care.  Xavier University School of Medicines admits students from the US, Canada and other countries to the undergraduate medical (MD course and also offers a premedical program. The present study was conducted to obtain student perception about working in rural US/Canada after graduation.   Methods: The study was conducted among premedical and preclinical undergraduate medical (MD students during October 2014. The questionnaire used was modified from a previous study. Semester of study, gender, nationality, place of residence and occupation of parents were noted. Information about whether students plan to work in rural US/Canada after graduation, possible reasons why doctors are reluctant to work in rural areas, how the government can encourage rural practice, possible problems respondents anticipate while working in rural areas were among the topics studied. Results: Ninety nine of the 108 students (91.7% participated. Forty respondents were in favor of working in rural US/Canada after graduation. Respondents mentioned good housing, regular electricity, water supply, telecommunication facilities, and schools for education of children as important conditions to be fulfilled. The government should provide higher salaries to rural doctors, help with loan repayment, and provide opportunities for professional growth.  Potential problems mentioned were difficulty in being accepted by the rural community, problems in convincing patients to follow medical advice, lack of exposure to rural life among the respondents, and cultural issues. Conclusions: About 40% of respondents would consider working in rural US/Canada. Conditions required to be fulfilled have been mentioned above. Graduates from Caribbean medical schools have a role in addressing rural physician shortage. Similar studies in other offshore Caribbean medical schools are required as Caribbean IMGs make an important contribution to the rural US and Canadian health workforce.

  13. Student perception about working in rural United States/Canada after graduation: a study in an offshore Caribbean medical school [v2; ref status: indexed, http://f1000r.es/5ac

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    P Ravi Shankar

    2015-04-01

    Full Text Available Introduction: Rural residents of the United States (US and Canada face problems in accessing healthcare. International medical graduates (IMGs play an important role in delivering rural healthcare. IMGs from Caribbean medical schools have the highest proportion of physicians in primary care.  Xavier University School of Medicines admits students from the US, Canada and other countries to the undergraduate medical (MD course and also offers a premedical program. The present study was conducted to obtain student perception about working in rural US/Canada after graduation.   Methods: The study was conducted among premedical and preclinical undergraduate medical (MD students during October 2014. The questionnaire used was modified from a previous study. Semester of study, gender, nationality, place of residence and occupation of parents were noted. Information about whether students plan to work in rural US/Canada after graduation, possible reasons why doctors are reluctant to work in rural areas, how the government can encourage rural practice, possible problems respondents anticipate while working in rural areas were among the topics studied. Results: Ninety nine of the 108 students (91.7% participated. Forty respondents were in favor of working in rural US/Canada after graduation. Respondents mentioned good housing, regular electricity, water supply, telecommunication facilities, and schools for education of children as important conditions to be fulfilled. The government should provide higher salaries to rural doctors, help with loan repayment, and provide opportunities for professional growth.  Potential problems mentioned were difficulty in being accepted by the rural community, problems in convincing patients to follow medical advice, lack of exposure to rural life among the respondents, and cultural issues. Conclusions: About 40% of respondents would consider working in rural US/Canada. Conditions required to be fulfilled have been mentioned above. Graduates from Caribbean medical schools have a role in addressing rural physician shortage. Similar studies in other offshore Caribbean medical schools are required as Caribbean IMGs make an important contribution to the rural US and Canadian health workforce.

  14. A salp bloom (Tunicata, Thaliacea along the Apulian coast and in the Otranto Channel between March-May 2013 [v1; ref status: indexed, http://f1000r.es/1ok

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    Ferdinando Boero

    2013-09-01

    Full Text Available Between March-May 2013 a massive Salpa maxima bloom was recorded by a citizen science study along the Ionian and Adriatic coast of the Salento peninsula (Italy. Citizen records were substantiated with field inspections along the coast and during an oceanographic campaign in the Otranto Channel. Salps clogged nets, impairing fishing activities along the coast. Swimmers were scared by the gelatinous appearance of the salps, and thought they were jellyfish. At the end of the bloom the dead bodies of the colonies, that were up to 6-7 m long, were accumulated along the coast and stirred by the waves, forming foams along dozens of kilometers of coast. The bloom also occurred at the Tremiti Islands, north of the Gargano Peninsula. The possible impacts of such events on the  functioning of pelagic systems are discussed.

  15. Reversion of the Arabidopsis rpn12a-1 exon-trap mutation by an intragenic suppressor that weakens the chimeric 5’ splice site [v2; ref status: indexed, http://f1000r.es/18y

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    Jasmina Kurepa

    2013-06-01

    Full Text Available Background: In the Arabidopsis 26S proteasome mutant rpn12a-1, an exon-trap T-DNA is inserted 531 base pairs downstream of the RPN12a STOP codon. We have previously shown that this insertion activates a STOP codon-associated latent 5' splice site that competes with the polyadenylation signal during processing of the pre-mRNA. As a result of this dual input from splicing and polyadenylation in the rpn12a-1 mutant, two RPN12a transcripts are produced and they encode the wild-type RPN12a and a chimeric RPN12a-NPTII protein. Both proteins form complexes with other proteasome subunits leading to the formation of wild-type and mutant proteasome versions. The net result of this heterogeneity of proteasome particles is a reduction of total cellular proteasome activity. One of the consequences of reduced proteasomal activity is decreased sensitivity to the major plant hormone cytokinin. Methods: We performed ethyl methanesulfonate mutagenesis of rpn12a-1 and isolated revertants with wild-type cytokinin sensitivity. Results: We describe the isolation and analyses of suppressor of rpn12a-1 (sor1. The sor1 mutation is intragenic and located at the fifth position of the chimeric intron. This mutation weakens the activated 5' splice site associated with the STOP codon and tilts the processing of the RPN12a mRNA back towards polyadenylation. Conclusions: These results validate our earlier interpretation of the unusual nature of the rpn12a-1 mutation. Furthermore, the data show that optimal 26S proteasome activity requires RPN12a accumulation beyond a critical threshold. Finally, this finding reinforces our previous conclusion that proteasome function is critical for the cytokinin-dependent regulation of plant growth.

  16. Tweets from the forest: using Twitter to increase student engagement in an undergraduate field biology course [v1; ref status: indexed, http://f1000r.es/56w

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    Lauren Soluk

    2015-03-01

    Full Text Available Twitter is a cold medium that allows users to deliver content-rich but small packets of information to other users, and provides an opportunity for active and collaborative communication. In an education setting, this social media tool has potential to increase active learning opportunities, and increase student engagement with course content. The effects of Twitter on learning dynamics was tested in a field biology course offered by a large Canadian University: 29 students agreed to take part in the Twitter project and quantitative and qualitative data were collected, including survey data from 18 students. Students published 200% more public Tweets than what was required, and interacted frequently with the instructor and teaching assistant, their peers, and users external to the course. Almost 80% of students stated that Twitter increased opportunities for among-group communication, and 94% of students felt this kind of collaborative communication was beneficial to their learning. Although students did not think they would use Twitter after the course was over, 77% of the students still felt it was a good learning tool, and 67% of students felt Twitter had a positive impact on how they engaged with course content. These results suggest social media tools such as Twitter can help achieve active and collaborative learning in higher education.

  17. A resistant-starch enriched yogurt: fermentability, sensory characteristics, and a pilot study in children [v1; ref status: indexed, http://f1000r.es/5cb

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    Kayanush Aryana

    2015-06-01

    Full Text Available The rising prevalence of obesity and the vulnerability of the pediatric age group have highlighted the critical need for a careful consideration of effective, safe, remedial and preventive dietary interventions.  Amylose starch (RS2 from high-amylose maize (HAM ferments in the gut and affects body weight.   One hundred and ten children, of 7-8 (n=91 or 13-14 (n=19 years of age scored the sensory qualities of a yogurt supplemented with either HAM-RS2 or an amylopectin starch.  The amylopectin starch yogurt was preferred to the HAM-RS2-enriched yogurt by 7-8 year old panelists (P<0.0001.  Appearance, taste, and sandiness scores given by 13- to 14-year-old panelists were more favorable for the amylopectin starch yogurt than for HAM-RS2-enriched yogurt (P<0.05.  HAM-RS2 supplementation resulted in acceptable (≥6 on a 1-9 scale sensory and hedonic ratings of the yogurt in 74% of subjects.  Four children consumed a HAM-RS2-enriched yogurt for four weeks to test its fermentability in a clinical trial.  Three adolescents, but not the single pre-pubertal child, had reduced stool pH (P=0.1 and increased stool short-chain fatty acids (SCFAs (P<0.05 including increased fecal acetate (P=0.02, and butyrate (P=0.089 from resistant starch (RS fermentation and isobutyrate (P=0.01 from protein fermentation post-treatment suggesting a favorable change to the gut microbiota.  HAM-RS2 was not modified by pasteurization of the yogurt, and may be a palatable way to increase fiber intake and stimulate colonic fermentation in adolescents.  Future studies are planned to determine the concentration of HAM-RS2 that offers the optimal safe and effective strategy to prevent excessive fat gain in children.

  18. Casanovas are liars: behavioral syndromes, sperm competition risk, and the evolution of deceptive male mating behavior in live-bearing fishes [v3; ref status: indexed, http://f1000r.es/1zi

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    David Bierbach

    2013-10-01

    Full Text Available Male reproductive biology can by characterized through competition over mates as well as mate choice. Multiple mating and male mate choice copying, especially in internally fertilizing species, set the stage for increased sperm competition, i.e., sperm of two or more males can compete for fertilization of the female’s ova. In the internally fertilizing fish Poecilia mexicana, males respond to the presence of rivals with reduced expression of mating preferences (audience effect, thereby lowering the risk of by-standing rivals copying their mate choice. Also, males interact initially more with a non-preferred female when observed by a rival, which has been interpreted in previous studies as a strategy to mislead rivals, again reducing sperm competition risk (SCR. Nevertheless, species might differ consistently in their expression of aggressive and reproductive behaviors, possibly due to varying levels of SCR. In the current study, we present a unique data set comprising ten poeciliid species (in two cases including multiple populations and ask whether species can be characterized through consistent differences in the expression of aggression, sexual activity and changes in mate choice under increased SCR. We found consistent species-specific differences in aggressive behavior, sexual activity as well as in the level of misleading behavior, while decreased preference expression under increased SCR was a general feature of all but one species examined. Furthermore, mean sexual activity correlated positively with the occurrence of potentially misleading behavior. An alternative explanation for audience effects would be that males attempt to avoid aggressive encounters, which would predict stronger audience effects in more aggressive species. We demonstrate a positive correlation between mean aggressiveness and sexual activity (suggesting a hormonal link as a mechanistic explanation, but did not detect a correlation between aggressiveness and audience effects. Suites of correlated behavioral tendencies are termed behavioral syndromes, and our present study provides correlational evidence for the evolutionary significance of SCR in shaping a behavioral syndrome at the species level across poeciliid taxa.

  19. Improving educational environment in medical colleges through transactional analysis practice of teachers [v1; ref status: indexed, http://f1000r.es/R3KKeG

    Directory of Open Access Journals (Sweden)

    Marina Rajan

    2012-10-01

    Full Text Available Context: A FAIMER (Foundation for Advancement in International Medical Education and Research fellow organized a comprehensive faculty development program to improve faculty awareness resulting in changed teaching practices and better teacher student relationships using Transactional Analysis (TA. Practicing TA tools help development of ‘awareness’ about intrapersonal and interpersonal processes. Objectives: To improve self-awareness among medical educators. To bring about self-directed change in practices among medical educators. To assess usefulness of TA tools for the same.Methods: An experienced trainer conducted a basic course (12 hours in TA for faculty members. The PAC model of personality structure, functional fluency model of personal functioning, stroke theory on motivation, passivity and script theories of adult functional styles were taught experientially with examples from the Medical Education Scenario. Self-reported improvement in awareness and changes in practices were assessed immediately after, at three months, and one year after training. Findings: The mean improvement in self-'awareness' is 13.3% (95% C.I 9.3-17.2 among nineteen participants. This persists one year after training. Changes in practices within a year include, collecting feedback, new teaching styles and better relationship with students. Discussion and Conclusions: These findings demonstrate sustainable and measurable improvement in self-awareness by practice of TA tools. Improvement in self-'awareness' of faculty resulted in self-directed changes in teaching practices. Medical faculty has judged the TA tools effective for improving self-awareness leading to self-directed changes.

  20. Can primary care nurse administered pelvic floor muscle training (PFMT be implemented for the prevention and treatment of urinary incontinence? A study protocol [v1; ref status: indexed, http://f1000r.es/wo

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    Sue Child

    2013-02-01

    Full Text Available Background: We aim to evaluate if Pelvic Floor Muscle Training (PFMT delivered in primary care results in fewer referrals to secondary care for urinary incontinence (UI, thereby reducing the number and associated costs of surgical procedures for UI. Methods / design: The study will consist of two populations – a prevention group and a treatment group who will both be offered PFMT in primary care. The prevention group will consist of parous women aged 25-64 attending for a routine cervical smear. Their pelvic floor will be assessed using the Modified Oxford Scale (MOS and a baseline data form will be completed that asks about the frequency and associated bother of urine leakage. From the answers given, the group will be subdivided into two groups. The first (prevention group will be subdivided into a primary prevention arm (no symptoms of urinary incontinence and pelvic floor strength ≤2 on MOS and a secondary prevention arm (women reporting symptoms of urine leakage irrespective of MOS. The second (treatment group will be women of any age who may or may not have had a vaginal birth presenting to their GP with UI. Semi-structured, in-depth interviews will be conducted with a subset of patients and staff with the aim of identifying barriers and facilitators in delivering PFMT in primary care. Discussion: A recently completed community study showed good outcomes with practice nurse delivery of PFMT. We suggest if this were to be implemented more widely it would reduce the need for referral to secondary care. We believe that this study will show whether implementing a package of PFMT delivered in primary care can treat as well as prevent UI and will also be helpful in exploring the benefits / drawbacks of such implementation, thus providing lessons for implementation in other Primary Care Trusts (PCTs.