Post Irradiation TEM Investigation of ZrN Coated U(Mo) Particles Prepared with FIB

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

Van Renterghem, W.; Leenaers, A.; Van den Berghe, S.

2015-10-01

In the framework of the Selenium project, two dispersion fuel plates were fabricated with Si and ZrN coated fuel particles and irradiated in the Br2 reactor of SCK•CEN to high burn-up. The first analysis of the irradiated plate proved the reduced swelling of the fuel plate and interaction layer growth up to 70% burn-up. The question was raised how the structure of the interaction layer had been affected by the irradiation and how the structure of the fuel particles had evolved. Hereto, samples from the ZrN coated UMo particles were prepared for transmission electron microscopy (TEM) using focused ion beammore » milling (FIB) at INL. The FIB technique allowed to precisely select the area of the interaction layer and/or fuel to produce a sample that is TEM transparent over an area of 20 by 20 µm. In this contribution, the first TEM results will be presented from the 66% burn-up sample.« less

Making the practically impossible "Merely difficult"--Cryogenic FIB lift-out for "Damage free" soft matter imaging.

PubMed

Parmenter, Christopher D J; Fay, Michael W; Hartfield, Cheryl; Eltaher, Hoda M

2016-04-01

The preparation of thinned lamellae from bulk samples for transmission electron microscopy (TEM) analysis has been possible in the focussed ion beam scanning electron microscope (FIB-SEM) for over 20 years via the in situ lift-out method. Lift-out offers a fast and site specific preparation method for TEM analysis, typically in the field of materials science. More recently it has been applied to a low-water content biological sample (Rubino 2012). This work presents the successful lift-out of high-water content lamellae, under cryogenic conditions (cryo-FIB lift-out) and using a nanomanipulator retaining its full range of motion, which are advances on the work previously done by Rubino (2012). Strategies are explored for maintaining cryogenic conditions, grid attachment using cryo-condensation of water and protection of the lamella when transferring to the TEM. © 2016 Wiley Periodicals, Inc.

In situ hydride formation in titanium during focused ion milling.

PubMed

Ding, Rengen; Jones, Ian P

2011-01-01

It is well known that titanium and its alloys are sensitive to electrolytes and thus hydrides are commonly observed in electropolished foils. In this study, focused ion beam (FIB) milling was used to prepare thin foils of titanium and its alloys for transmission electron microscopy. The results show the following: (i) titanium hydrides were observed in pure titanium, (ii) the preparation of a bulk sample in water or acid solution resulted in the formation of more hydrides and (iii) FIB milling aids the precipitation of hydrides, but there were never any hydrides in Ti64 and Ti5553.

Glancing-incidence focussed ion beam milling: A coherent X-ray diffraction study of 3D nano-scale lattice strains and crystal defects

DOE PAGES

Hofmann, Felix; Harder, Ross J.; Liu, Wenjun; ...

2018-05-11

Here, this study presents a detailed examination of the lattice distortions introduced by glancing incidence Focussed Ion Beam (FIB) milling. Using non-destructive multi-reflection Bragg coherent X-ray diffraction we probe damage formation in an initially pristine gold micro-crystal following several stages of FIB milling. These experiments allow access to the full lattice strain tensor in the micro-crystal with ~25 nm 3D spatial resolution, enabling a nano-scale analysis of residual lattice strains and defects formed. Our results show that 30 keV glancing incidence milling produces fewer large defects than normal incidence milling at the same energy. However the resulting residual lattice strainsmore » have similar magnitude and extend up to ~50 nm into the sample. At the edges of the milled surface, where the ion-beam tails impact the sample at near-normal incidence, large dislocation loops with a range of Burgers vectors are formed. Further glancing incidence FIB polishing with 5 keV ion energy removes these dislocation loops and reduces the lattice strains caused by higher energy FIB milling. However, even at the lower ion energy, damage-induced lattice strains are present within a ~20 nm thick surface layer. These results highlight the need for careful consideration and management of FIB damage. They also show that low-energy FIB-milling is an effective tool for removing FIB-milling induced lattice strains. This is important for the preparation of micro-mechanical test specimens and strain microscopy samples.« less

Glancing-incidence focussed ion beam milling: A coherent X-ray diffraction study of 3D nano-scale lattice strains and crystal defects

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

Hofmann, Felix; Harder, Ross J.; Liu, Wenjun

Here, this study presents a detailed examination of the lattice distortions introduced by glancing incidence Focussed Ion Beam (FIB) milling. Using non-destructive multi-reflection Bragg coherent X-ray diffraction we probe damage formation in an initially pristine gold micro-crystal following several stages of FIB milling. These experiments allow access to the full lattice strain tensor in the micro-crystal with ~25 nm 3D spatial resolution, enabling a nano-scale analysis of residual lattice strains and defects formed. Our results show that 30 keV glancing incidence milling produces fewer large defects than normal incidence milling at the same energy. However the resulting residual lattice strainsmore » have similar magnitude and extend up to ~50 nm into the sample. At the edges of the milled surface, where the ion-beam tails impact the sample at near-normal incidence, large dislocation loops with a range of Burgers vectors are formed. Further glancing incidence FIB polishing with 5 keV ion energy removes these dislocation loops and reduces the lattice strains caused by higher energy FIB milling. However, even at the lower ion energy, damage-induced lattice strains are present within a ~20 nm thick surface layer. These results highlight the need for careful consideration and management of FIB damage. They also show that low-energy FIB-milling is an effective tool for removing FIB-milling induced lattice strains. This is important for the preparation of micro-mechanical test specimens and strain microscopy samples.« less

Si amorphization by focused ion beam milling: Point defect model with dynamic BCA simulation and experimental validation.

PubMed

Huang, J; Loeffler, M; Muehle, U; Moeller, W; Mulders, J J L; Kwakman, L F Tz; Van Dorp, W F; Zschech, E

2018-01-01

A Ga focused ion beam (FIB) is often used in transmission electron microscopy (TEM) analysis sample preparation. In case of a crystalline Si sample, an amorphous near-surface layer is formed by the FIB process. In order to optimize the FIB recipe by minimizing the amorphization, it is important to predict the amorphous layer thickness from simulation. Molecular Dynamics (MD) simulation has been used to describe the amorphization, however, it is limited by computational power for a realistic FIB process simulation. On the other hand, Binary Collision Approximation (BCA) simulation is able and has been used to simulate ion-solid interaction process at a realistic scale. In this study, a Point Defect Density approach is introduced to a dynamic BCA simulation, considering dynamic ion-solid interactions. We used this method to predict the c-Si amorphization caused by FIB milling on Si. To validate the method, dedicated TEM studies are performed. It shows that the amorphous layer thickness predicted by the numerical simulation is consistent with the experimental data. In summary, the thickness of the near-surface Si amorphization layer caused by FIB milling can be well predicted using the Point Defect Density approach within the dynamic BCA model. Copyright © 2017 Elsevier B.V. All rights reserved.

A novel approach to TEM preparation with a (7-axis stage) triple-beam FIB-SEM system

NASA Astrophysics Data System (ADS)

Clarke, Jamil J.

2015-10-01

Preparation of lamellae from bulk to grid for Cs-corrected Transmission Electron Microscope (TEM) observation has mostly become routine work on the latest FIB-SEM systems, with standardized techniques that often are left to automation for the initial steps. The finalization of lamellae however, has mostly become, non-routine, non-repeatable and often driven by user experience level in most cases to produce high quality damage-less cross section. Materials processing of the latest technologies, with ever-shrinking Nano-sized structures pose challenges to modern FIB-SEM systems. This can often lead to specialized techniques and hyper-specific functions for producing ultra-thin high quality lamellae that often are lab specific, preventing practical use of such techniques across multiple materials and applications. Several factors that should be incorporated in processing fine structured materials successfully include how the use of electron and ion scan conditions can affect a thin section during ion milling, the type of ion species applied for material processing during the finalization of lamellae with gallium ions or of a smaller ion species type such as Ar/Xe, sample orientation of the lamella during the thinning process which is linked to ion beam incident angle as a direct relationship in the creation of waterfall effects or curtain effects, and how software can be employed to aid in the reduction of these artifacts with reproducible results regardless of FIB-SEM experience for site-specific lift outs. A traditional TEM preparation was performed of a fine structure specimen in pursuit of a process technique to produce a high quality TEM lamella which would address all of the factors mentioned. These new capabilities have been refined and improved upon during the FIB-SEM design and development stages with an end result of a new approach that yields an improvement in quality by the reduction of common ion milling artifacts such as curtain effects, amorphous material, and better pin pointing of the area of interest while reducing overall processing time for the TEM sample preparation process and enhancing repeatability through ease of use via software controls. The development of these new technologies, incorporating a third Ar/Xe ion beam column in conjunction with the electron and gallium ion beam column, a 7-axis stage for enhanced sample orientation with tilt functions in two axes and automated swing control along with a host of additional functions which address the factors aforementioned such as electron and ion scan techniques and curtain effect removal by the use of hardware and software components that are key to reduce typical FIB related artifacts, all of which are called "ACE [Anti Curtaining Effect] Technologies" are explained. The overall developments of these technologies are to address a significant point that productivity, throughput and repeatability are comprised by synergy between the user, application, software and hardware within a FIB-SEM system. The latest Hitachi FIB-SEM platform offers these innovations for reliability, repeatability and high quality lamella preparation for Cs-corrected (S)TEMs.

KSC-07pd1491

NASA Image and Video Library

2007-06-13

KENNEDY SPACE CENTER, FLA. -- United Space Alliance employees prepared three test articles that will be used in wind tunnel testing by NASA to collect data for analysis of the detached Flexible Insulation Blanket, or FIB, on Atlantis. The test articles each feature three tiles (Low Temperature Reusable Surface Insulation, or LRSI) affixed next to two FIB blankets, simulating the thermal protection system set-up on Atlantis' OMS pod in the vicinity of the in-flight anomaly. These test articles were flown to Texas the morning of June 14. The TPS team at KSC has also provided a total of 22 FIB samples for other testing and analysis. Photo credit: NASA/Kim Shiflett

FIB-SEM imaging of carbon nanotubes in mouse lung tissue.

PubMed

Købler, Carsten; Saber, Anne Thoustrup; Jacobsen, Nicklas Raun; Wallin, Håkan; Vogel, Ulla; Qvortrup, Klaus; Mølhave, Kristian

2014-06-01

Ultrastructural characterisation is important for understanding carbon nanotube (CNT) toxicity and how the CNTs interact with cells and tissues. The standard method for this involves using transmission electron microscopy (TEM). However, in particular, the sample preparation, using a microtome to cut thin sample sections for TEM, can be challenging for investigation of regions with agglomerations of large and stiff CNTs because the CNTs cut with difficulty. As a consequence, the sectioning diamond knife may be damaged and the uncut CNTs are left protruding from the embedded block surface excluding them from TEM analysis. To provide an alternative to ultramicrotomy and subsequent TEM imaging, we studied focused ion beam scanning electron microscopy (FIB-SEM) of CNTs in the lungs of mice, and we evaluated the applicability of the method compared to TEM. FIB-SEM can provide serial section volume imaging not easily obtained with TEM, but it is time-consuming to locate CNTs in the tissue. We demonstrate that protruding CNTs after ultramicrotomy can be used to locate the region of interest, and we present FIB-SEM images of CNTs in lung tissue. FIB-SEM imaging was applied to lung tissue from mice which had been intratracheally instilled with two different multiwalled CNTs; one being short and thin, and the other longer and thicker. FIB-SEM was found to be most suitable for detection of the large CNTs (Ø ca. 70 nm), and to be well suited for studying CNT agglomerates in biological samples which is challenging using standard TEM techniques.

3D lattice distortions and defect structures in ion-implanted nano-crystals

PubMed Central

Hofmann, Felix; Tarleton, Edmund; Harder, Ross J.; Phillips, Nicholas W.; Ma, Pui-Wai; Clark, Jesse N.; Robinson, Ian K.; Abbey, Brian; Liu, Wenjun; Beck, Christian E.

2017-01-01

Focussed Ion Beam (FIB) milling is a mainstay of nano-scale machining. By manipulating a tightly focussed beam of energetic ions, often gallium (Ga+), FIB can sculpt nanostructures via localised sputtering. This ability to cut solid matter on the nano-scale revolutionised sample preparation across the life, earth and materials sciences. Despite its widespread usage, detailed understanding of the FIB-induced structural damage, intrinsic to the technique, remains elusive. Here we examine the defects caused by FIB in initially pristine objects. Using Bragg Coherent X-ray Diffraction Imaging (BCDI), we are able to spatially-resolve the full lattice strain tensor in FIB-milled gold nano-crystals. We find that every use of FIB causes large lattice distortions. Even very low ion doses, typical of FIB imaging and previously thought negligible, have a dramatic effect. Our results are consistent with a damage microstructure dominated by vacancies, highlighting the importance of free-surfaces in determining which defects are retained. At larger ion fluences, used during FIB-milling, we observe an extended dislocation network that causes stresses far beyond the bulk tensile strength of gold. These observations provide new fundamental insight into the nature of the damage created and the defects that lead to a surprisingly inhomogeneous morphology. PMID:28383028

3D lattice distortions and defect structures in ion-implanted nano-crystals.

PubMed

Hofmann, Felix; Tarleton, Edmund; Harder, Ross J; Phillips, Nicholas W; Ma, Pui-Wai; Clark, Jesse N; Robinson, Ian K; Abbey, Brian; Liu, Wenjun; Beck, Christian E

2017-04-06

Focussed Ion Beam (FIB) milling is a mainstay of nano-scale machining. By manipulating a tightly focussed beam of energetic ions, often gallium (Ga + ), FIB can sculpt nanostructures via localised sputtering. This ability to cut solid matter on the nano-scale revolutionised sample preparation across the life, earth and materials sciences. Despite its widespread usage, detailed understanding of the FIB-induced structural damage, intrinsic to the technique, remains elusive. Here we examine the defects caused by FIB in initially pristine objects. Using Bragg Coherent X-ray Diffraction Imaging (BCDI), we are able to spatially-resolve the full lattice strain tensor in FIB-milled gold nano-crystals. We find that every use of FIB causes large lattice distortions. Even very low ion doses, typical of FIB imaging and previously thought negligible, have a dramatic effect. Our results are consistent with a damage microstructure dominated by vacancies, highlighting the importance of free-surfaces in determining which defects are retained. At larger ion fluences, used during FIB-milling, we observe an extended dislocation network that causes stresses far beyond the bulk tensile strength of gold. These observations provide new fundamental insight into the nature of the damage created and the defects that lead to a surprisingly inhomogeneous morphology.

A Coordinated Focused Ion Beam/Ultramicrotomy Technique for Serial Sectioning of Hayabusa Particles and Other Returned Samples

NASA Technical Reports Server (NTRS)

Berger, E. L.; Keller, L. P.

2014-01-01

Recent sample return missions, such as NASA's Stardust mission to comet 81P/Wild 2 and JAXA's Hayabusa mission to asteroid 25143 Itokawa, have returned particulate samples (typically 5-50 µm) that pose tremendous challenges to coordinated analysis using a variety of nano- and micro-beam techniques. The ability to glean maximal information from individual particles has become increasingly important and depends critically on how the samples are prepared for analysis. This also holds true for other extraterrestrial materials, including interplanetary dust particles, micrometeorites and lunar regolith grains. Traditionally, particulate samples have been prepared using microtomy techniques (e.g., [1]). However, for hard mineral particles ?20 µm, microtome thin sections are compromised by severe chatter and sample loss. For these difficult samples, we have developed a hybrid technique that combines traditional ultramicrotomy with focused ion beam (FIB) techniques, allowing for the in situ investigation of grain surfaces and interiors. Using this method, we have increased the number of FIB-SEM prepared sections that can be recovered from a particle with dimensions on the order of tens of µms. These sections can be subsequently analyzed using a variety of electron beam techniques. Here, we demonstrate this sample preparation technique on individual lunar regolith grains in order to study their space-weathered surfaces. We plan to extend these efforts to analyses of individual Hayabusa samples.

Comparison of mechanical characteristics of focused ion beam fabricated silicon nanowires

NASA Astrophysics Data System (ADS)

Ina, Ginnosuke; Fujii, Tatsuya; Kozeki, Takahiro; Miura, Eri; Inoue, Shozo; Namazu, Takahiro

2017-06-01

In this study, we investigate the effects of focused ion beam (FIB)-induced damage and specimen size on the mechanical properties of Si nanowires (NWs) by a microelectromechanical system (MEMS)-based tensile testing technique. By an FIB fabrication technique, three types of Si NWs, which are as-FIB-fabricated, annealed, and FIB-implanted NWs, are prepared. A sacrificial-oxidized NW is also prepared to compare the mechanical properties of these FIB-based NWs. The quasi-static uniaxial tensile tests of all the NWs are conducted by scanning electron microscopy (SEM). The fabrication process and specimen size dependences on Young’s modulus and fracture strength are observed. Annealing is effective for improving the Young’s modulus of the FIB-damaged Si. Transmission electron microscopy (TEM) suggests that the mechanism behind the process dependence on the mechanical characteristics is related to the crystallinity of the FIB-damaged portion.

High Resolution Chemical Study of ALH84001

NASA Technical Reports Server (NTRS)

Conrad, Pamela G.; Douglas, Susanne; Kuhlman, Kimberly R.

2001-01-01

We have studied the chemistry of a sample of the SNC meteorite ALH84001 using an environmental scanning electron microscope (ESEM) with an energy dispersive chemical analytical detector and a focused ion beam secondary ion mass spectrometer (FIB-SIMS). Here we present the chemical data, both spectra and images, from two techniques that do not require sample preparation with a conductive coating, thus eliminating the possibility of preparation-induced textural artifacts. The FIB-SIMS instrument includes a column optimized for SEM with a quadrupole type mass spectrometer. Its spatial and spectral resolution are 20 nm and 0.4 AMU, respectively. The spatial resolution of the ESEM for chemical analysis is about 100 nm. Limits of detection for both instruments are mass dependent. Both the ESEM and the FIB-SIMS instrument revealed contrasting surficial features; crumbled, weathered appearance of the matrix in some regions as well as a rather ubiquitous presence of euhedral halite crystals, often associated with cracks or holes in the surface of the rock. Other halogen elements present in the vicinity of the NaCl crystals include K and Br. In this report, elemental inventories are shown as mass spectra and as X-ray maps.

Cryo-FIB specimen preparation for use in a cartridge-type cryo-TEM.

PubMed

He, Jie; Hsieh, Chyongere; Wu, Yongping; Schmelzer, Thomas; Wang, Pan; Lin, Ying; Marko, Michael; Sui, Haixin

2017-08-01

Cryo-electron tomography (cryo-ET) is a well-established technique for studying 3D structural details of subcellular macromolecular complexes and organelles in their nearly native context in the cell. A primary limitation of the application of cryo-ET is the accessible specimen thickness, which is less than the diameters of almost all eukaryotic cells. It has been shown that focused ion beam (FIB) milling can be used to prepare thin, distortion-free lamellae of frozen biological material for high-resolution cryo-ET. Commercial cryosystems are available for cryo-FIB specimen preparation, however re-engineering and additional fixtures are often essential for reliable results with a particular cryo-FIB and cryo-transmission electron microscope (cryo-TEM). Here, we describe our optimized protocol and modified instrumentation for cryo-FIB milling to produce thin lamellae and subsequent damage-free cryotransfer of the lamellae into our cartridge-type cryo-TEM. Published by Elsevier Inc.

Ultrastructural characterization of tooth-biomaterial interfaces prepared with broad and focused ion beams.

PubMed

Coutinho, E; Jarmar, T; Svahn, F; Neves, A A; Verlinden, B; Van Meerbeek, B; Engqvist, H

2009-11-01

Current available techniques for transmission electron microscopy (TEM) of tooth-biomaterial interfaces are mostly ineffective for brittle phases and impair integrated chemical and morphological characterization. The aims of this study were (1) to determine the applicability of new focused ion beam (FIB) and broad ion beam (BIB) techniques for TEM preparation of tooth-biomaterial interfaces; (2) to characterize the interfacial interaction with enamel and dentin of a conventional glass-ionomer (Chemfil Superior, DeTrey Dentsply, Germany), a 2-step self-etch (Clearfil SE, Kuraray, Japan) and a 3-step etch-and-rinse (OptiBond FL, Kerr, USA) adhesives; and (3) to characterize clinically relevant interfaces obtained from actual Class-I cavities. After bonding to freshly extracted human third molars, non-demineralized and non-stained sections were obtained using the FIB/BIB techniques and examined under TEM. The main structures generally disclosed in conventional ultramicrotomy samples were recognized in FIB/BIB-based ones. There were not any major differences between FIB and BIB concerning the resulting ultrastructural morphology. FIB/BIB-sections enabled to clearly resolve sub-micron hydroxyapatite crystals on top of hard tissues and the interface between matrix and filler in all materials, even at nano-scale. Some investigated interfaces disclosed areas with a distinct "fog" or "melted look", which is probably an artifact due to surface damage caused by the high-energy beam. Interfaces with enamel clearly disclosed the distinct "keyhole" shape of enamel rods sectioned at 90 degrees , delimited by a thin electron-lucent layer of inter-rod enamel. At regions where enamel crystals ran parallel with the interface, we observed a lack of interaction and some de-bonding along with interfacial void formation. The FIB/BIB methods are viable and reliable alternatives to conventional ultramicrotomy for preparation of thin sections of brittle and thus difficult to cut biomaterial-hard tissue interfaces. They disclose additional ultrastructural information about both substrates and are more suitable for advanced analytic procedures.

First evidence of tyre debris characterization at the nanoscale by focused ion beam

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

Milani, M.; Pucillo, F.P.; Ballerini, M.

2004-07-15

In this paper, we present a novel technique for the nanoscale characterization of the outer and inner structure of tyre debris. Tyre debris is produced by the normal wear of tyres. In previous studies, the microcharacterization and identification were performed by analytical electron microscopy. This study is a development of the characterization of surface and microstructure of tyre debris. For the first time, tyre debris was analysed by focused ion beam (FIB), a technique with 2- to 5-nm resolution that does not require any sample preparation. We studied tyre debris produced in the laboratory. We made electron and ionic imagingmore » of the surface of the material, and after a ionic cut, we studied the internal microstructure of the same sample. The tyre debris was analysed by FIB without any sample preparations unlike the case of scanning and transmission electron microscopy (SEM and TEM). Useful information was derived to improve detection and monitoring techniques of pollution by tyre degradation processes.« less

RECENT DEVELOPMENT IN TEM CHARACTERIZATION OF IRRADIATED RERTR FUELS

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

J. Gan; B.D. Miller; D.D. Keiser Jr.

2011-10-01

The recent development on TEM work of irradiated RERTR fuels includes microstructural characterization of the irradiated U-10Mo/alloy-6061 monolithic fuel plate, the RERTR-7 U-7Mo/Al-2Si and U-7Mo/Al-5Si dispersion fuel plates. It is the first time that a TEM sample of an irradiated nuclear fuel was prepared using the focused-ion-beam (FIB) lift-out technical at the Idaho National Laboratory. Multiple FIB TEM samples were prepared from the areas of interest in a SEM sample. The characterization was carried out using a 200kV TEM with a LaB6 filament. The three dimensional orderings of nanometer-sized fission gas bubbles are observed in the crystalline region of themore » U-Mo fuel. The co-existence of bubble superlattice and dislocations is evident. Detailed microstructural information along with composition analysis is obtained. The results and their implication on the performance of these fuels are discussed.« less

3D Structure Determination of Native Mammalian Cells using Cryo-FIB and Cryo-electron Tomography

PubMed Central

Wang, Ke; Strunk, Korrinn; Zhao, Gongpu; Gray, Jennifer L.; Zhang, Peijun

2012-01-01

Cryo-electron tomography (cryo-ET) has enabled high resolution three-dimensional (3D) structural analysis of virus and host cell interactions and many cell signaling events; these studies, however, have largely been limited to very thin, peripheral regions of eukaryotic cells or to small prokaryotic cells. Recent efforts to make thin, vitreous sections using cryo-ultramicrotomy have been successful, however, this method is technically very challenging and with many artifacts. Here, we report a simple and robust method for creating in situ, frozen-hydrated cell lamellas using a focused ion beam at cryogenic temperature (cryo-FIB), allowing access to any interior cellular regions of interest. We demonstrate the utility of cryo-FIB with high resolution 3D cellular structures from both bacterial cells and large mammalian cells. The method will not only facilitate high-throughput 3D structural analysis of biological specimens, but is also broadly applicable to sample preparation of thin films and surface materials without the need for FIB “lift-out”. PMID:22796867

Automated radiosynthesis of no-carrier-added 4-[18F]fluoroiodobenzene: a versatile building block in 18F radiochemistry.

PubMed

Way, Jenilee Dawn; Wuest, Frank

2014-02-01

4-[18F]Fluoroiodobenzene ([18F]FIB) is a versatile building block in 18F radiochemistry used in various transition metal-mediated C-C and C-N cross-coupling reactions and [18F]fluoroarylation reactions. Various synthesis routes have been described for the preparation of [18F]FIB. However, to date, no automated synthesis of [18F]FIB has been reported to allow access to larger amounts of [18F]FIB in high radiochemical and chemical purity. Herein, we describe an automated synthesis of no-carrier-added [18F]FIB on a GE TRACERlab™ FX automated synthesis unit starting from commercially available(4-iodophenyl)diphenylsulfonium triflate as the labelling precursor. [18F]FIB was prepared in high radiochemical yields of 89 ± 10% (decay-corrected, n = 7) within 60 min, including HPLC purification. The radiochemical purity exceeded 95%, and specific activity was greater than 40 GBq/μmol. Typically, from an experiment, 6.4 GBq of [18F]FIB could be obtained starting from 10.4 GBq of [18F]fluoride.

Three-dimensional imaging of adherent cells using FIB/SEM and STEM.

PubMed

Villinger, Clarissa; Schauflinger, Martin; Gregorius, Heiko; Kranz, Christine; Höhn, Katharina; Nafeey, Soufi; Walther, Paul

2014-01-01

In this chapter we describe three different approaches for three-dimensional imaging of electron microscopic samples: serial sectioning transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM) tomography, and focused ion beam/scanning electron microscopy (FIB/SEM) tomography. With these methods, relatively large volumes of resin-embedded biological structures can be analyzed at resolutions of a few nm within a reasonable expenditure of time. The traditional method is serial sectioning and imaging the same area in all sections. Another method is TEM tomography that involves tilting a section in the electron beam and then reconstruction of the volume by back projection of the images. When the scanning transmission (STEM) mode is used, thicker sections (up to 1 μm) can be analyzed. The third approach presented here is focused ion beam/scanning electron microscopy (FIB/SEM) tomography, in which a sample is repeatedly milled with a focused ion beam (FIB) and each newly produced block face is imaged with the scanning electron microscope (SEM). This process can be repeated ad libitum in arbitrary small increments allowing 3D analysis of relatively large volumes such as eukaryotic cells. We show that resolution of this approach is considerably improved when the secondary electron signal is used. However, the most important prerequisite for three-dimensional imaging is good specimen preparation. For all three imaging methods, cryo-fixed (high-pressure frozen) and freeze-substituted samples have been used.

KSC-07pd1499

NASA Image and Video Library

2007-06-13

KENNEDY SPACE CENTER, FLA. -- United Space Alliance employees prepare test articles to be used in wind tunnel testing by NASA to collect data for analysis of the detached Flexible Insulation Blanket, or FIB, on Atlantis. A tear occurred in an area of the OMS pod on Atlantis during launch of mission STS-117 on June 8, 2007. The test articles each feature three tiles (Low Temperature Reusable Surface Insulation, or LRSI) affixed next to two FIB blankets, simulating the thermal protection system set-up on Atlantis' OMS pod in the vicinity of the in-flight anomaly. These test articles will be flown to Texas the morning of June 14. The TPS team at KSC has also provided a total of 22 FIB samples for other testing and analysis. Repair is under consideration following testing at KSC and Houston. Photo credit: NASA/Amanda Diller

KSC-07pd1498

NASA Image and Video Library

2007-06-13

KENNEDY SPACE CENTER, FLA. -- United Space Alliance employees prepare test articles to be used in wind tunnel testing by NASA to collect data for analysis of the detached Flexible Insulation Blanket, or FIB, on Atlantis. A tear occurred in an area of the OMS pod on Atlantis during launch of mission STS-117 on June 8, 2007. The test articles each feature three tiles (Low Temperature Reusable Surface Insulation, or LRSI) affixed next to two FIB blankets, simulating the thermal protection system set-up on Atlantis' OMS pod in the vicinity of the in-flight anomaly. These test articles will be flown to Texas the morning of June 14. The TPS team at KSC has also provided a total of 22 FIB samples for other testing and analysis. Repair is under consideration following testing at KSC and Houston. Photo credit: NASA/Amanda Diller

KSC-07pd1497

NASA Image and Video Library

2007-06-13

KENNEDY SPACE CENTER, FLA. -- United Space Alliance employees prepare test articles to be used in wind tunnel testing by NASA to collect data for analysis of the detached Flexible Insulation Blanket, or FIB, on Atlantis. A tear occurred in an area of the OMS pod on Atlantis during launch of mission STS-117 on June 8, 2007. The test articles each feature three tiles (Low Temperature Reusable Surface Insulation, or LRSI) affixed next to two FIB blankets, simulating the thermal protection system set-up on Atlantis' OMS pod in the vicinity of the in-flight anomaly. These test articles will be flown to Texas the morning of June 14. The TPS team at KSC has also provided a total of 22 FIB samples for other testing and analysis. Repair is under consideration following testing at KSC and Houston. Photo credit: NASA/Amanda Diller

KSC-07pd1501

NASA Image and Video Library

2007-06-13

KENNEDY SPACE CENTER, FLA. -- United Space Alliance employees prepare test articles to be used in wind tunnel testing by NASA to collect data for analysis of the detached Flexible Insulation Blanket, or FIB, on Atlantis. A tear occurred in an area of the OMS pod on Atlantis during launch of mission STS-117 on June 8, 2007. The test articles each feature three tiles (Low Temperature Reusable Surface Insulation, or LRSI) affixed next to two FIB blankets, simulating the thermal protection system set-up on Atlantis' OMS pod in the vicinity of the in-flight anomaly. These test articles will be flown to Texas the morning of June 14. The TPS team at KSC has also provided a total of 22 FIB samples for other testing and analysis. Repair is under consideration following testing at KSC and Houston. Photo credit: NASA/Amanda Diller

KSC-07pd1496

NASA Image and Video Library

2007-06-13

KENNEDY SPACE CENTER, FLA. -- A United Space Alliance employee prepares a test article that will be used in wind tunnel testing by NASA to collect data for analysis of the detached Flexible Insulation Blanket, or FIB, on Atlantis. A tear occurred in an area of the OMS pod on Atlantis during launch of mission STS-117 on June 8, 2007. The test articles each feature three tiles (Low Temperature Reusable Surface Insulation, or LRSI) affixed next to two FIB blankets, simulating the thermal protection system set-up on Atlantis' OMS pod in the vicinity of the in-flight anomaly. These test articles will be flown to Texas the morning of June 14. The TPS team at KSC has also provided a total of 22 FIB samples for other testing and analysis. Repair is under consideration following testing at KSC and Houston. Photo credit: NASA/Amanda Diller

KSC-07pd1500

NASA Image and Video Library

2007-06-13

KENNEDY SPACE CENTER, FLA. -- United Space Alliance employees prepare test articles to be used in wind tunnel testing by NASA to collect data for analysis of the detached Flexible Insulation Blanket, or FIB, on Atlantis. A tear occurred in an area of the OMS pod on Atlantis during launch of mission STS-117 on June 8, 2007. The test articles each feature three tiles (Low Temperature Reusable Surface Insulation, or LRSI) affixed next to two FIB blankets, simulating the thermal protection system set-up on Atlantis' OMS pod in the vicinity of the in-flight anomaly. These test articles will be flown to Texas the morning of June 14. The TPS team at KSC has also provided a total of 22 FIB samples for other testing and analysis. Repair is under consideration following testing at KSC and Houston. Photo credit: NASA/Amanda Diller

Microstructural characterization of Ti-6Al-4V metal chips by focused ion beam (FIB) and transmission electron microscopy (TEM)

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

Schneider, Judy; Dong, Lei; Howe, Jane Y

2011-01-01

The microstructure of the secondary deformation zone (SDZ) near the cutting surface in metal chips of Ti-6Al-4V formed during machining was investigated using focused ion beam (FIB) specimen preparation and transmission electron microscopy (TEM) imaging. Use of the FIB allowed precise extraction of the specimen across this region to reveal its inhomogeneous microstructure resulting from the non-uniform distribution of strain, strain rate, and temperature generated during the cutting process. Initial imaging from conventional TEM foil preparation revealed microstructures ranging from heavily textured to regions of fine grains. Using FIB preparation, the transverse microstructure could be interpreted as fine grains nearmore » the cutting surface which transitioned to coarse grains toward the free surface. At the cutting surface a 10 nm thick recrystallized layer was observed capping a 20 nm thick amorphous layer.« less

Three-Dimensional FIB/EBSD Characterization of Irradiated HfAl3-Al Composite

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

Hua, Zilong; Guillen, Donna Post; Harris, William

2016-09-01

A thermal neutron absorbing material, comprised of 28.4 vol% HfAl3 in an Al matrix, was developed to serve as a conductively cooled thermal neutron filter to enable fast flux materials and fuels testing in a pressurized water reactor. In order to observe the microstructural change of the HfAl3-Al composite due to neutron irradiation, an EBSD-FIB characterization approach is developed and presented in this paper. Using the focused ion beam (FIB), the sample was fabricated to 25µm × 25µm × 20 µm and mounted on the grid. A series of operations were carried out repetitively on the sample top surface tomore » prepare it for scanning electron microscopy (SEM). First, a ~100-nm layer was removed by high voltage FIB milling. Then, several cleaning passes were performed on the newly exposed surface using low voltage FIB milling to improve the SEM image quality. Last, the surface was scanned by Electron Backscattering Diffraction (EBSD) to obtain the two-dimensional image. After 50 to 100 two-dimensional images were collected, the images were stacked to reconstruct a three-dimensional model using DREAM.3D software. Two such reconstructed three-dimensional models were obtained from samples of the original and post-irradiation HfAl3-Al composite respectively, from which the most significant microstructural change caused by neutron irradiation apparently is the size reduction of both HfAl3 and Al grains. The possible reason is the thermal expansion and related thermal strain from the thermal neutron absorption. This technique can be applied to three-dimensional microstructure characterization of irradiated materials.« less

FIB/SEM and SEM/EDS microstructural analysis of metal-ceramic and zirconia-ceramic interfaces.

PubMed

Massimi, F; Merlati, G; Sebastiani, M; Battaini, P; Menghini, P; Bemporad, E

2012-01-10

Recently introduced FIB/SEM analysis in microscopy seems to provide a high-resolution characterization of the samples by 3D (FIB) cross-sectioning and (SEM) high resolution imaging. The aim of this study was to apply the FIB/SEM and SEM/EDS analysis to the interfaces of a metal-ceramic vs. two zirconia-ceramic systems. Plate samples of three different prosthetic systems were prepared in the dental lab following the manufacturers' instructions, where metal-ceramic was the result of a ceramic veneering (porcelain-fused-to-metal) and the two zirconia-ceramic systems were produced by the dedicated CAD-CAM procedures of the zirconia cores (both with final sintering) and then veneered by layered or heat pressed ceramics. In a FIB/SEM equipment (also called DualBeam), a thin layer of platinum (1 μm) was deposited on samples surface crossing the interfaces, in order to protect them during milling. Then, increasingly deeper trenches were milled by a focused ion beam, first using a relatively higher and later using a lower ion current (from 9 nA to 0.28 nA, 30KV). Finally, FEG-SEM (5KV) micrographs (1000-50,000X) were acquired. In a SEM the analysis of the morphology and internal microstructure was performed by 13KV secondary and backscattered electrons signals (in all the samples). The compositional maps were then performed by EDS probe only in the metal-ceramic system (20kV). Despite the presence of many voids in all the ceramic layers, it was possible to identify: (1) the grain structures of the metallic and zirconia substrates, (2) the thin oxide layer at the metal-ceramic interface and its interactions with the first ceramic layer (wash technique), (3) the roughness of the two different zirconia cores and their interactions with the ceramic interface, where the presence of zirconia grains in the ceramic layer was reported in two system possibly due to sandblasting before ceramic firing.

Fundamentals of Focused Ion Beam Nanostructural Processing: Below, At, and Above the Surface

DOE PAGES

MoberlyChan, Warren J.; Adams, David P.; Aziz, Michael J.; ...

2007-05-01

This paper considers the fundamentals of what happens in a solid when it is impacted by a medium-energy gallium ion. The study of the ion/sample interaction at the nanometer scale is applicable to most focused ion beam (FIB)–based work even if the FIB/sample interaction is only a step in the process, for example, micromachining or microelectronics device processing. Whereas the objective in other articles in this issue is to use the FIB tool to characterize a material or to machine a device or transmission electron microscopy sample, the goal of the FIB in this article is to have the FIB/samplemore » interaction itself become the product. To that end, the FIB/sample interaction is considered in three categories according to geometry: below, at, and above the surface. First, the FIB ions can penetrate the top atom layer(s) and interact below the surface. Ion implantation and ion damage on flat surfaces have been comprehensively examined; however, FIB applications require the further investigation of high doses in three-dimensional profiles. Second, the ions can interact at the surface, where a morphological instability can lead to ripples and surface self-organization, which can depend on boundary conditions for site-specific and compound FIB processing. Third, the FIB may interact above the surface (and/or produce secondary particles that interact above the surface). Such ion beam–assisted deposition, FIB–CVD (chemical vapor deposition), offers an elaborate complexity in three dimensions with an FIB using a gas injection system. Finally, at the nanometer scale, these three regimes—below, at, and above the surface—can require an interdependent understanding to be judiciously controlled by the FIB.« less

DIY Tomography sample holder

NASA Astrophysics Data System (ADS)

Lari, L.; Wright, I.; Boyes, E. D.

2015-10-01

A very simple tomography sample holder at minimal cost was developed in-house. The holder is based on a JEOL single tilt fast exchange sample holder where its exchangeable tip was modified to allow high angle degree tilt. The shape of the tip was designed to retain mechanical stability while minimising the lateral size of the tip. The sample can be mounted on as for a standard 3mm Cu grids as well as semi-circular grids from FIB sample preparation. Applications of the holder on different sample systems are shown.

Stratification and loading of fecal indicator bacteria (FIB) in a tidally muted urban salt marsh.

PubMed

Johnston, Karina K; Dorsey, John H; Saez, Jose A

2015-03-01

Stratification and loading of fecal indicator bacteria (FIB) were assessed in the main tidal channel of the Ballona Wetlands, an urban salt marsh receiving muted tidal flows, to (1) determine FIB concentration versus loading within the water column at differing tidal flows, (2) identify associations of FIB with other water quality parameters, and (3) compare wetland FIB concentrations to the adjacent estuary. Sampling was conducted four times during spring-tide events; samples were analyzed for FIB and turbidity (NTU) four times over a tidal cycle at pre-allocated depths, depending on the water level. Additional water quality parameters measured included temperature, salinity, oxygen, and pH. Loadings were calculated by integrating the stratified FIB concentrations with water column cross-sectional volumes corresponding to each depth. Enterococci and Escherichia coli were stratified both by concentration and loading, although these variables portrayed different patterns over a tidal cycle. Greatest concentrations occurred in surface to mid-strata levels, during flood tides when contaminated water flowed in from the estuary, and during ebb flows when sediments were suspended. Loading was greatest during flood flows and diminished during low tide periods. FIB concentrations within the estuary often were significantly greater than those within the wetland tide channel, supporting previous studies that the wetlands act as a sink for FIB. For public health water quality monitoring, these results indicate that more accurate estimates of FIB concentrations would be obtained by sampling a number of points within a water column rather than relying only on single surface samples.

TEM observations of radiation damage in tungsten irradiated by 20 MeV W ions

NASA Astrophysics Data System (ADS)

Ciupiński, Ł.; Ogorodnikova, O. V.; Płociński, T.; Andrzejczuk, M.; Rasiński, M.; Mayer, M.; Kurzydłowski, K. J.

2013-12-01

Polycrystalline, recrystallized W targets were subjected to implantation with 20 MeV W6+ ions in order to simulate radiation damage caused by fusion neutrons. Three samples with cumulative damage of 0.01, 0.1 and 0.89 dpa were produced. The near-surface zone of each sample has been analyzed by transmission electron microscopy (TEM). To this end, lamellae oriented perpendicularly to the targets implanted surface were milled out using focused ion beam (FIB). A reference lamella from non-irradiated, recrystallized W target was also prepared to estimate the damage introduced during FIB processing. TEM studies revealed a complex microstructure of the damaged zones as well as its evolution with cumulative damage level. The experimentally observed damage depth agrees very well with the one calculated using the Stopping and Range of Ions in Matter (SRIM) software.

Post-ion beam induced degradation of copper layers in transmission electron microscopy specimens

NASA Astrophysics Data System (ADS)

Seidel, F.; Richard, O.; Bender, H.; Vandervorst, W.

2015-11-01

Copper containing transmission electron microscopy (TEM) specimens frequently show corrosion after focused ion beam (FIB) preparation. This paper reveals that the corrosion product is a Cu-S phase growing over the specimen surface. The layer is identified by energy-dispersive x-ray spectroscopy, and lattice spacing indexing of power spectra patterns. The corrosion process is further studied by TEM on cone-shaped specimens, which are intentionally stored after FIB preparation with S flakes for short time. Furthermore, a protective method against corrosion is developed by varying the time in the FIB vacuum and the duration of a subsequent plasma cleaning.

Characterization of nutrients and fecal indicator bacteria at a concentrated swine feeding operation in Wake County, North Carolina, 2009-2011

USGS Publications Warehouse

Harden, Stephen L.; Rogers, Shane W.; Jahne, Michael A.; Shaffer, Carrie E.; Smith, Douglas G.

2012-01-01

Study sites were sampled for laboratory analysis of nutrients, total suspended solids (TSS), and (or) fecal indicator bacteria (FIB). Nutrient analyses included measurement of dissolved ammonia, total and dissolved ammonia + organic nitrogen, dissolved nitrate + nitrite, dissolved orthophosphate, and total phosphorus. The FIB analyses included measurement of Escherichia coli and enterococci. Samples of wastewater at the swine facility were collected from a pipe outfall from the swine housing units, two storage lagoons, and the spray fields for analysis of nutrients, TSS, and FIB. Soil samples collected from a spray field were analyzed for FIB. Monitoring locations were established for collecting discharge and water-quality data during storm events at three in-field runoff sites and two sites on the headwater stream (one upstream and one downstream) next to the swine facility. Stormflow samples at the five monitoring locations were collected for four storm events during 2009 to 2010 and analyzed for nutrients, TSS, and FIB. Monthly water samples also were collected during base-flow conditions at all four stream sites for laboratory analysis of nutrients, TSS, and (or) FIB.

Detection of Helicobacter pylori and fecal indicator bacteria in five North American rivers.

USGS Publications Warehouse

Voytek, M.A.; Ashen, J.B.; Fogarty, L.R.; Kirshtein, J.D.; Landa, E.R.

2005-01-01

This study examines the use of fecal indicator bacteria (FIB) as a predictor of the presence of Helicobacter spp. A combination of standard culture and molecular techniques were used to detect and quantify FIB, Helicobacter spp. and H. pylori from five North American rivers of different size and with different land use characteristics. Primers designed to amplify genes specific to Helicobacter spp. and H. pylori were evaluated for their efficacy in detection and quantification in environmental samples. Helicobacter spp. were detected in 18/33 (55%) of river samples. H. pylori was detected in 11/33 (33%) of river samples. FIB were found in 32/33 (96%) of river samples. When FIB abundance exceeded USEPA water quality standards for single samples, Helicobacter or H. pylori were detected in 7/15 (47%) cases. No numerical correlation was found between the presence of FIB and either Helicobacter spp. or H. pylori. This suggests that the presence of FIB will be of limited use for detection of Helicobacter spp. or H. pylori by public health agencies.

Microstructural analysis of 800H steel exposed at test operation in HTHL by using FIB-SEM and HRTEM techniques

NASA Astrophysics Data System (ADS)

Marušáková, Daniela; Bublíková, Petra; Berka, Jan; Vávrovcová, Zuzana; Burda, Jaroslav

2017-09-01

To understand the degradation process of metal materials which are used in power engineering, appropriate evaluation procedure is necessary to ensure. In that order, the degradation of alloy 800H during the first period of test operation in High Temperature Helium Loop (HTHL) was tested. Experiment was carried out in atmosphere of pure technical helium with purity 4.6 containing only residual concentration of moisture up to 300 vppm. Parameters during the operation test were not constant, process was interrupted several times. The maximum temperature on specimens during this period was 750 °C, average temperature was 460 °C, gas pressure ranged from 3 to 6 MPa and gas flow from 3 to 9 gs-1. Total duration of the test was 264 h. After the exposure the degradation of specimens was investigated by Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM). Using the technique of Focused Ion Beam (FIB) integrated within SEM the transparent samples with quality surface parameters were obtained for TEM analysis. FIB technique in combination with High Resolution TEM ensured the guaranteed methodology of exposed sample preparation and precise description of changes in this kind of material.

Long-range crystalline order in spicules from the calcareous sponge Paraleucilla magna (Porifera, Calcarea).

PubMed

Rossi, Andre L; Campos, Andrea P C; Barroso, Madalena M S; Klautau, Michelle; Archanjo, Bráulio S; Borojevic, Radovan; Farina, Marcos; Werckmann, Jacques

2014-09-01

We investigated the ultrastructure and crystallographic orientation of spicules from the calcareous sponge Paraleucilla magna (subclass Calcaronea) by transmission and scanning electron microscopy using two different methods of sample preparation: ultramicrotomy and focused ion beam (FIB). It was found that the unpaired actine from the spicules was oriented in the [211] zone axis. The plane that contains the unpaired actine and divides symmetrically the paired actines is the (-120). This plane is a mirror plane of the hexagonal lattice system. All the spicule types analyzed presented the same crystallographic orientation. Electron nanodiffraction maps from 4μm×4μm regions prepared by FIB showed disorientation of <2° between diffraction patterns obtained from neighbor regions, indicating the presence of a unique, highly aligned calcite crystalline phase. Among the eight FIB sections obtained, four presented high pore density. In one section perpendicular to the actine axis pores were observed only in the center of the spicule aligned in a circular pattern and surrounded by a faint circular contour with a larger radius. The presence of amorphous carbon representative of organic molecules detected by electron energy loss spectroscopy was correlated neither with porosity nor with specific lattice planes. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Focused Ion Beam Recovery and Analysis of Interplanetary Dust Particles (IDPs) and Stardust Analogues

NASA Technical Reports Server (NTRS)

Graham, G. A.; Bradley, J. P.; Bernas, M.; Stroud, R. M.; Dai, Z. R.; Floss, C.; Stadermann, F. J.; Snead, C. J.; Westphal, A. J.

2004-01-01

Meteoritics research is a major beneficiary of recent developments in analytical instrumentation [1,2]. Integrated studies in which multiple analytical techniques are applied to the same specimen are providing new insight about the nature of IDPs [1]. Such studies are dependent on the ability to prepare specimens that can be analyzed in multiple instruments. Focused ion beam (FIB) microscopy has revolutionized specimen preparation in materials science [3]. Although FIB has successfully been used for a few IDP and meteorite studies [1,4-6], it has yet to be widely utilized in meteoritics. We are using FIB for integrated TEM/NanoSIMS/synchrotron infrared (IR) studies [1].

Coordinated STEM/FIB/NanoSIMS Analyses of Presolar Silicates in Comet Dust and Primitive Meteorites

NASA Technical Reports Server (NTRS)

Keller, Lindsay; Nguyen, A.; Rahman, Z.; Messenger, S.

2012-01-01

Silicate grains were among the most abundant mineralogical building blocks of our Solar System. These grains were the detritus from earlier generations of stars that have been recycled in the early solar nebula. Rare sub-micrometer survivors of this processing have been identified in meteorites, micrometeorites and interplanetary dust particles (IDPs). These silicate grains are recognized as presolar in origin because of their extremely anomalous isotopic compositions that reflect nucleosynthetic processes in their stellar sources (evolved stars, novae and supernovae). We perform coordinated chemical, mineralogical and isotopic studies of these grains to determine their origins and histories. We examine the complex mineralogy and petrography of presolar silicates using imaging, diffraction and chemical data obtained from thin sections with the JSC JEOL 2500 field-emission STEM equipped with a Noran thin window energy dispersive x-ray (EDX) spectrometer and a Gatan Tridiem GIF. Quantitative element x-ray maps (spectrum images) are acquired by rastering a 4 nm incident probe whose dwell time is minimized to avoid beam damage and element diffusion during mapping. Successive image layers are acquired and combined in order to achieve approx 1% counting statistics for major elements. The IDP samples are prepared by ultramicrotomy of particles embedded in epoxy or elemental sulfur. After EDX mapping, the sections are subjected to C, N, and O isotopic imaging with the JSC NanoSIMS 50L ion microprobe. We prepare sections of some meteorite grains using the JSC FEI Quanta 3D focused ion beam (FIB) instrument. The specimen surface is protected from the FIB milling process by layers of electron beam-deposited C and Pt followed by an ion-deposited Pt layer. We also use the FIB to preferentially remove surrounding grains to reduce the background in subsequent NanoSIMS measurements. For mineralogical studies, we again employ the FIB instrument to deposit a protective cap over the grain of interest and then extract the grain and thin it to electron transparency for TEM analysis.

Modern Focused-Ion-Beam-Based Site-Specific Specimen Preparation for Atom Probe Tomography.

PubMed

Prosa, Ty J; Larson, David J

2017-04-01

Approximately 30 years after the first use of focused ion beam (FIB) instruments to prepare atom probe tomography specimens, this technique has grown to be used by hundreds of researchers around the world. This past decade has seen tremendous advances in atom probe applications, enabled by the continued development of FIB-based specimen preparation methodologies. In this work, we provide a short review of the origin of the FIB method and the standard methods used today for lift-out and sharpening, using the annular milling method as applied to atom probe tomography specimens. Key steps for enabling correlative analysis with transmission electron-beam backscatter diffraction, transmission electron microscopy, and atom probe tomography are presented, and strategies for preparing specimens for modern microelectronic device structures are reviewed and discussed in detail. Examples are used for discussion of the steps for each of these methods. We conclude with examples of the challenges presented by complex topologies such as nanowires, nanoparticles, and organic materials.

Depletion region surface effects in electron beam induced current measurements.

PubMed

Haney, Paul M; Yoon, Heayoung P; Gaury, Benoit; Zhitenev, Nikolai B

2016-09-07

Electron beam induced current (EBIC) is a powerful characterization technique which offers the high spatial resolution needed to study polycrystalline solar cells. Current models of EBIC assume that excitations in the p - n junction depletion region result in perfect charge collection efficiency. However we find that in CdTe and Si samples prepared by focused ion beam (FIB) milling, there is a reduced and nonuniform EBIC lineshape for excitations in the depletion region. Motivated by this, we present a model of the EBIC response for excitations in the depletion region which includes the effects of surface recombination from both charge-neutral and charged surfaces. For neutral surfaces we present a simple analytical formula which describes the numerical data well, while the charged surface response depends qualitatively on the location of the surface Fermi level relative to the bulk Fermi level. We find the experimental data on FIB-prepared Si solar cells is most consistent with a charged surface, and discuss the implications for EBIC experiments on polycrystalline materials.

Characterization of Meteorites by Focused Ion Beam Sectioning: Recent Applications to CAIs and Primitive Meteorite Matrices

NASA Technical Reports Server (NTRS)

Christoffersen, Roy; Keller, Lindsay P.; Han, Jangmi; Rahman, Zia; Berger, Eve L.

2015-01-01

Focused ion beam (FIB) sectioning has revolutionized preparation of meteorite samples for characterization by analytical transmission electron microscopy (TEM) and other techniques. Although FIB is not "non-destructive" in the purest sense, each extracted section amounts to no more than nanograms (approximately 500 cubic microns) removed intact from locations precisely controlled by SEM imaging and analysis. Physical alteration of surrounding material by ion damage, fracture or sputter contamination effects is localized to within a few micrometers around the lift-out point. This leaves adjacent material intact for coordinate geochemical analysis by SIMS, microdrill extraction/TIMS and other techniques. After lift out, FIB sections can be quantitatively analyzed by electron microprobe prior to final thinning, synchrotron x-ray techniques, and by the full range of state-of-the-art analytical field-emission scanning transmission electron microscope (FE-STEM) techniques once thinning is complete. Multiple meteorite studies supported by FIB/FE-STEM are currently underway at NASA-JSC, including coordinated analysis of refractory phase assemblages in CAIs and fine-grained matrices in carbonaceous chondrites. FIB sectioning of CAIs has uncovered epitaxial and other overgrowth relations between corundum-hibonite-spinel consistent with hibonite preceding corundum and/or spinel in non-equilibrium condensation sequences at combinations of higher gas pressures, dust-gas enrichments or significant nebular transport. For all of these cases, the ability of FIB to allow for coordination with spatially-associated isotopic data by SIMS provides immense value for constraining the formation scenarios of the particular CAI assemblage. For carbonaceous chondrites matrix material, FIB has allowed us to obtain intact continuous sections of the immediate outer surface of Murchison (CM2) after it has been experimentally ion processed to simulate solar wind space weathering. The surface amorphization and loss of OH produced by the irradiation provides important clues regarding space weathering on primitive asteroids such as the OSIRIS-Rex target 101955 Bennu.

High quality lamella preparation of gallium nitride compound semiconductor using Triple Beam™ system

NASA Astrophysics Data System (ADS)

Sato, T.; Nakano, K.; Matsumoto, H.; Torikawa, S.; Nakatani, I.; Kiyohara, M.; Isshiki, T.

2017-09-01

Gallium nitride (GaN) compound semiconductors have been known to be very sensitive to Ga focused ion beam (FIB) processing. Due to the nature of GaN based materials it is often difficult to produce damage-free lamellae, therefore applying the Triple Beam™ system which incorporates an enhanced method for amorphous removal is presented to make a high quality lamella. The damage or distortion layer thickness of GaN single crystal prepared with 30 kV Ga FIB and 1 kV Ga FIB were about 17 nm and 1.5 nm respectively. The crystallinity at the uppermost surface remained unaffected when the condition of 1 kV Ar ion milling with the Triple Beam™ system was used. The technique of combining traditional Ga FIB processing with an enhanced method for amorphous layer removal by low energy Ar ion milling allows us to analyse the InGaN/GaN interface using aberration corrected scanning transmission electron microscopy at atomic resolution levels.

Three-Phase 3D Reconstruction of a LiCoO 2 Cathode via FIB-SEM Tomography

DOE PAGES

Liu, Zhao; Chen-Wiegart, Yu-chen K.; Wang, Jun; ...

2016-01-14

Three-phase three-dimensional (3D) microstructural reconstructions of lithium-ion battery electrodes are critical input for 3D simulations of electrode lithiation/delithiation, which provide a detailed understanding of battery operation. In this report, 3D images of a LiCoO 2electrode are achieved using focused ion beam-scanning electron microscopy (FIB-SEM), with clear contrast among the three phases: LiCoO 2particles, carbonaceous phases (carbon and binder) and the electrolyte space. The good contrast was achieved by utilizing an improved FIB-SEM sample preparation method that combined infiltration of the electrolyte space with a low-viscosity silicone resin and triple ion-beam polishing. Morphological parameters quantified include phase volume fraction, surface area,more » feature size distribution, connectivity, and tortuosity. Electrolyte tortuosity was determined using two different geometric calculations that were in good agreement. In conclusion, the electrolyte tortuosity distribution versus position within the electrode was found to be highly inhomogeneous; this will lead to inhomogeneous electrode lithiation/delithiation at high C-rates that could potentially cause battery degradation.« less

Implementation of focused ion beam (FIB) system in characterization of nuclear fuels and materials

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

A. Aitkaliyeva; J. W. Madden; B. D. Miller

2014-10-01

Beginning in 2007, a program was established at the Idaho National Laboratory to update key capabilities enabling microstructural and micro-chemical characterization of highly irradiated and/or radiologically contaminated nuclear fuels and materials at scales that previously had not been achieved for these types of materials. Such materials typically cannot be contact handled and pose unique hazards to instrument operators, facilities, and associated personnel. One of the first instruments to be acquired was a Dual Beam focused ion beam (FIB)-scanning electron microscope (SEM) to support preparation of transmission electron microscopy and atom probe tomography samples. Over the ensuing years, techniques have beenmore » developed and operational experience gained that has enabled significant advancement in the ability to characterize a variety of fuel types including metallic, ceramic, and coated particle fuels, obtaining insights into in-reactor degradation phenomena not obtainable by any other means. The following article describes insights gained, challenges encountered, and provides examples of unique results obtained in adapting Dual Beam FIB technology to nuclear fuels characterization.« less

Effects of Antiadhesion preparation on free fibrinogen and fibrin degrading products in abdominal exudates of rabbits postoperatively

PubMed Central

Wang, You-Li; Pan, Cheng-En; Yang, Ping-Lin; Tian, Yuan; Pei, Shu-Wen; Dong, Ming

2004-01-01

AIM: To observe effects of ACOL on fibrinogen (FIB), fibrin degrading products (FDP) and changes of FIB and FDP concentration in rabbits with intro-abdominal exudates during 7 d after major abdominal surgery. METHODS: Sixty New Zealand rabbits were randomly divided into 4 groups: ACOL group, the control group, DCT group and the normal group. After being modeled, except the normal group, the other 3 groups were treated with different ways for a week; the intro-abdominal exudates of rabbits in the 4 groups were drawn for FIB and FDP measurement once daily during 7 d after major abdominal surgery. RESULTS: FIB and FDP in the intro-abdominal exudates altered in a regular way and ACOL could change the concentration of FIB and FDP in the intra-abdominal exudates after major abdominal surgery. CONCLUSION: ACOL can prevent intestinal adhesion by reducing the concentration of FIB and raising that of FDP in the intro-abdominal exudates after major abdominal surgery. PMID:15309738

Preparation of MgB2 superconducting microbridges by focused ion beam direct milling

NASA Astrophysics Data System (ADS)

Zhang, Xuena; Li, Yanli; Xu, Zhuang; Kong, Xiangdong; Han, Li

2017-01-01

MgB2 superconducting microbridges were prepared by focused ion beam (FIB) direct milling on MgB2 films. The surface topography of the microbridges were observed using SEM and AFM and the superconductivity was measured in this paper. Lots of cracks and holes were found near the milled area. And the superconducting transition temperature was decreased a lot and the bridges prepared were not superconducting due to ion damage after milled with large dose. Through these works, we explored the effect regular of FIB milling and experimental parameters on the performance of microbridges.

Insights into Regolith Dynamics from the Irradiation Record Preserved in Hayabusa Samples

NASA Technical Reports Server (NTRS)

Keller, Lindsay P.; Berger, E. L.

2014-01-01

The rates of space weathering processes are poorly constrained for asteroid surfaces, with recent estimates ranging over 5 orders of magnitude. The return of the first surface samples from a space-weathered asteroid by the Hayabusa mission and their laboratory analysis provides "ground truth" to anchor the timescales for space weathering. We determine the rates of space weathering on Itokawa by measuring solar flare track densities and the widths of solar wind damaged rims on grains. These measurements are made possible through novel focused ion beam (FIB) sample preparation methods.

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

Thangadurai, P.; Lumelsky, Yulia; Silverstein, Michael S.

Transmission electron microscopy (TEM) cross-section specimens of PMMA in contact with gold and Si were prepared by focused ion beam (FIB) and compared with plan-view PMMA specimens prepared by a dip-coating technique. The specimens were characterized by TEM and electron energy loss spectroscopy (EELS). In the cross-section specimens, the thin films of PMMA were located in a Si-PMMA-Au multilayer. Different thicknesses of PMMA films were spin-coated on the Si substrates. The thickness of the TEM specimens prepared by FIB was estimated using EELS to be 0.65 of the plasmon mean-free-path. Along the PMMA-Au interface, Au particle diffusion into the PMMAmore » was observed, and the size of the Au particles was in the range of 2-4 nm. Dip-coating of PMMA directly on Cu TEM grids resulted in thin specimens with a granular morphology, with a thickness of 0.58 of the plasmon mean-free-path. The dip-coated specimens were free from ion milling induced artifacts, and thus serve as control specimens for comparison with the cross-sectioned specimens prepared by FIB.« less

Dual drug encapsulated thermo-sensitive fibrinogen-graft-poly (N-isopropyl acrylamide) nanogels for breast cancer therapy.

PubMed

Rejinold, N Sanoj; Baby, Thejus; Chennazhi, K P; Jayakumar, R

2014-02-01

5-FU/Megestrol acetate loaded fibrinogen-graft-PNIPAAm Nanogels (5-FU/Meg-fib-graft-PNIPAAm NGs) were prepared for thermo responsive drug delivery toward α5β1-integrins expressing breast cancer cells in vitro (MCF-7 cells). The 60-100 nm sized fib-graft-PNIPAAm nanogels (LCST=35 °C) were prepared by CaCl2 cross-linker. 5-FU/Meg-fib-graft-PNIPAAm NGs showed particle size of 165-195 nm size. The drug loading efficiency with 5-FU was 60% and 70% for Meg. "Drug release was greater above the lower critical solution temperature (LCST). Above LCST, drug release system triggers apopotosis and enhance toxicity to MCF-7 cells when compared to the equivalent dose of the free drug. This effect was due to the greater uptake of the drug by MCF-7 cells". 5-FU/Meg-fib-graft-PNIPAAm NGs is portrayed here as a new combinatorial thermo-responsive drug delivery agent for breast cancer therapy. Copyright © 2013 Elsevier B.V. All rights reserved.

Improving yield and reliability of FIB modifications using electrical testing

NASA Astrophysics Data System (ADS)

Desplats, Romain; Benbrik, Jamel; Benteo, Bruno; Perdu, Philippe

1998-08-01

Focused Ion Beam technology has two main areas of application for ICs: modification and preparation for technological analysis. The most solicited area is modification. This involves physically modifying a circuit by cutting lines and creating new ones in order to change the electrical function of the circuit. IC planar technologies have an increasing number of metal interconnections making FIB modifications more complex and decreasing their changes of success. The yield of FIB operations on ICs reflects a downward trend that imposes a greater number of circuits to be modified in order to successfully correct a small number of them. This requires extended duration, which is not compatible with production line turn around times. To respond to this problem, two solutions can be defined: either, reducing the duration of each FIB operation or increasing the success rate of FIB modifications. Since reducing the time depends mainly on FIB operator experience, insuring a higher success rate represents a more crucial aspect as both experienced and novice operators could benefit from this improvement. In order to insure successful modifications, it is necessary to control each step of a FIB operation. To do this, we have developed a new method using in situ electrical testing which has a direct impact on the yield of FIB modifications. We will present this innovative development through a real case study of a CMOS ASIC for high-speed communications. Monitoring the electrical behavior at each step in a FIB operation makes it possible to reduce the number of circuits to be modified and consequently reduces system costs thanks to better yield control. Knowing the internal electrical behavior also gives us indications about the impact on reliability of FIB modified circuits. Finally, this approach can be applied to failure analysis and FIB operations on flip chip circuits.

Site-Specific Preparation of Intact Solid–Liquid Interfaces by Label-Free In Situ Localization and Cryo-Focused Ion Beam Lift-Out

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

Zachman, Michael J.; Asenath-Smith, Emily; Estroff, Lara A.

Abstract Scanning transmission electron microscopy (STEM) allows atomic scale characterization of solid–solid interfaces, but has seen limited applications to solid–liquid interfaces due to the volatility of liquids in the microscope vacuum. Although cryo-electron microscopy is routinely used to characterize hydrated samples stabilized by rapid freezing, sample thinning is required to access the internal interfaces of thicker specimens. Here, we adapt cryo-focused ion beam (FIB) “lift-out,” a technique recently developed for biological specimens, to prepare intact internal solid–liquid interfaces for high-resolution structural and chemical analysis by cryo-STEM. To guide the milling process we introduce a label-freein situmethod of localizing subsurface structuresmore » in suitable materials by energy dispersive X-ray spectroscopy (EDX). Monte Carlo simulations are performed to evaluate the depth-probing capability of the technique, and show good qualitative agreement with experiment. We also detail procedures to produce homogeneously thin lamellae, which enable nanoscale structural, elemental, and chemical analysis of intact solid–liquid interfaces by analytical cryo-STEM. This work demonstrates the potential of cryo-FIB lift-out and cryo-STEM for understanding physical and chemical processes at solid–liquid interfaces.« less

Depletion region surface effects in electron beam induced current measurements

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

Haney, Paul M.; Zhitenev, Nikolai B.; Yoon, Heayoung P.

2016-09-07

Electron beam induced current (EBIC) is a powerful characterization technique which offers the high spatial resolution needed to study polycrystalline solar cells. Current models of EBIC assume that excitations in the p-n junction depletion region result in perfect charge collection efficiency. However, we find that in CdTe and Si samples prepared by focused ion beam (FIB) milling, there is a reduced and nonuniform EBIC lineshape for excitations in the depletion region. Motivated by this, we present a model of the EBIC response for excitations in the depletion region which includes the effects of surface recombination from both charge-neutral and chargedmore » surfaces. For neutral surfaces, we present a simple analytical formula which describes the numerical data well, while the charged surface response depends qualitatively on the location of the surface Fermi level relative to the bulk Fermi level. We find that the experimental data on FIB-prepared Si solar cells are most consistent with a charged surface and discuss the implications for EBIC experiments on polycrystalline materials.« less

FIB-SEM tomography in biology.

PubMed

Kizilyaprak, Caroline; Bittermann, Anne Greet; Daraspe, Jean; Humbel, Bruno M

2014-01-01

Three-dimensional information is much easier to understand than a set of two-dimensional images. Therefore a layman is thrilled by the pseudo-3D image taken in a scanning electron microscope (SEM) while, when seeing a transmission electron micrograph, his imagination is challenged. First approaches to gain insight in the third dimension were to make serial microtome sections of a region of interest (ROI) and then building a model of the object. Serial microtome sectioning is a tedious and skill-demanding work and therefore seldom done. In the last two decades with the increase of computer power, sophisticated display options, and the development of new instruments, an SEM with a built-in microtome as well as a focused ion beam scanning electron microscope (FIB-SEM), serial sectioning, and 3D analysis has become far easier and faster.Due to the relief like topology of the microtome trimmed block face of resin-embedded tissue, the ROI can be searched in the secondary electron mode, and at the selected spot, the ROI is prepared with the ion beam for 3D analysis. For FIB-SEM tomography, a thin slice is removed with the ion beam and the newly exposed face is imaged with the electron beam, usually by recording the backscattered electrons. The process, also called "slice and view," is repeated until the desired volume is imaged.As FIB-SEM allows 3D imaging of biological fine structure at high resolution of only small volumes, it is crucial to perform slice and view at carefully selected spots. Finding the region of interest is therefore a prerequisite for meaningful imaging. Thin layer plastification of biofilms offers direct access to the original sample surface and allows the selection of an ROI for site-specific FIB-SEM tomography just by its pronounced topographic features.

Mechanisms of material removal and mass transport in focused ion beam nanopore formation

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

Das, Kallol, E-mail: das7@illinois.edu; Johnson, Harley T., E-mail: htj@illinois.edu; Freund, Jonathan B., E-mail: jbfreund@illinois.edu

2015-02-28

Despite the widespread use of focused ion beam (FIB) processing as a material removal method for applications ranging from electron microscope sample preparation to nanopore processing for DNA sequencing, the basic material removal mechanisms of FIB processing are not well understood. We present the first complete atomistic simulation of high-flux FIB using large-scale parallel molecular dynamics (MD) simulations of nanopore fabrication in freestanding thin films. We focus on the root mechanisms of material removal and rearrangement and describe the role of explosive boiling in forming nanopores. FIB nanopore fabrication is typically understood to occur via sputter erosion. This can bemore » shown to be the case in low flux systems, where individual ion impacts are sufficiently separated in time that they may be considered as independent events. But our detailed MD simulations show that in high flux FIB processing, above a threshold level at which thermal effects become significant, the primary mechanism of material removal changes to a significantly accelerated, thermally dominated process. Under these conditions, the target is heated by the ion beam faster than heat is conducted away by the material, leading quickly to melting, and then continued heating to nearly the material critical temperature. This leads to explosive boiling of the target material with spontaneous bubble formation and coalescence. Mass is rapidly rearranged at the atomistic scale, and material removal occurs orders of magnitude faster than would occur by simple sputtering. While the phenomenology is demonstrated computationally in silicon, it can be expected to occur at lower beam fluxes in other cases where thermal conduction is suppressed due to material properties, geometry, or ambient thermal conditions.« less

In-situ integrity control of frozen-hydrated, vitreous lamellas prepared by the cryo-focused ion beam-scanning electron microscope.

PubMed

de Winter, D A Matthijs; Mesman, Rob J; Hayles, Michael F; Schneijdenberg, Chris T W M; Mathisen, Cliff; Post, Jan A

2013-07-01

Recently a number of new approaches have been presented with the intention to produce electron beam transparent cryo-sections (lamellas in FIB-SEM terminology) from hydrated vitreously frozen cryo samples with a Focused Ion Beam (FIB) system, suitable for cryo-Transmission Electron Microscopy (cryo-TEM). As the workflow is still challenging and time consuming, it is important to be able to determine the integrity and suitability (cells vs. no cells; vitreous vs. crystalline) of the lamellas. Here we present an in situ method that tests both conditions by using the cryo-Scanning Electron Microscope (cryo-SEM) in transmission mode (TSEM; Transmission Scanning Electron Microscope) once the FIB-made lamella is ready. Cryo-TSEM imaging of unstained cells yields strong contrast, enabling direct imaging of material present in the lamellas. In addition, orientation contrast is shown to be suitable for distinguishing crystalline lamellas from vitreous lamellas. Tilting the stage a few degrees results in changes of contrast between ice grains as a function of the tilt angle, whereas the contrast of areas with vitreous ice remains unchanged as a function of the tilt angle. This orientation contrast has subsequently been validated by cryo-Electron BackScattered Diffraction (EBSD) in transmission mode. Integration of the presented method is discussed and the role it can play in future developments for a new and innovative all-in-one cryo-FIB-SEM life sciences instrument. Copyright © 2013 Elsevier Inc. All rights reserved.

Comparing wastewater chemicals, indicator bacteria concentrations, and bacterial pathogen genes as fecal pollution indicators

USGS Publications Warehouse

Haack, S.K.; Duris, J.W.; Fogarty, L.R.; Kolpin, D.W.; Focazio, M.J.; Furlong, E.T.; Meyer, M.T.

2009-01-01

The objective of this study was to compare fecal indicator bacteria (FIB) (fecal coliforms, Escherichia coli [EC], and enterococci [ENT]) concentrations with a wide array of typical organic wastewater chemicals and selected bacterial genes as indicators of fecal pollution in water samples collected at or near 18 surface water drinking water intakes. Genes tested included esp (indicating human-pathogenic ENT) and nine genes associated with various animal sources of shiga-toxin-producing EC (STEC). Fecal pollution was indicated by genes and/or chemicals for 14 of the 18 tested samples, with little relation to FIB standards. Of 13 samples with <50 EC 100 mL-1, human pharmaceuticals or chemical indicators of wastewater treatment plant effluent occurred in six, veterinary antibiotics were detected in three, and stx1 or stx2 genes (indicating varying animal sources of STEC) were detected in eight. Only the EC eaeA gene was positively correlated with FIB concentrations. Human-source fecal pollution was indicated by the esp gene and the human pharmaceutical carbamazepine in one of the nine samples that met all FIB recreational water quality standards. Escherichia coli rfbO157 and stx2c genes, which are typically associated with cattle sources and are of potential human health significance, were detected in one sample in the absence of tested chemicals. Chemical and gene-based indicators of fecal contamination may be present even when FIB standards are met, and some may, unlike FIB, indicate potential sources. Application of multiple water quality indicators with variable environmental persistence and fate may yield greater confidence in fecal pollution assessment and may inform remediation decisions. Copyright ?? 2009 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Spin-coated epoxy resin embedding technique enables facile SEM/FIB thickness determination of porous metal oxide ultra-thin films.

PubMed

Peña, B; Owen, G Rh; Dettelbach, K E; Berlinguette, C P

2018-01-25

A facile nonsubjective method was designed to measure porous nonconductive iron oxide film thickness using a combination of a focused ion beam (FIB) and scanning electron microscopy. Iron oxide films are inherently nonconductive and porous, therefore the objective of this investigation was to optimize a methodology that would increase the conductivity of the film to facilitate high resolution imaging with a scanning electron microscopy and to preserve the porous nature of the film that could potentially be damaged by the energy of the FIB. Sputter coating the sample with a thin layer of iridium before creating the cross section with the FIB decreased sample charging and drifting, but differentiating the iron layer from the iridium coating with backscattered electron imaging was not definitive, making accurate assumptions of the delineation between the two metals difficult. Moreover, the porous nature of the film was lost due to beam damage following the FIB process. A thin layer plastication technique was therefore used to embed the porous film in epoxy resin that would provide support for the film during the FIB process. However, the thickness of the resin created using conventional thin layer plastication processing varied across the sample, making the measuring process only possible in areas where the resin layer was at its thinnest. Such variation required navigating the area for ideal milling areas, which increased the subjectivity of the process. We present a method to create uniform thin resin layers, of controlled thickness, that are ideal for quantifying the thickness of porous nonconductive films with FIB/scanning electron microscopy. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Metal oxide multilayer hard mask system for 3D nanofabrication

NASA Astrophysics Data System (ADS)

Han, Zhongmei; Salmi, Emma; Vehkamäki, Marko; Leskelä, Markku; Ritala, Mikko

2018-02-01

We demonstrate the preparation and exploitation of multilayer metal oxide hard masks for lithography and 3D nanofabrication. Atomic layer deposition (ALD) and focused ion beam (FIB) technologies are applied for mask deposition and mask patterning, respectively. A combination of ALD and FIB was used and a patterning procedure was developed to avoid the ion beam defects commonly met when using FIB alone for microfabrication. ALD grown Al2O3/Ta2O5/Al2O3 thin film stacks were FIB milled with 30 keV gallium ions and chemically etched in 5% tetramethylammonium hydroxide at 50 °C. With metal evaporation, multilayers consisting of amorphous oxides Al2O3 and Ta2O5 can be tailored for use in 2D lift-off processing, in preparation of embedded sub-100 nm metal lines and for multilevel electrical contacts. Good pattern transfer was achieved by lift-off process from the 2D hard mask for micro- and nano-scaled fabrication. As a demonstration of the applicability of this method to 3D structures, self-supporting 3D Ta2O5 masks were made from a film stack on gold particles. Finally, thin film resistors were fabricated by utilizing controlled stiction of suspended Ta2O5 structures.

Preparation and characterization of biohybrid poly (3-hydroxybutyrate-co-3-hydroxyvalerate) based nanofibrous scaffolds

NASA Astrophysics Data System (ADS)

Kouhi, Monireh; Fathi, Mohammadhossein; Venugopal, Jayarama Reddy; Shamanian, Morteza; Ramakrishna, Seeram

2018-01-01

Development of bioengineered scaffolds for bone tissue regeneration is a growing area of research, especially those involving biodegradable electrospun nanofibers incorporated with ceramic nanoparticles, since they can mimic the extracellular matrix (ECM) of the native bone. In the current study, a biocomposite nanofibrous scaffolds consisting of poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), fibrinogen (FIB) and bredigite (BR) nanoparticles was fabricated through electrospinning. The morphological, chemical and mechanical characteristics of the resultant scaffolds were studied by using field emission-scanning electron microscopy (FESEM), Fourier transform infrared spectroscopy (FTIR) and tensile tester, respectively. It was found that PHBV-FIB-BR scaffolds exhibited enhanced tensile strength and young modulus compared to PHBV and PHBV-FIB scaffolds. In addition, the measurements of the water contact angle suggested that incorporation of bredigite and fibrinogen into PHBV could improve the hydrophilicity of the composites. The results of bioactivity assessment performed in the simulated body fluid (SBF) demonstrated that the presence of the bredigite nanoparticles induced the nucleation and growth of apatite layer on the surface of PHBV-FIB-BR scaffold in SBF. Furthermore, the ion concentration changes of SBF solutions with composite scaffolds showed that PHBV-FIB-BR scaffolds released Ca and Si ions, which can stimulate osteoblast proliferation. The results of cell culture studies revealed the higher osteoblast proliferation, mineralization and differentiation on PHBV-FIB-BR and PHBV-FIB scaffolds than on PHBV. Our results suggest that PHBV-FIB-BR nanofibrous scaffold would be a promising candidate as a biocomposite nanofibrous scaffold material for tissue engineering applications.

Focused-ion-beam-inflicted surface amorphization and gallium implantation--new insights and removal by focused-electron-beam-induced etching.

PubMed

Roediger, P; Wanzenboeck, H D; Waid, S; Hochleitner, G; Bertagnolli, E

2011-06-10

Recently focused-electron-beam-induced etching of silicon using molecular chlorine (Cl(2)-FEBIE) has been developed as a reliable and reproducible process capable of damage-free, maskless and resistless removal of silicon. As any electron-beam-induced processing is considered non-destructive and implantation-free due to the absence of ion bombardment this approach is also a potential method for removing focused-ion-beam (FIB)-inflicted crystal damage and ion implantation. We show that Cl(2)-FEBIE is capable of removing FIB-induced amorphization and gallium ion implantation after processing of surfaces with a focused ion beam. TEM analysis proves that the method Cl(2)-FEBIE is non-destructive and therefore retains crystallinity. It is shown that Cl(2)-FEBIE of amorphous silicon when compared to crystalline silicon can be up to 25 times faster, depending on the degree of amorphization. Also, using this method it has become possible for the first time to directly investigate damage caused by FIB exposure in a top-down view utilizing a localized chemical reaction, i.e. without the need for TEM sample preparation. We show that gallium fluences above 4 × 10(15) cm(-2) result in altered material resulting from FIB-induced processes down to a depth of ∼ 250 nm. With increasing gallium fluences, due to a significant gallium concentration close beneath the surface, removal of the topmost layer by Cl(2)-FEBIE becomes difficult, indicating that gallium serves as an etch stop for Cl(2)-FEBIE.

The Effect of Molybdenum Substrate Oxidation on Molybdenum Splat Formation

NASA Astrophysics Data System (ADS)

Wang, Jun; Li, Chang-Jiu

2018-01-01

Disk splats are usually observed when the deposition temperature exceeds the transition temperature, whereas thick oxide layer will reduce the adhesion resulting from high deposition temperature. In present study, single molybdenum splats were deposited onto polished molybdenum substrates with different preheating processes to clarify the effect of surface oxidation on the splat formation. Three substrate samples experienced three different preheating processes in an argon atmosphere. Two samples were preheated to 350 and 550 °C, and another sample was cooled to 350 °C after it was preheated to 550 °C. The chemistry and compositions of substrate surface were examined by XPS. The cross sections of splats were prepared by focus ion beam (FIB) and then characterized by SEM. Nearly disk-shaped splat with small fingers in the periphery was observed on the sample preheated to 350 °C. A perfect disk-shape splat was deposited at 550 °C. With the sample on the substrate preheated to 350 °C (cooling down from 550 °C), flower-shaped splat exhibited a central core and discrete periphery detached by some voids. The results of peeling off splats by carbon tape and the morphology of FIB sampled cross sections indicated that no effective bonding formed at the splat-substrate interface for the substrate ever heated to 550 °C, due to the increasing content of MoO3 on the preheated molybdenum surface.

FIB-SEM cathodoluminescence tomography: practical and theoretical considerations.

PubMed

De Winter, D A M; Lebbink, M N; Wiggers De Vries, D F; Post, J A; Drury, M R

2011-09-01

Focused ion beam-scanning electron microscope (FIB-SEM) tomography is a powerful application in obtaining three-dimensional (3D) information. The FIB creates a cross section and subsequently removes thin slices. The SEM takes images using secondary or backscattered electrons, or maps every slice using X-rays and/or electron backscatter diffraction patterns. The objective of this study is to assess the possibilities of combining FIB-SEM tomography with cathodoluminescence (CL) imaging. The intensity of CL emission is related to variations in defect or impurity concentrations. A potential problem with FIB-SEM CL tomography is that ion milling may change the defect state of the material and the CL emission. In addition the conventional tilted sample geometry used in FIB-SEM tomography is not compatible with conventional CL detectors. Here we examine the influence of the FIB on CL emission in natural diamond and the feasibility of FIB-SEM CL tomography. A systematic investigation establishes that the ion beam influences CL emission of diamond, with a dependency on both the ion beam and electron beam acceleration voltage. CL emission in natural diamond is enhanced particularly at low ion beam and electron beam voltages. This enhancement of the CL emission can be partly explained by an increase in surface defects induced by ion milling. CL emission enhancement could be used to improve the CL image quality. To conduct FIB-SEM CL tomography, a recently developed novel specimen geometry is adopted to enable sequential ion milling and CL imaging on an untilted sample. We show that CL imaging can be manually combined with FIB-SEM tomography with a modified protocol for 3D microstructure reconstruction. In principle, automated FIB-SEM CL tomography should be feasible, provided that dedicated CL detectors are developed that allow subsequent milling and CL imaging without manual intervention, as the current CL detector needs to be manually retracted before a slice can be milled. Due to the required high electron beam acceleration voltage for CL emission, the resolution for FIB-SEM CL tomography is currently limited to several hundreds of nm in XY and up to 650 nm in Z for diamonds. Opaque materials are likely to have an improved Z resolution, as CL emission generated deeper in the material is not able to escape from it. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Electrical characterization of FIB processed metal layers for reliable conductive-AFM on ZnO microstructures

NASA Astrophysics Data System (ADS)

Pea, M.; Maiolo, L.; Giovine, E.; Rinaldi, A.; Araneo, R.; Notargiacomo, A.

2016-05-01

We report on the conductive-atomic force microscopy (C-AFM) study of metallic layers in order to find the most suitable configuration for electrical characterization of individual ZnO micro-pillars fabricated by focused ion beam (FIB). The electrical resistance between the probe tip and both as deposited and FIB processed metal layers (namely, Cr, Ti, Au and Al) has been investigated. Both chromium and titanium evidenced a non homogenous and non ohmic behaviour, non negligible scanning probe induced anodic oxidation associated to electrical measurements, and after FIB milling they exhibited significantly higher tip-sample resistance. Aluminium had generally a more apparent non conductive behaviour. Conversely, gold films showed very good tip-sample conduction properties being less sensitive to FIB processing than the other investigated metals. We found that a reliable C-AFM electrical characterization of ZnO microstructures obtained by FIB machining is feasible by using a combination of metal films as top contact layer. An Au/Ti bilayer on top of ZnO was capable to sustain the FIB fabrication process and to form a suitable ohmic contact to the semiconductor, allowing for reliable C-AFM measurement. To validate the consistency of this approach, we measured the resistance of ZnO micropillars finding a linear dependence on the pillar height, as expected for an ohmic conductor, and evaluated the resistivity of the material. This procedure has the potential to be downscaled to nanometer size structures by a proper choice of metal films type and thickness.

Two novel approaches to study arthropod anatomy by using dualbeam FIB/SEM.

PubMed

Di Giulio, Andrea; Muzzi, Maurizio

2018-03-01

Transmission Electron Microscopy (TEM) has always been the conventional method to study arthropod ultrastructure, while the use of Scanning Electron Microscopy (SEM) was mainly devoted to the examination of the external cuticular structures by secondary electrons. The new generation field emission SEMs are capable to generate images at sub-cellular level, comparable to TEM images employing backscattered electrons. The potential of this kind of acquisition becomes very powerful in the dual beam FIB/SEM where the SEM column is combined with a Focused Ion Beam (FIB) column. FIB uses ions as a nano-scalpel to slice samples fixed and embedded in resin, replacing traditional ultramicrotomy. We here present two novel methods, which optimize the use of FIB/SEM for studying arthropod anatomy. Copyright © 2017 Elsevier Ltd. All rights reserved.

Association of Fecal Indicator Bacteria with Human Viruses and Microbial Source Tracking Markers at Coastal Beaches Impacted by Nonpoint Source Pollution

PubMed Central

McQuaig, Shannon; Griffith, John

2012-01-01

Water quality was assessed at two marine beaches in California by measuring the concentrations of culturable fecal indicator bacteria (FIB) and by library-independent microbial source tracking (MST) methods targeting markers of human-associated microbes (human polyomavirus [HPyV] PCR and quantitative PCR, Methanobrevibacter smithii PCR, and Bacteroides sp. strain HF183 PCR) and a human pathogen (adenovirus by nested PCR). FIB levels periodically exceeded regulatory thresholds at Doheny and Avalon Beaches for enterococci (28.5% and 31.7% of samples, respectively) and fecal coliforms (20% and 5.8%, respectively). Adenoviruses were detected at four of five sites at Doheny Beach and were correlated with detection of HPyVs and human Bacteroides HF183; however, adenoviruses were not detected at Avalon Beach. The most frequently detected human source marker at both beaches was Bacteroides HF183, which was detected in 27% of samples. Correlations between FIBs and human markers were much more frequent at Doheny Beach than at Avalon Beach; e.g., adenovirus was correlated with HPyVs and HF183. Human sewage markers and adenoviruses were routinely detected in samples meeting FIB regulatory standards. The toolbox approach of FIB measurement coupled with analysis of several MST markers targeting human pathogens used here demonstrated that human sewage is at least partly responsible for the degradation of water quality, particularly at Doheny Beach, and resulted in a more definitive assessment of recreational water quality and human health risk than reliance on FIB concentrations alone could have provided. PMID:22773625

Complexities of Focused Ion Beam Preparation of Electron-Transparent Sections for Meteorite Studies

NASA Astrophysics Data System (ADS)

Ishii, H. A.; Bradley, J. P.; Teslich, N.

2012-09-01

Focused Ion Beam is increasingly used to prepare site-specific, electron-transparent sections for meteorite micro-texture and -chemistry studies. We discuss technical challenges and frequently-overlooked FIB artifacts relevant to meteorite analyses.

Thinning of Large Biological Cells for Cryo-TEM Characterization by Cryo-FIB Milling

PubMed Central

Strunk, Korrinn M.; Ke, Danxia; Gray, Jennifer L.; Zhang, Peijun

2013-01-01

SUMMARY Focused ion beam milling at cryogenic temperatures (cryo-FIB) is a valuable tool that can be used to thin vitreous biological specimens for subsequent imaging and analysis in a cryo-transmission electron microscope (cryo-TEM) in their frozen-hydrated state. This technique offers the potential benefit of eliminating the mechanical artifacts that are typically found with cryo-ultramicrotomy. However, due to the additional complexity in transferring samples in and out of the FIB, contamination and devitrification of the amorphous ice is commonly encountered. In order to address these problems, we have designed a new sample cryo-shuttle that specifically accepts Polara TEM cartridges directly in order to simplify the transfer process between the FIB and TEM. We used the quality of the ice in the sample as an indicator to test various parameters used the process, and demonstrated with successful milling of large mammalian cells. By comparing the results from larger HeLa cells to those from E. coli cells, we discuss some of the artifacts and challenges we have encountered using this technique. PMID:22906009

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

Liu, Zhao; Chen-Wiegart, Yu-chen K.; Wang, Jun

Three-phase three-dimensional (3D) microstructural reconstructions of lithium-ion battery electrodes are critical input for 3D simulations of electrode lithiation/delithiation, which provide a detailed understanding of battery operation. In this report, 3D images of a LiCoO 2electrode are achieved using focused ion beam-scanning electron microscopy (FIB-SEM), with clear contrast among the three phases: LiCoO 2particles, carbonaceous phases (carbon and binder) and the electrolyte space. The good contrast was achieved by utilizing an improved FIB-SEM sample preparation method that combined infiltration of the electrolyte space with a low-viscosity silicone resin and triple ion-beam polishing. Morphological parameters quantified include phase volume fraction, surface area,more » feature size distribution, connectivity, and tortuosity. Electrolyte tortuosity was determined using two different geometric calculations that were in good agreement. In conclusion, the electrolyte tortuosity distribution versus position within the electrode was found to be highly inhomogeneous; this will lead to inhomogeneous electrode lithiation/delithiation at high C-rates that could potentially cause battery degradation.« less

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

Liu, Zhao; Chen-Wiegart, Yu-chen K.; Wang, Jun

Abstract Three-phase three-dimensional (3D) microstructural reconstructions of lithium-ion battery electrodes are critical input for 3D simulations of electrode lithiation/delithiation, which provide a detailed understanding of battery operation. In this report, 3D images of a LiCoO 2electrode are achieved using focused ion beam-scanning electron microscopy (FIB-SEM), with clear contrast among the three phases: LiCoO 2particles, carbonaceous phases (carbon and binder) and the electrolyte space. The good contrast was achieved by utilizing an improved FIB-SEM sample preparation method that combined infiltration of the electrolyte space with a low-viscosity silicone resin and triple ion-beam polishing. Morphological parameters quantified include phase volume fraction, surfacemore » area, feature size distribution, connectivity, and tortuosity. Electrolyte tortuosity was determined using two different geometric calculations that were in good agreement. The electrolyte tortuosity distribution versus position within the electrode was found to be highly inhomogeneous; this will lead to inhomogeneous electrode lithiation/delithiation at high C-rates that could potentially cause battery degradation.« less

Storm drains are sources of human fecal pollution during dry weather in three urban southern California watersheds.

PubMed

Sercu, Bram; Van De Werfhorst, Laurie C; Murray, Jill; Holden, Patricia A

2009-01-15

Coastal urbanized areas in Southern California experience frequent beach water quality warnings in summer due to high concentrations of fecal indicator bacteria (FIB). Remediation can be difficult, as sources are often unknown. During two summers, we sampled three urbanized watersheds in Santa Barbara, CA at sites with historically high FIB concentrations to determine if human fecal matter was influencing water quality. By quantification of a human-specific Bacteroides marker (HBM), human waste was evidenced throughout both transects, and concentrations were highest in the discharges of several flowing storm drains. The HBM concentrations in storm drain discharges varied by up to 5 orders of magnitude on the same day. While the exact points of entry into the storm drain systems were not definitively determined, further inspection of the drain infrastructure suggested exfiltrating sanitary sewers as possible sources. The HBM and FIB concentrations were not consistently correlated, although the exclusive occurrence of high HBM concentrations with high FIB concentrations warrants the use of FIB analyses for a first tier of sampling. The association of human fecal pollution with dry weather drainage could be a window into a larger problem for other urbanized coastal areas with Mediterranean-type climates.

Recent improvement of a FIB-SEM serial-sectioning method for precise 3D image reconstruction - application of the orthogonally-arranged FIB-SEM.

PubMed

Hara, Toru

2014-11-01

IntroductionWe installed the first "orthogonally-arranged" FIB-SEM in 2011. The most characteristic point of this instrument is that the FIB and SEM columns are perpendicularly mounted; this is specially designed to obtain a serial-sectioning dataset more accurately and precisely with higher contrast and higher spatial resolution compare to other current FIB-SEMs [1]. Since the installation in 2011, we have developed the hardware and methodology of the serial-sectioning based on this orthogonal FIB-SEM. In order to develop this technique, we have widely opened this instrument to every researcher of all fields. In the presentation, I would like to introduce some of application results that are obtained by users of this instrument. The characteristic points of the orthogonal systemFigure 1 shows a difference between the standard and the orthogonal FIB-SEM systems: In the standard system, shown in Fig.1(a), optical axes of a FIB and a SEM crosses around 60deg., while in the orthogonal system (Fig.1(b)), they are perpendicular to each other. The standard arrangement (a) is certainly suitable for TEM lamellae preparation etc. because the FIB and the SEM can see the same position simultaneously. However, for a serial-sectioning, it is not to say the best arrangement. One of the reasons is that the sliced plane by the FIB is not perpendicular to the electron beam so that the background contrast is not uniform and observed plane is distorted. On the other hand, in case of the orthogonally-arranged system,(b), these problems are resolved. In addition, spatial resolution can keep high enough even in a low accelerating voltage (e.g. 500V) because a working distance is set very small, 2mm. From these special design, we can obtain the serial-sectioning dataset from rather wide area (∼100um) with high spatial resolution (Max. 2×2×2nm). As this system has many kinds of detectors: SE, ET, Backscatter Electron(Energy-selective), EDS, EBSD, STEM(BF&ADF), with Ar+ ion-gun and a plasma cleaner, many kinds of signals can be obtained simultaneously.jmicro;63/suppl_1/i5-a/DFU077F1F1DFU077F1Fig. 1.Schematic illustration described (a) a standard type arrangement, (b) an orthogonal type arrangement. Recent topics and Future prospectsWe have applied this instrument for wide area of microstructure analysis; Metals and Alloys, Semiconductor devices, Battery electrodes, Minerals, Biomaterials, and so on. In my presentation, I would like to introduce some of our application results and will discuss about future development of the methodology of a FIB-SEM serial sectioning. As the applied research field becomes wider, various requests for the method were arisen. However, most requests can be summarized as follows: observation of larger area, expansion of applicable sample, obtain many kind of information, linkage with other instruments. AcknowledgmentsThe instrument introduced in this work was installed at NIMS by a part of "Low-carbon research network Japan" funded by the MEXT,Japan. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

TEM Analysis of Diffusion-Bonded Silicon Carbide Ceramics Joined Using Metallic Interlayers

NASA Technical Reports Server (NTRS)

Ozaki, T.; Hasegawa, Y.; Tsuda, H.; Mori, S.; Halbig, M. C.; Asthana, R.; Singh, M.

2017-01-01

SiC fiber-bonded ceramics (SA-Tyrannohex: SA-THX) diffusion-bonded with TiCu metallic interlayers were investigated. Thin samples of the ceramics were prepared with a focused ion beam (FIB) and the interfacial microstructure of the prepared samples was studied by transmission electron microscopy (TEM) and scanning TEM (STEM). In addition to conventional microstructure observation, for detailed analysis of reaction compounds in diffusion-bonded area, we performed STEM-EDS measurements and selected area electron diffraction (SAD) experiments. The TEM and STEM experiments revealed the diffusion-bonded area was composed of only one reaction layer, which was characterized by TiC precipitates in Cu-Si compound matrix. This reaction layer was in good contact with the SA-THX substrates, and it is concluded that the joint structure led to the excellent bonding strength.

Mapping the Complex Morphology of Cell Interactions with Nanowire Substrates Using FIB-SEM

PubMed Central

Jensen, Mikkel R. B.; Łopacińska, Joanna; Schmidt, Michael S.; Skolimowski, Maciej; Abeille, Fabien; Qvortrup, Klaus; Mølhave, Kristian

2013-01-01

Using high resolution focused ion beam scanning electron microscopy (FIB-SEM) we study the details of cell-nanostructure interactions using serial block face imaging. 3T3 Fibroblast cellular monolayers are cultured on flat glass as a control surface and on two types of nanostructured scaffold substrates made from silicon black (Nanograss) with low- and high nanowire density. After culturing for 72 hours the cells were fixed, heavy metal stained, embedded in resin, and processed with FIB-SEM block face imaging without removing the substrate. The sample preparation procedure, image acquisition and image post-processing were specifically optimised for cellular monolayers cultured on nanostructured substrates. Cells display a wide range of interactions with the nanostructures depending on the surface morphology, but also greatly varying from one cell to another on the same substrate, illustrating a wide phenotypic variability. Depending on the substrate and cell, we observe that cells could for instance: break the nanowires and engulf them, flatten the nanowires or simply reside on top of them. Given the complexity of interactions, we have categorised our observations and created an overview map. The results demonstrate that detailed nanoscale resolution images are required to begin understanding the wide variety of individual cells’ interactions with a structured substrate. The map will provide a framework for light microscopy studies of such interactions indicating what modes of interactions must be considered. PMID:23326412

Atomistic simulations of focused ion beam machining of strained silicon

NASA Astrophysics Data System (ADS)

Guénolé, J.; Prakash, A.; Bitzek, E.

2017-09-01

The focused ion beam (FIB) technique has established itself as an indispensable tool in the material science community, both to analyze samples and to prepare specimens by FIB milling. In combination with digital image correlation (DIC), FIB milling can, furthermore, be used to evaluate intrinsic stresses by monitoring the strain release during milling. The irradiation damage introduced by such milling, however, results in a change in the stress/strain state and elastic properties of the material; changes in the strain state in turn affect the bonding strength, and are hence expected to implicitly influence irradiation damage formation and sputtering. To elucidate this complex interplay between strain, irradiation damage and sputtering, we perform TRIM calculations and molecular dynamics simulations on silicon irradiated by Ga+ ions, with slab and trench-like geometries, whilst simultaneously applying uniaxial tensile and compressive strains up to 4%. In addition we calculate the threshold displacement energy (TDE) and the surface binding energy (SBE) for various strain states. The sputter rate and amount of damage produced in the MD simulations show a clear influence of the strain state. The SBE shows no significant dependence on strain, but is strongly affected by surface reconstructions. The TDE shows a clear strain-dependence, which, however, cannot explain the influence of strain on the extent of the induced irradiation damage or the sputter rate.

Distinction between amorphous and healed planar deformation features in shocked quartz using composite color scanning electron microscope cathodoluminescence (SEM-CL) imaging

NASA Astrophysics Data System (ADS)

Hamers, Maartje F.; Pennock, Gill M.; Herwegh, Marco; Drury, Martyn R.

2016-10-01

Planar deformation features (PDFs) in quartz are one of the most reliable and most widely used forms of evidence for hypervelocity impact. PDFs can be identified in scanning electron microscope cathodoluminescence (SEM-CL) images, but not all PDFs show the same CL behavior: there are nonluminescent and red luminescent PDFs. This study aims to explain the origin of the different CL emissions in PDFs. Focused ion beam (FIB) thin foils were prepared of specific sample locations selected in composite color SEM-CL images and were analyzed in a transmission electron microscope (TEM). The FIB preparation technique allowed a direct, often one-to-one correlation between the CL images and the defect structure observed in TEM. This correlation shows that composite color SEM-CL imaging allows distinction between amorphous PDFs on one hand and healed PDFs and basal Brazil twins on the other: nonluminescent PDFs are amorphous, while healed PDFs and basal Brazil twins are red luminescent, with a dominant emission peak at 650 nm. We suggest that the red luminescence is the result of preferential beam damage along dislocations, fluid inclusions, and twin boundaries. Furthermore, a high-pressure phase (possibly stishovite) in PDFs can be detected in color SEM-CL images by its blue luminescence.

3D-profile measurement of advanced semiconductor features by using FIB as reference metrology

NASA Astrophysics Data System (ADS)

Takamasu, Kiyoshi; Iwaki, Yuuki; Takahashi, Satoru; Kawada, Hiroki; Ikota, Masami

2017-03-01

A novel method of sub-nanometer uncertainty for the 3D-profile measurement and LWR (Line Width Roughness) measurement by using FIB (Focused Ion Beam) processing, and TEM (Transmission Electron Microscope) and CD-SEM (Critical Dimension Scanning Electron Microscope) images measurement is proposed to standardize 3D-profile measurement through reference metrology. In this article, we apply the methodology to line profile measurements and roughness measurement of advanced FinFET (Fin-shaped Field-Effect Transistor) features. The FinFET features are horizontally sliced as a thin specimen by FIB micro sampling system. Horizontally images of the specimens are obtained then by a planar TEM. LWR is calculated from the edges positions on TEM images. Moreover, we already have demonstrated the novel on-wafer 3D-profile metrology as "FIB-to-CDSEM method" with FIB slope cut and CD-SEM measuring. Using the method, a few micrometers wide on a wafer is coated and cut by 45-degree slope using FIB tool. Then, the wafer is transferred to CD-SEM to measure the cross section image by top down CD-SEM measurement. We applied FIB-to-CDSEM method to a CMOS image sensor feature. The 45-degree slope cut surface is observed using AFM. The surface profile of slope cut surface and line profiles are analyzed for improving the accuracy of FIB-to-CDSEM method.

Formation of the YBa2Cu2NbOy Phase in Thin Films (POSTPRINT)

DTIC Science & Technology

2010-03-01

protective layer was deposited on the top of YBCNO film by dc sputtering . A 200 nm 200 nm area film was selected and cut with a Ga ion beam (30 kV...200 TEM at 200 kV. Samples for TEM were prepared using a focused ion beam (FIB (Eindhoven, The Netherlands)) microscope. For TEM examination, a thin Pt...by dc magnetron sputtering deposition of Ag with 93 mm thickness. Transport current measurements were made in liquid nitrogen with the 4-probe method

Determination of the sequence of intersecting lines using Focused Ion Beam/Scanning Electron Microscope.

PubMed

Kim, Jiye; Kim, MinJung; An, JinWook; Kim, Yunje

2016-05-01

The aim of this study was to verify that the combination of focused ion beam (FIB) and scanning electron microscope/energy-dispersive X-ray (SEM/EDX) could be applied to determine the sequence of line crossings. The samples were transferred into FIB/SEM for FIB milling and an imaging operation. EDX was able to explore the chemical components and the corresponding elemental distribution in the intersection. The technique was successful in determining the sequence of heterogeneous line intersections produced using gel pens and red sealing ink with highest success rate (100% correctness). These observations show that the FIB/SEM was the appropriate instrument for an overall examination of document. © 2016 American Academy of Forensic Sciences.

The Interior Analysis and 3-D Reconstruction of Internally-Mixed Light-Absorbing Atmospheric Particles

NASA Astrophysics Data System (ADS)

Conny, J. M.; Collins, S. M.; Anderson, I.; Herzing, A.

2010-12-01

Carbon-containing atmospheric particles may either absorb solar or outgoing long-wave radiation or scatter solar radiation, and thus, affect Earth’s radiative balance in multiple ways. Light-absorbing carbon that is common in urban air particles such as industrial coke dust, road dust, and diesel soot, often exists in the same particle with other phases that contain, for example, aluminum, calcium, iron, and sulfur. While the optical properties of atmospheric particles in general depend on overall particle size and shape, the inhomogeneity of chemical phases within internally-mixed particles may also greatly affect particle optical properties. In this study, a series of microscopic approaches were used to identify individual light-absorbing coarse-mode particles and to assess their interior structure and composition. Particle samples were collected in 2004 from one of the U.S. EPA’s Los Angeles Particulate Matter Supersites, and were likely affected substantially by road dust and construction dust. First, bright-field and dark-field light microscopy and computer-controlled scanning electron microscopy (SEM) with energy-dispersive x-ray spectroscopy (EDX) were used to distinguish predominantly light-absorbing carbonaceous particles from other particle types such as mineral dust, sea salt, and brake wear. Second, high-resolution SEM-EDX elemental mapping of individual carbonaceous particles was used to select particles with additional elemental phases that exhibited spatial inhomogeneity. Third, focused ion-beam SEM (FIB-SEM) with EDX was used to slice through selected particles to expose interior surfaces and to determine the spatial distribution of element phases throughout the particles. Fourth, study of the interior phases of a particle was augmented by the transmission electron microscopy (TEM) of a thin section of the particle prepared by FIB-SEM. Here, electron energy loss spectroscopy with TEM was used to study chemical bonding in the carbonaceous phase. Finally, automated serial slicing and imaging in the FIB-SEM generated a stack of secondary electron images of the particles’ interior surfaces that allowed for the 3-D reconstruction of the particles, a process known as FIB tomography. Interior surface of light-absorbing carbonaceous particle from FIB-SEM analysis.

Probing the magnetic moment of FePt micromagnets prepared by focused ion beam milling

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

Overweg, H. C.; Haan, A. M. J. den; Eerkens, H. J.

2015-08-17

We investigate the degradation of the magnetic moment of a 300 nm thick FePt film induced by Focused Ion Beam (FIB) milling. A 1 μm × 8 μm rod is milled out of a film by a FIB process and is attached to a cantilever by electron beam induced deposition. Its magnetic moment is determined by frequency-shift cantilever magnetometry. We find that the magnetic moment of the rod is μ = 1.1 ± 0.1 × 10{sup −12} Am{sup 2}, which implies that 70% of the magnetic moment is preserved during the FIB milling process. This result has important implications for atom trapping and magnetic resonance force microscopy, which are addressed inmore » this paper.« less

Amorphization induced by focused ion beam milling in metallic and electronic materials.

PubMed

Huh, Yoon; Hong, Ki Jung; Shin, Kwang Soo

2013-08-01

Focused ion beam (FIB) milling using high-energy gallium ions is widely used in the preparation of specimens for transmission electron microscopy (TEM). However, the energetic ion beam induces amorphization on the edge of specimens during milling, resulting in a mischievous influence on the clearness of high-quality transmission electron micrographs. In this work, the amorphization induced by the FIB milling was investigated by TEM for three kinds of materials, metallic materials in bulk shape, and semiconductive and electronic ceramic materials as a substrate for the deposition of thin films.

Long-term monitoring of molecular markers can distinguish different seasonal patterns of fecal indicating bacteria sources.

PubMed

Riedel, Timothy E; Thulsiraj, Vanessa; Zimmer-Faust, Amity G; Dagit, Rosi; Krug, Jenna; Hanley, Kaitlyn T; Adamek, Krista; Ebentier, Darcy L; Torres, Robert; Cobian, Uriel; Peterson, Sophie; Jay, Jennifer A

2015-03-15

Elevated levels of fecal indicator bacteria (FIB) have been observed at Topanga Beach, CA, USA. To identify the FIB sources, a microbial source tracking study using a dog-, a gull- and two human-associated molecular markers was conducted at 10 sites over 21 months. Historical data suggest that episodic discharge from the lagoon at the mouth of Topanga Creek is the main source of bacteria to the beach. A decline in creek FIB/markers downstream from upper watershed development and a sharp increase in FIB/markers at the lagoon sites suggest sources are local to the lagoon. At the lagoon and beach, human markers are detected sporadically, dog marker peaks in abundance mid-winter, and gull marker is chronically elevated. Varied seasonal patterns of FIB and source markers were identified showing the importance of applying a suite of markers over long-term spatial and temporal sampling to identify a complex combination of sources of contamination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Temporal and spatial patterns for surf zone bacteria before and after disinfection of the orange county sanitation district effluent

USGS Publications Warehouse

Robertson, G.L.; Noble, M.A.; Xu, J. P.; Rosenfeld, L.K.; McGee, C.D.

2005-01-01

Data from pre- and post-disinfection fecal indicator bacteria (FIB) samples from final effluent, an offshore ocean outfall, and surf zone stations off Huntington Beach, CA were compared. Analysis of the results from these data sets confirmed that the ocean outfall was not the FIB source responsible for the postings and closures of local beaches that have occurred each summer since 1999. While FIB counts in the final effluent and offshore showed several order of magnitude reductions after disinfection, there were no significant reductions at the nearby surf zone stations. Additionally, the FIB spectral patterns suggest different sources. The dominant fortnightly cycle suggested that the source was related to the wetting and draining of the land from large spring tide tidal excursions.

COMPARATIVE STUDY OF FIB-4 INDEX AND TRANSIENT ELASTOGRAPHY AMONG PATIENTS WITH CHRONIC HEPATITIS C VIRUS INFECTION IN GEORGIA.

PubMed

Dolmazashvili, E; Karchava, M; Abutidze, A; Sharvadze, L; Tsertsvadze, T

2017-03-01

Liver biopsy remains the reference standard for fibrosis staging. However, it has several limitations, which have led to the development of non-invasive methods. We evaluated liver fibrosis severity among HCV infected patients by comparing transient elastography (TE) and FIB-4 index. Retrospective study was conducted. Clinical data for 750 patients were obtained. The mean age of the study population was 51 years; 595 (79.3%) were male and 155 (20.7%) were female. TE and tests on biological samples were performed within one-week timeframe. Additional analyses of prothrombin index, albumin concentration, splenomegaly on abdominal ultrasound and esophageal varices on upper gastrointestinal endoscopy were performed among selected patients. Comparable results were observed among 534 patients (71.2%). FIB-4<1.45 had a negative predictive value of 89% to exclude significant fibrosis and FIB-4>3.25 had a positive predictive value of 100 % to confirm the existence of significant fibrosis. Inconclusive FIB-4 score was obtained in 170 (22.7%) patients. Of them 127 (74.7%) had significant fibrosis (F3-F4) by TE. Discordant results (FIB-4 <1.45 and Liver Stiffness Measurement (LSM) >9.5 kpa) were observed in 46 (6.1%) of patients. Low prothrombin index, low albumin concentration, splenomegaly and esophageal varices were significantly (p<0.001) correlated with TE results. Discrepancy showing high FIB-4 score and low LSM was not observed in our cohort. There was a good correlation between TE and FIB-4 score. FIB-4 could rapidly replace expensive methods to assess liver fibrosis severity in some scenarios. However, our study demonstrated superiority of TE. LSM correlated better with indirect markers of significant fibrosis.

Impacts of beach wrack removal via grooming on surf zone water quality.

PubMed

Russell, Todd L; Sassoubre, Lauren M; Zhou, Christina; French-Owen, Darien; Hassaballah, Abdulrahman; Boehm, Alexandria B

2014-02-18

Fecal indicator bacteria (FIB) are used to assess the microbial water quality of recreational waters. Increasingly, nonfecal sources of FIB have been implicated as causes of poor microbial water quality in the coastal environment. These sources are challenging to quantify and difficult to remediate. The present study investigates one nonfecal FIB source, beach wrack (decaying aquatic plants), and its impacts on water quality along the Central California coast. The prevalence of FIB on wrack was studied using a multibeach survey, collecting wrack throughout Central California. The impacts of beach grooming, to remove wrack, were investigated at Cowell Beach in Santa Cruz, California using a long-term survey (two summers, one with and one without grooming) and a 48 h survey during the first ever intensive grooming event. FIB were prevalent on wrack but highly variable spatially and temporally along the nine beaches sampled in Central California. Beach grooming was generally associated with either no change or a slight increase in coastal FIB concentrations and increases in surf zone turbidity and silicate, phosphate, and dissolved inorganic nitrogen concentrations. The findings suggest that beach grooming for wrack removal is not justified as a microbial pollution remediation strategy.

Improving microstructural quantification in FIB/SEM nanotomography.

PubMed

Taillon, Joshua A; Pellegrinelli, Christopher; Huang, Yi-Lin; Wachsman, Eric D; Salamanca-Riba, Lourdes G

2018-01-01

FIB/SEM nanotomography (FIB-nt) is a powerful technique for the determination and quantification of the three-dimensional microstructure in subsurface features. Often times, the microstructure of a sample is the ultimate determiner of the overall performance of a system, and a detailed understanding of its properties is crucial in advancing the materials engineering of a resulting device. While the FIB-nt technique has developed significantly in the 15 years since its introduction, advanced nanotomographic analysis is still far from routine, and a number of challenges remain in data acquisition and post-processing. In this work, we present a number of techniques to improve the quality of the acquired data, together with easy-to-implement methods to obtain "advanced" microstructural quantifications. The techniques are applied to a solid oxide fuel cell cathode of interest to the electrochemistry community, but the methodologies are easily adaptable to a wide range of material systems. Finally, results from an analyzed sample are presented as a practical example of how these techniques can be implemented. Copyright © 2017 Elsevier B.V. All rights reserved.

Nano-inclusions in diamond: Evidence of diamond genesis

NASA Astrophysics Data System (ADS)

Wirth, R.

2015-12-01

The use of Focused Ion Beam technology (FIB) for TEM sample preparation introduced approximately 15 years ago revolutionized the application of TEM in Geosciences. For the first time, FIB enabled cutting samples for TEM use from exactly the location we are interested in. Applied to diamond investigation, this technique revealed the presence of nanometre-sized inclusions in diamond that have been simply unknown before. Nanoinclusions in diamond from different location and origin such as diamonds from the Lower and Upper Mantle, metamorphic diamonds (Kazakhstan, Erzgebirge, Bohemia), diamonds from ophiolites (Tibet, Mongolia, Xinjiang, Ural Mountains), diamonds from igneous rocks (Hawaii, Kamchatka) and impact diamonds (Popigai Crater, Siberia) have been investigated during the last 15 years. The major conclusion of all these TEM studies is, that the nanoinclusions, their phases and phase composition together with the micro- and nanostructure evidence the origin of diamond and genesis of diamond. We can discriminate Five different mechanisms of diamond genesis in nature are observed: Diamond crystallized from a high-density fluid (Upper mantle and metamorphic diamond). Diamond crystallized from carbonatitic melt (Lower mantle diamond). Diamond precipitates from a metal alloy melt (Diamond from ophiolites). Diamond crystallized by gas phase condensation or chemical vapour condensation (CVD) (Lavas from Kamchatka, xenoliths in Hawaiian lavas). Direct transformation of graphite into diamond.

Atomic-scale thermocapillary flow in focused ion beam milling

NASA Astrophysics Data System (ADS)

Das, Kallol; Johnson, Harley; Freund, Jonathan

2016-11-01

Focused ion beams (FIB) offer an attractive tool for nanometer-scale manufacturing and material processing, particularly because they can be focused to a few nanometer diameter spot. This motivates their use for many applications, such as sample preparation for transmission electron microscopy (TEM), forming nanometer scale pores in thin films for DNA sequencing. Despite its widespread use, the specific mechanisms of FIB milling, especially at high ion fluxes for which significant phase change might occur, remains incompletely understood. Here we investigate the process of nanopore fabrication in thin Si films using molecular dynamics simulation where Ga+ ions are used as the focused ions. For a range of ion intensities in a realistic configuration, a recirculating melt region develops, which is seen to flow with a symmetrical pattern, counter to how it would flow were it is driven by the ion momentum flux. Such flow is potentially important for the shape and composition of the formed structures. Relevant stress scales and estimated physical properties of silicon under these extreme conditions support the importance thermocapillary effects. A continuum flow model with Marangoni forcing reproduces the flow.

Gene and antigen markers of Shiga-toxin producing E. coli from Michigan and Indiana river water: Occurrence and relation to recreational water quality criteria

USGS Publications Warehouse

Duris, J.W.; Haack, S.K.; Fogarty, L.R.

2009-01-01

The relation of bacterial pathogen occurrence to fecal indicator bacteria (FIB) concentrations used for recreational water quality criteria (RWQC) is poorly understood. This study determined the occurrence of Shiga-toxin producing Escherichia coli (STEC) markers and their relation to FIB concentrations in Michigan and Indiana river water. Using 67 fecal coliform (FC) bacteria cultures from 41 river sites in multiple watersheds, we evaluated the occurrence of five STEC markers: the Escherichia coli (EC) O157 antigen and gene, and the STEC virulence genes eaeA, stx1, and stx2. Simple isolations from selected FC cultures yielded viable EC O157. By both antigen and gene assays, EC O157 was detected in a greater proportion of samples exceeding rather than meeting FC RWQC (P < 0.05), but was unrelated to EC and enterococci RWQC. The occurrence of all other STEC markers was unrelated to any FIB RWQC. The eaeA, stx2, and stx1 genes were found in 93.3, 13.3, and in 46.7% of samples meeting FC RWQC and in 91.7, 0.0, and 37.5% of samples meeting the EC RWQC. Although not statistically significant, the percentage of samples positive for each STEC marker except stx1 was lower in samples that met, as opposed to exceeded, FIB RWQC. Viable STEC were common members of the FC communities in river water throughout southern Michigan and northern Indiana, regardless of FIB RWQC. Our study indicates that further information on the occurrence of pathogens in recreational waters, and research on alternative indicators of their occurrence, may help inform water-resource management and public health decision-making. Copyright ?? 2009 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Preparation of Regular Specimens for Atom Probes

NASA Technical Reports Server (NTRS)

Kuhlman, Kim; Wishard, James

2003-01-01

A method of preparation of specimens of non-electropolishable materials for analysis by atom probes is being developed as a superior alternative to a prior method. In comparison with the prior method, the present method involves less processing time. Also, whereas the prior method yields irregularly shaped and sized specimens, the present developmental method offers the potential to prepare specimens of regular shape and size. The prior method is called the method of sharp shards because it involves crushing the material of interest and selecting microscopic sharp shards of the material for use as specimens. Each selected shard is oriented with its sharp tip facing away from the tip of a stainless-steel pin and is glued to the tip of the pin by use of silver epoxy. Then the shard is milled by use of a focused ion beam (FIB) to make the shard very thin (relative to its length) and to make its tip sharp enough for atom-probe analysis. The method of sharp shards is extremely time-consuming because the selection of shards must be performed with the help of a microscope, the shards must be positioned on the pins by use of micromanipulators, and the irregularity of size and shape necessitates many hours of FIB milling to sharpen each shard. In the present method, a flat slab of the material of interest (e.g., a polished sample of rock or a coated semiconductor wafer) is mounted in the sample holder of a dicing saw of the type conventionally used to cut individual integrated circuits out of the wafers on which they are fabricated in batches. A saw blade appropriate to the material of interest is selected. The depth of cut and the distance between successive parallel cuts is made such that what is left after the cuts is a series of thin, parallel ridges on a solid base. Then the workpiece is rotated 90 and the pattern of cuts is repeated, leaving behind a square array of square posts on the solid base. The posts can be made regular, long, and thin, as required for samples for atom-probe analysis. Because of their small volume and regularity, the amount of FIB-milling time can be much less than that of the method of sharp shards. Individual posts can be broken off for mounting in a manner similar to that of the method of sharp shards. Alternatively, the posts can be left intact on the base and the base can be cut to a small square (e.g., 3 by 3 mm) suitable for mounting in an atom probe of a type capable of accepting multiple-tip specimens. The advantage of multiple-tip specimens is the possibility of analyzing many tips without the time-consuming interchange of specimens.

Electroless silver coating of rod-like glass particles.

PubMed

Moon, Jee Hyun; Kim, Kyung Hwan; Choi, Hyung Wook; Lee, Sang Wha; Park, Sang Joon

2008-09-01

An electroless silver coating of rod-like glass particles was performed and silver glass composite powders were prepared to impart electrical conductivity to these non-conducting glass particles. The low density Ag-coated glass particles may be utilized for manufacturing conducting inorganic materials for electromagnetic interference (EMI) shielding applications and the techniques for controlling the uniform thickness of silver coating can be employed in preparation of biosensor materials. For the surface pretreatment, Sn sensitization was performed and the coating powders were characterized by scanning electron microscopy (SEM), focused ion beam microscopy (FIB), and atomic force microscopy (AFM) along with the surface resistant measurements. In particular, the use of FIB technique for determining directly the Ag-coating thickness was very effective on obtaining the optimum conditions for coating. The surface sensitization and initial silver loading for electroless silver coating could be found and the uniform and smooth silver-coated layer with thickness of 46 nm was prepared at 2 mol/l of Sn and 20% silver loading.

The effect of SEM imaging on the Ar/Ar system in feldspars

NASA Astrophysics Data System (ADS)

Flude, S.; Sherlock, S.; Lee, M.; Kelley, S. P.

2010-12-01

Complex microtextures form in K-feldspar crystals as they cool and are affected by deuteric alteration. This complex structure is the cause of variable closure temperatures for Ar-Ar, a phenomenon which has been utilized in multi domain diffusion (MDD) modelling to recover thermal histories [1]. However, there has been substantial controversy regarding the precise interaction between feldspar microtextures and Ar-diffusion [2,3]. A number of studies have addressed this issue using coupled SEM imaging and Ar/Ar UV laser ablation microprobe (UV-LAMP) analysis on the same sample, to enable direct comparison of microtextures with Ar/Ar age data [4]. Here we have tested the idea that SEM work may affect Ar/Ar ages, leading to inaccurate results in subsequent Ar/Ar analyses. Three splits of alkali feldspar from the Dartmoor Granite in SW England were selected for Ar/Ar UV-LAMP analysis. Split 1 (“control”) was prepared as a polished thick section for Ar/Ar analysis. Split 2 (“SEM”) was prepared as a polished thick section, was chemically-mechanically polished with colloidal silica and underwent SEM imaging (uncoated) and focussed ion beam (FIB) milling (gold coated); electron beam damage in the SEM was maximised by leaving the sample at high magnification for eight minutes. Split 3 (“Etch”) is a cleavage fragment that was etched with HF vapour and underwent low to moderate magnification SEM imaging. The control split gave a range of laser-spot ages consistent with the expected cooling age of the granite and high yields of radiogenic 40Ar* (>90%). The area of the “SEM” split that experienced significant electron beam damage gave younger than expected ages and 40Ar* yields as low as 57%. These are interpreted as a combination of implantation of atmospheric Ar and local redistribution of K within the sample. The area of “SEM” that underwent FIB milling gave ages and 40Ar* yields comparable to the control split, suggesting that the Au-coat minimises FIB damage and that colloidal-polishing and low-magnification SEM imaging do not affect the Ar/Ar system. The “Etch” split gave younger than expected ages and 40Ar* yields as low as 58%, suggesting that HF etching also disrupts the Ar/Ar system. These results suggest that SEM techniques involving intense electron bombardment of an uncoated sample, such as charge contrast imaging and electron backscatter diffraction (EBSD), may disrupt the Ar/Ar system in the sample, leading to spurious results. Etching samples with HF, as is often done for routine Ar/Ar preparation of volcanic phenocrysts, introduces atmospheric Ar and may result in differential loss or gain of K and Ar isotopes, leading to spurious results. References [1] Lovera and Richter, 1989, J. Geophys. Res. 94, 17917-17935. [2] Parsons. et al., 1999, Cont. Min. Pet. 136, 92-110. [3] Mark et al., 2008, Geochim. Cosmochim. Acta, 72 2695-2710. [4] Reddy et al., 2001, Cont. Min. Pet., 141 186-200.

Practical aspects of the use of the X(2) holder for HRTEM-quality TEM sample preparation by FIB.

PubMed

van Mierlo, Willem; Geiger, Dorin; Robins, Alan; Stumpf, Matthias; Ray, Mary Louise; Fischione, Paul; Kaiser, Ute

2014-12-01

The X(2) holder enables the effective production of thin, electron transparent samples for high-resolution transmission electron microscopy (HRTEM). Improvements to the X(2) holder for high-quality transmission electron microscopy (TEM) sample preparation are presented in this paper. We discuss the influence of backscattered electrons (BSE) from the sample holder in determining the lamella thickness in situ and demonstrate that a significant improvement in thickness determination can be achieved by comparatively simple means using the relative BSE intensity. We show (using Monte Carlo simulations) that by taking into account the finite collection angle of the electron backscatter detector, an approximately 20% underestimation of the lamella thickness in a silicon sample can be avoided. However, a correct thickness determination for light-element lamellas still remains a problem with the backscatter method; we introduce a more accurate method using the energy dispersive X-ray spectroscopy (EDX) signal for in situ thickness determination. Finally, we demonstrate how to produce a thin lamella with a nearly damage-free surface using the X(2) holder in combination with sub-kV polishing in the Fischione Instruments׳ NanoMill(®) TEM specimen preparation system. Copyright © 2014 Elsevier B.V. All rights reserved.

An Examination of the Space Weathering Patina of Lunar Rock 76015

NASA Technical Reports Server (NTRS)

Noble, S.; Chrisoffersen, R.; Rahman, Z.

2011-01-01

Space weathering discussions have generally centered around soils but exposed rocks will also incur the effects of weathering. Rocks have much longer surface lifetimes than an individual soil grain and thus record a longer history of exposure. By studying the weathering products which have built up on a rock surface, we can gain a deeper perspective on the weathering process and better assess the relative importance of various weathering components. The weathered coating, or patina, of the lunar rock 76015 has been previously studied under SEM and also by TEM using ultramicrotome sample preparation methods. However, to really understand the products involved in creating these coatings, it is helpful to examine the patina in cross section, something which is now possible though the use of Focused Ion Beam (FIB) sample prep techniques, which allows us to preserve intact the delicate stratigraphy of the patina coating and provides a unique cross-sectional view of the space weathering process. Several samples have been prepared from the rock and the coatings are found to be quite variable in thickness and composition from one sample to the next.

Transmission electron microscopy investigation of neutron irradiated Si and ZrN coated UMo particles prepared using FIB

NASA Astrophysics Data System (ADS)

Van Renterghem, W.; Miller, B. D.; Leenaers, A.; Van den Berghe, S.; Gan, J.; Madden, J. W.; Keiser, D. D.

2018-01-01

Two fuel plates, containing Si and ZrN coated U-Mo fuel particles dispersed in an Al matrix, were irradiated in the BR2 reactor of SCK•CEN to a burn-up of ∼70% 235U. Five samples were prepared by INL using focused ion beam milling and transported to SCK•CEN for transmission electron microscopy (TEM) investigation. Two samples were taken from the Si coated U-Mo fuel particles at a burn-up of ∼42% and ∼66% 235U and three samples from the ZrN coated U-Mo at a burn-up of ∼42%, ∼52% and ∼66% 235U. The evolution of the coating, fuel structure, fission products and the formation of interaction layers are discussed. Both coatings appear to be an effective barrier against fuel matrix interaction and only on the samples having received the highest burn-up and power, the formation of an interaction between Al and U(Mo) can be observed on those locations where breaches in the coatings were formed during plate fabrication.

Sources of fecal indicator bacteria to groundwater, Malibu Lagoon and the near-shore ocean, Malibu, California, USA

USGS Publications Warehouse

Izbicki, John A.; Swarzenski, Peter W.; Burton, Carmen A.; Van De Werfhorst, Laurie; Holden, Patricia A.; Dubinsky, Eric A.

2012-01-01

Onsite wastewater treatment systems (OWTS) used to treat residential and commercial sewage near Malibu, California have been implicated as a possible source of fecal indicator bacteria (FIB) to Malibu Lagoon and the near-shore ocean. For this to occur, treated wastewater must first move through groundwater before discharging to the Lagoon or ocean. In July 2009 and April 2010, δ18O and δD data showed that some samples from water-table wells contained as much as 70% wastewater; at that time FIB concentrations in those samples were generally less than the detection limit of 1 Most Probable Number (MPN) per 100 milliliters (mL). In contrast, Malibu Lagoon had total coliform, Escherichia coli, and enterococci concentrations as high as 650,000, 130,000, and 5,500 MPN per 100 mL, respectively, and as many as 12% of samples from nearby ocean beaches exceeded the U.S. Environmental Protection Agency single sample enterococci standard for marine recreational water of 104 MPN per 100 mL. Human-associated Bacteroidales, an indicator of human-fecal contamination, were not detected in water from wells, Malibu Lagoon, or the near-shore ocean. Similarly, microarray (PhyloChip) data show Bacteroidales and Fimicutes Operational Taxanomic Units (OTUs) present in OWTS were largely absent in groundwater; in contrast, 50% of Bacteroidales and Fimicutes OTUs present in the near-shore ocean were also present in gull feces. Terminal-Restriction Length Fragment Polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) data showed that microbial communities in groundwater were different and less abundant than communities in OWTS, Malibu Lagoon, or the near-shore ocean. However, organic compounds indicative of wastewater (such as fecal sterols, bisphenol-A and cosmetics) were present in groundwater having a high percentage of wastewater and were present in groundwater discharging to the ocean. FIB in the near-shore ocean varied with tides, ocean swells, and waves. Movement of water from Malibu Lagoon through the sand berm at the mouth of the Lagoon contributed FIB to the adjacent beach at low tide. Similar increases in FIB concentrations did not occur at beaches adjacent to unsewered residential development, although wastewater indicator compounds and radon-222 (indicative of groundwater discharge) were present. High FIB concentrations at high tide were not related to groundwater discharge, but may be related to FIB associated with debris accumulated along the high-tide line.

A density gradient of VAPG peptides on a cell-resisting surface achieves selective adhesion and directional migration of smooth muscle cells over fibroblasts.

PubMed

Yu, Shan; Zuo, Xingang; Shen, Tao; Duan, Yiyuan; Mao, Zhengwei; Gao, Changyou

2018-05-01

Selective adhesion and migration of smooth muscle cells (SMCs) over fibroblasts (FIBs) is required to prevent adventitia fibrosis in vascular regeneration. In this study, a uniform cell-resisting layer of poly(ethylene glycol) (PEG) with a density gradient of azide groups was generated on a substrate by immobilizing two kinds of PEG molecules in a gradient manner. A density gradient of alkynyl-functionalized Val-Ala-Pro-Gly (VAPG) peptides was then prepared on the PEG layer via click chemistry. The VAPG density gradient was characterized by fluorescence imaging, revealing the gradual enhancement of the fluorescent intensity along the substrate direction. The adhesion and mobility of SMCs were selectively enhanced on the VAPG density gradient, leading to directional migration toward the higher peptide density (up to 84%). In contrast, the adhesion and mobility of FIBs were significantly weakened. The net displacement of SMCs also significantly increased compared with that on tissue culture polystyrene (TCPS) and that of FIBs on the gradient. The mitogen-activated protein kinase (MAPK) signaling pathways related to cell migration were studied, showing higher expressions of functional proteins from SMCs on the VAPG-modified surface in a density-dependent manner. For the first time the selective adhesion and directional migration of SMCs over FIBs was achieved by an elaborative design of a gradient surface, leading to a new insight in design of novel vascular regenerative materials. Selective cell adhesion and migration guided by regenerative biomaterials are extremely important for the regeneration of targeted tissues, which can avoid the drawbacks of incorrect and uncontrolled responses of tissue cells to implants. For example, selectivity of smooth muscle cells (SMCs) over fibroblasts (FIBs) is required to prevent adventitia fibrosis in vascular regeneration. Herein we prepare a uniform cell-repelling layer, on which SMCs-selective Val-Ala-Pro-Gly (VAPG) peptides are immobilized in a continuous manner. Selective adhesion and enhanced and directional migration of SMCs over FIBs are achieved by the interplay of cell-repelling layer and gradient SMCs-selective VAPG peptides, paving a new way for the design of novel vascular grafts with enhanced biological performance. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Evaluation of methods to sample fecal indicator bacteria in foreshore sand and pore water at freshwater beaches.

PubMed

Vogel, Laura J; Edge, Thomas A; O'Carroll, Denis M; Solo-Gabriele, Helena M; Kushnir, Caitlin S E; Robinson, Clare E

2017-09-15

Fecal indicator bacteria (FIB) are known to accumulate in foreshore beach sand and pore water (referred to as foreshore reservoir) where they act as a non-point source for contaminating adjacent surface waters. While guidelines exist for sampling surface waters at recreational beaches, there is no widely-accepted method to collect sand/sediment or pore water samples for FIB enumeration. The effect of different sampling strategies in quantifying the abundance of FIB in the foreshore reservoir is unclear. Sampling was conducted at six freshwater beaches with different sand types to evaluate sampling methods for characterizing the abundance of E. coli in the foreshore reservoir as well as the partitioning of E. coli between different components in the foreshore reservoir (pore water, saturated sand, unsaturated sand). Methods were evaluated for collection of pore water (drive point, shovel, and careful excavation), unsaturated sand (top 1 cm, top 5 cm), and saturated sand (sediment core, shovel, and careful excavation). Ankle-depth surface water samples were also collected for comparison. Pore water sampled with a shovel resulted in the highest observed E. coli concentrations (only statistically significant at fine sand beaches) and lowest variability compared to other sampling methods. Collection of the top 1 cm of unsaturated sand resulted in higher and more variable concentrations than the top 5 cm of sand. There were no statistical differences in E. coli concentrations when using different methods to sample the saturated sand. Overall, the unsaturated sand had the highest amount of E. coli when compared to saturated sand and pore water (considered on a bulk volumetric basis). The findings presented will help determine the appropriate sampling strategy for characterizing FIB abundance in the foreshore reservoir as a means of predicting its potential impact on nearshore surface water quality and public health risk. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Solla, E.L., E-mail: esolla@uvigo.es

Herein, we report on the micro- and nanostructure of the calcium phosphate coating produced by pulsed laser deposition (PLD), using focused ion beam (FIB) lamella sample preparation and transmission electron microscopy (TEM) as the characterization technique. The initial selected area electron diffraction (SAED) data demonstrated the presence of hydroxyapatite (HA) over any other possible calcium phosphate crystalline structure and the polycrystalline nature of the coating. Moreover, the SAED analyses showed clear textured ring patterns coherent with the presence of a preferred orientation in the HA nano-crystal growth. The SAED data also indicated that the coating appears to be textured inmore » the 〈002〉 crystalline direction. Dark-field images obtained using 002 as the working reflection showed a clear oriented crystal growth in columns, from bottom to top. These columns have a peculiar arrangement of nano-crystals since, in some cases, the preferred orientation appears to start at a certain distance from the substrate. Direct d-spacing measurements on high-resolution TEM images provided further proof of the presence of an HA nano-crystal structure. The reported data may be of interest in the future to adjust the microstructure of the HA coatings. - Highlights: •The FIB lift-out technique allows a very site-specific sample preparation method for HRTEM analysis. •It also permits a fast assessment of the HA coating thickness and elemental composition (EDS). •The coatings exhibit a nano-crystalline nature, with a texturing effect along the 002 planes. •PLD is suitable for the production of crystalline c-axis oriented hydroxyapatite coatings. •The crystalline HA phase in the PLD coating is very similar to the present in bone.« less

Three-dimensional microstructural characterization of bulk plutonium and uranium metals using focused ion beam technique

NASA Astrophysics Data System (ADS)

Chung, Brandon W.; Erler, Robert G.; Teslich, Nick E.

2016-05-01

Nuclear forensics requires accurate quantification of discriminating microstructural characteristics of the bulk nuclear material to identify its process history and provenance. Conventional metallographic preparation techniques for bulk plutonium (Pu) and uranium (U) metals are limited to providing information in two-dimension (2D) and do not allow for obtaining depth profile of the material. In this contribution, use of dual-beam focused ion-beam/scanning electron microscopy (FIB-SEM) to investigate the internal microstructure of bulk Pu and U metals is demonstrated. Our results demonstrate that the dual-beam methodology optimally elucidate microstructural features without preparation artifacts, and the three-dimensional (3D) characterization of inner microstructures can reveal salient microstructural features that cannot be observed from conventional metallographic techniques. Examples are shown to demonstrate the benefit of FIB-SEM in improving microstructural characterization of microscopic inclusions, particularly with respect to nuclear forensics.

Three-dimensional microstructural characterization of bulk plutonium and uranium metals using focused ion beam technique

DOE PAGES

Chung, Brandon W.; Erler, Robert G.; Teslich, Nick E.

2016-03-03

Nuclear forensics requires accurate quantification of discriminating microstructural characteristics of the bulk nuclear material to identify its process history and provenance. Conventional metallographic preparation techniques for bulk plutonium (Pu) and uranium (U) metals are limited to providing information in two-dimension (2D) and do not allow for obtaining depth profile of the material. In this contribution, use of dual-beam focused ion-beam/scanning electron microscopy (FIB-SEM) to investigate the internal microstructure of bulk Pu and U metals is demonstrated. Our results demonstrate that the dual-beam methodology optimally elucidate microstructural features without preparation artifacts, and the three-dimensional (3D) characterization of inner microstructures can revealmore » salient microstructural features that cannot be observed from conventional metallographic techniques. As a result, examples are shown to demonstrate the benefit of FIB-SEM in improving microstructural characterization of microscopic inclusions, particularly with respect to nuclear forensics.« less

Three dimensional rock microstructures: insights from FIB-SEM tomography

NASA Astrophysics Data System (ADS)

Drury, Martyn; Pennock, Gill; de Winter, Matthijs

2016-04-01

Most studies of rock microstructures investigate two-dimensional sections or thin slices of three dimensional grain structures. With advances of X-ray and electron tomography methods the 3-D microstructure can be(relatively) routinely investigated on scales from a few microns to cm. 3D studies are needed to investigate the connectivity of microstructures and to test the assumptions we use to calculate 3D properties from 2D sections. We have used FIB-SEM tomography to study the topology of melts in synthetic olivine rocks, 3D crystal growth microstructures, pore networks and subgrain structures. The technique uses a focused ion beam to make serial sections with a spacing of tens to hundreds of nanometers. Each section is then imaged or mapped using the electron beam. The 3D geometry of grains and subgrains can be investigated using orientation contrast or EBSD mapping. FIB-SEM tomography of rocks and minerals can be limited by charging of the uncoated surfaces exposed by the ion beam. The newest generation of FIB-SEMs have much improved low voltage imaging capability allowing high resolution charge free imaging. Low kV FIB-SEM tomography is now widely used to study the connectivity of pore networks. In-situ fluids can also be studied using cryo-FIB-SEM on frozen samples, although special freezing techniques are needed to avoid artifacts produced by ice crystallization. FIB-SEM tomography is complementary, in terms of spatial resolution and sampled volume, to TEM tomography and X-ray tomography, and the combination of these methods can cover a wide range of scales. Our studies on melt topology in synthetic olivine rocks with a high melt content show that many grain boundaries are wetted by nanometre scale melt layers that are too thin to resolve by X-ray tomography. A variety of melt layer geometries occur consistent with several mechanisms of melt layer formation. The nature of melt geometries along triple line junctions and quadruple points can be resolved. Quadruple point junctions between four grains cannot be investigated in 2D studies. 3D microstructural studies suggest that triple lines and quadruple points are important sites for the initiation of recrystallization, reaction and fracture.

Understanding the Earth's Mantle Through Advanced Elasticity Measurements

NASA Astrophysics Data System (ADS)

Marquardt, Hauke; Schulze, Kirsten; Kurnosov, Alexander; Buchen, Johannes; Frost, Daniel; Boffa Ballaran, Tiziana; Marquardt, Katharina; Kawazoe, Takaaki

2017-04-01

Constraints on the inner structure, chemical and mineralogical composition as well as dynamics of Earth's mantle can be derived through comparison of laboratory elasticity data to seismological observables. A quantitative knowledge of the elastic properties of mantle minerals, and their variations with chemical composition, at pressure and temperature conditions of Earth's mantle is key to construct reliable synthetic mineral physics-based seismic velocity models to be compared to seismic observables. We will discuss results of single-crystal elasticity measurements on Earth mantle minerals that have been conducted using the combined Brillouin scattering and x-ray diffraction (XRD) system at BGI Bayreuth in combination with advanced sample preparation using the focused ion beam (FIB) technique [1] that allows for tailoring sizes and shapes of tiny single-crystals. In our experiments, multiple FIB-prepared single-crystals were loaded in a single sample chamber of a resistively-heated diamond-anvil cell (DAC). The possiblity to measure simultaneously acoustic wave velocities and density (unit-cell parameters) in the DAC in combination with the multi-sample approach facilitates direct quantification of the effects of chemical substitution on the elasticity and seismic wave velocities at non-ambient conditions. Our experimental approach eliminates uncertainties arising from the combination of data collected under (potentially) different conditions in several DAC runs, in different laboratories and/or from using different pressure-temperature sensors. We will present our recent experiments on the elasticity of single-crystal Fe-Al-bearing bridgmanite in the lower mantle and discuss implications for the composition and oxidation state of Earth's lower mantle. We will further discuss our laboratory data on the effects of 'water' and iron on the seismic wave velocities of ringwoodite in Earth's transition zone and outline implications for mapping 'water' in the transition zone using geophysical observables. [1] Marquardt, H. and K. Marquardt, 2012. American Mineralogist 97, 299-304.

TEM Analysis of Interfaces in Diffusion-Bonded Silicon Carbide Ceramics Joined Using Metallic Interlayers

NASA Technical Reports Server (NTRS)

Ozaki, T.; Tsuda, H.; Halbig, M. C.; Singh, M.; Hasegawa, Y.; Mori, S.; Asthana R.

2016-01-01

Silicon Carbide (SiC) is a promising material for thermo-structural applications due to its excellent high-temperature mechanical properties, oxidation resistance, and thermal stability. However, joining and integration technologies are indispensable for this material in order to fabricate large size and complex shape components with desired functionalities. Although diffusion bonding techniques using metallic interlayers have been commonly utilized to bond various SiC ceramics, detailed microstructural observation by Transmission Electron Microscopy (TEM) of the bonded area has not been carried out due to difficulty in preparing TEM samples. In this study, we tried to prepare TEM samples from joints of diffusion bonded SiC ceramics by Focused Ion Beam (FIB) system and carefully investigated the interfacial microstructure by TEM analysis. The samples used in this study were SiC fiber bonded ceramics (SA-Tyrannohex: SA-THX) diffusion bonded with metallic interlayers such as Ti, TiMo, and Mo-B. In this presentation, the result of microstructural analysis obtained by TEM observations and the influence of metallic interlayers and fiber orientation of SA-THX on the joint microstructure will be discussed.

TEM Analysis of Diffusion-Bonded Silicon Carbide Ceramics Joined Using Metallic Interlayers

NASA Technical Reports Server (NTRS)

Ozaki, T.; Tsuda, H.; Halbig, M. C.; Singh, M.; Hasegawa, Y; Mori, S.; Asthana, R.

2017-01-01

Silicon Carbide (SiC) is a promising material for thermostructural applications due to its excellent high-temperature mechanical properties, oxidation resistance, and thermal stability. However, joining and integration technologies are indispensable for this material in order to fabricate large size and complex shape components with desired functionalities. Although diffusion bonding techniques using metallic interlayers have been commonly utilized to bond various SiC ceramics, detailed microstructural observation by Transmission Electron Microscopy (TEM) of the bonded area has not been carried out due to difficulty in preparing TEM samples. In this study, we tried to prepare TEM samples from joints of diffusion bonded SiC ceramics by Focused Ion Beam (FIB) system and carefully investigated the interfacial microstructure by TEM analysis. The samples used in this study were SiC fiber bonded ceramics (SA-Tyrannohex: SA-THX) diffusion bonded with metallic interlayers such as Ti, TiMo, Mo-B and TiCu. In this presentation, we report the microstructure of diffusion bonded SA-THX mainly with TiCu interlayers obtained by TEM observations, and the influence of metallic interlayers on the joint microstructure and microhardness will be discussed.

Superconductivity in the system Mo{sub x}C{sub y}Ga{sub z}O{sub δ} prepared by focused ion beam induced deposition

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

Weirich, P. M., E-mail: p.weirich@Physik.uni-frankfurt.de; Schwalb, C. H.; Winhold, M.

2014-05-07

We have prepared the new amorphous superconductor Mo{sub x}C{sub y}Ga{sub z}O{sub δ} with a maximum critical temperature T{sub c} of 3.8 K by the direct-write nano-patterning technique of focused (gallium) ion beam induced deposition (FIBID) using Mo(CO){sub 6} as precursor gas. From a detailed analysis of the temperature-dependent resistivity and the upper critical field, we found clear evidence for proximity of the samples to a disorder-induced metal-insulator transition. We observed a strong dependence of T{sub c} on the deposition parameters and identified clear correlations between T{sub c}, the localization tendency visible in the resistance data and the sample composition. By anmore » in-situ feedback-controlled optimization process in the FIB-induced growth, we were able to identify the beam parameters which lead to samples with the largest T{sub c}-value and sharpest transition into the superconducting state.« less

Morphologies and optical and electrical properties of InGaN/GaN micro-square array light-emitting diode chips.

PubMed

Han, Dan; Ma, Shufang; Jia, Zhigang; Liu, Peizhi; Jia, Wei; Shang, Lin; Zhai, Guangmei; Xu, Bingshe

2018-04-10

InGaN/GaN micro-square array light-emitting diode (LED) chips (micro-chips) have been prepared via the focused ion beam (FIB) etching technique, which can not only reduce ohmic contact degradation but also control the aspect ratio precisely in three-dimensional (3D) structure LED (3D-LED) device fabrication. The effects of FIB beam current and micro-square array depth on morphologies and optical and electrical properties of the micro-chips have been studied. Our results show that sidewall surface morphology and optical and electrical properties of the micro-chips degrade with increased beam current. After potassium hydroxide etching with different times, an optimal current-voltage and luminescence performance can be obtained. Combining the results of cathodoluminescence mappings and light output-current characteristics, the light extraction efficiency of the micro-chips is reduced as FIB etch depth increases. The mechanisms of micro-square depth on light extraction have been revealed by 3D finite difference time domain.

The Relationship Between Land Management, Fecal Indicator Bacteria, and the Occurrence of Campylobacter and Listeria Spp. in Water and Sediments During Synoptic Sampling In The South Fork Broad River Watershed, Northeast Georgia, U.S.A.

EPA Science Inventory

Fecal indicator bacteria (FIB) and pathogens stored in the bed sediments of streams and rivers may be mobilized into the water column affecting overall water quality. Furthermore, land management may play an important role in the concentrations of FIB and the occurrence of pathog...

Synovial Fluid Response to Extensional Flow: Effects of Dilution and Intermolecular Interactions

PubMed Central

Haward, Simon J.

2014-01-01

In this study, a microfluidic cross-slot device is used to examine the extensional flow response of diluted porcine synovial fluid (PSF) samples using flow-induced birefringence (FIB) measurements. The PSF sample is diluted to 10× 20× and 30× its original mass in a phosphate-buffered saline and its FIB response measured as a function of the strain rate at the stagnation point of the cross-slots. Equivalent experiments are also carried out using trypsin-treated PSF (t-PSF) in which the protein content is digested away using an enzyme. The results show that, at the synovial fluid concentrations tested, the protein content plays a negligible role in either the fluid's bulk shear or extensional flow behaviour. This helps support the validity of the analysis of synovial fluid HA content, either by microfluidic or by other techniques where the synovial fluid is first diluted, and suggests that the HA and protein content in synovial fluid must be higher than a certain minimum threshold concentration before HA-protein or protein-protein interactions become significant. However a systematic shift in the FIB response as the PSF and t-PSF samples are progressively diluted indicates that HA-HA interactions remain significant at the concentrations tested. These interactions influence FIB-derived macromolecular parameters such as the relaxation time and the molecular weight distribution and therefore must be minimized for the best validity of this method as an analytical technique, in which non-interaction between molecules is assumed. PMID:24651529

Synovial fluid response to extensional flow: effects of dilution and intermolecular interactions.

PubMed

Haward, Simon J

2014-01-01

In this study, a microfluidic cross-slot device is used to examine the extensional flow response of diluted porcine synovial fluid (PSF) samples using flow-induced birefringence (FIB) measurements. The PSF sample is diluted to 10× 20× and 30× its original mass in a phosphate-buffered saline and its FIB response measured as a function of the strain rate at the stagnation point of the cross-slots. Equivalent experiments are also carried out using trypsin-treated PSF (t-PSF) in which the protein content is digested away using an enzyme. The results show that, at the synovial fluid concentrations tested, the protein content plays a negligible role in either the fluid's bulk shear or extensional flow behaviour. This helps support the validity of the analysis of synovial fluid HA content, either by microfluidic or by other techniques where the synovial fluid is first diluted, and suggests that the HA and protein content in synovial fluid must be higher than a certain minimum threshold concentration before HA-protein or protein-protein interactions become significant. However a systematic shift in the FIB response as the PSF and t-PSF samples are progressively diluted indicates that HA-HA interactions remain significant at the concentrations tested. These interactions influence FIB-derived macromolecular parameters such as the relaxation time and the molecular weight distribution and therefore must be minimized for the best validity of this method as an analytical technique, in which non-interaction between molecules is assumed.

Water Quality Conditions Associated with Cattle Grazing and Recreation on National Forest Lands

PubMed Central

Roche, Leslie M.; Kromschroeder, Lea; Atwill, Edward R.; Dahlgren, Randy A.; Tate, Kenneth W.

2013-01-01

There is substantial concern that microbial and nutrient pollution by cattle on public lands degrades water quality, threatening human and ecological health. Given the importance of clean water on multiple-use landscapes, additional research is required to document and examine potential water quality issues across common resource use activities. During the 2011 grazing-recreation season, we conducted a cross sectional survey of water quality conditions associated with cattle grazing and/or recreation on 12 public lands grazing allotments in California. Our specific study objectives were to 1) quantify fecal indicator bacteria (FIB; fecal coliform and E. coli), total nitrogen, nitrate, ammonium, total phosphorus, and soluble-reactive phosphorus concentrations in surface waters; 2) compare results to a) water quality regulatory benchmarks, b) recommended maximum nutrient concentrations, and c) estimates of nutrient background concentrations; and 3) examine relationships between water quality, environmental conditions, cattle grazing, and recreation. Nutrient concentrations observed throughout the grazing-recreation season were at least one order of magnitude below levels of ecological concern, and were similar to U.S. Environmental Protection Agency (USEPA) estimates for background water quality conditions in the region. The relative percentage of FIB regulatory benchmark exceedances widely varied under individual regional and national water quality standards. Relative to USEPA’s national E. coli FIB benchmarks–the most contemporary and relevant standards for this study–over 90% of the 743 samples collected were below recommended criteria values. FIB concentrations were significantly greater when stream flow was low or stagnant, water was turbid, and when cattle were actively observed at sampling. Recreation sites had the lowest mean FIB, total nitrogen, and soluble-reactive phosphorus concentrations, and there were no significant differences in FIB and nutrient concentrations between key grazing areas and non-concentrated use areas. Our results suggest cattle grazing, recreation, and provisioning of clean water can be compatible goals across these national forest lands. PMID:23826370

Occurrence and distribution of fecal indicator bacteria and gene markers of pathogenic bacteria in Great Lakes tributaries, March-October 2011

USGS Publications Warehouse

Brennan, Angela K.; Johnson, Heather E.; Totten, Alexander R.; Duris, Joseph W.

2015-01-01

Water samples were analyzed for the presence of FIB concentrations (FIB; fecal coliform bacteria, Escherichia coli [E. coli], and enterococci) by using membrane filtration and serial dilution methods. The resulting enrichments from standard culturing of the samples were then analyzed by using polymerase chain reaction (PCR) to determine the occurrence of pathogen gene markers for Shigella species, Campylobacter jejuni and coli, Salmonellaspecies, and pathogenic E. coli, including Shiga toxin-producing E. coli (STEC).

Spatial and temporal microbial pollution patterns in a tropical estuary during high and low river flow conditions.

PubMed

Wiegner, T N; Edens, C J; Abaya, L M; Carlson, K M; Lyon-Colbert, A; Molloy, S L

2017-01-30

Spatial and temporal patterns of coastal microbial pollution are not well documented. Our study examined these patterns through measurements of fecal indicator bacteria (FIB), nutrients, and physiochemical parameters in Hilo Bay, Hawai'i, during high and low river flow. >40% of samples tested positive for the human-associated Bacteroides marker, with highest percentages near rivers. Other FIB were also higher near rivers, but only Clostridium perfringens concentrations were related to discharge. During storms, FIB concentrations were three times to an order of magnitude higher, and increased with decreasing salinity and water temperature, and increasing turbidity. These relationships and high spatial resolution data for these parameters were used to create Enterococcus spp. and C. perfringens maps that predicted exceedances with 64% and 95% accuracy, respectively. Mapping microbial pollution patterns and predicting exceedances is a valuable tool that can improve water quality monitoring and aid in visualizing FIB hotspots for management actions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Attempt of correlative observation of morphological synaptic connectivity by combining confocal laser-scanning microscope and FIB-SEM for immunohistochemical staining technique.

PubMed

Sonomura, Takahiro; Furuta, Takahiro; Nakatani, Ikuko; Yamamoto, Yo; Honma, Satoru; Kaneko, Takeshi

2014-11-01

Ten years have passed since a serial block-face scanning electron microscopy (SBF-SEM) method was developed [1]. In this innovative method, samples were automatically sectioned with an ultramicrotome placed inside a scanning electron microscope column, and the block surfaces were imaged one after another by SEM to capture back-scattered electrons. The contrast-inverted images obtained by the SBF-SEM were very similar to those acquired using conventional TEM. SFB-SEM has made easy to acquire image stacks of the transmission electron microscopy (TEM) in the mesoscale, which is taken with the confocal laser-scanning microcopy(CF-LSM).Furthermore, serial-section SEM has been combined with the focused ion beam (FIB) milling method [2]. FIB-incorporated SEM (FIB-SEM) has enabled the acquisition of three-dimensional images with a higher z-axis resolution com- pared to ultramicrotome-equipped SEM.We tried immunocytochemistry for FIB-SEM and correlated this immunoreactivity with that in CF-LSM. Dendrites of neurons in the rat neostriatum were visualized using a recombinant viral vector. Moreover, the thalamostriatal afferent terminals were immunolabeled with Cy5 fluorescence for vesicular glutamate transporter 2 (VGluT2). After detection of the sites of terminals apposed to the dendrites by using CF-LSM, GFP and VGluT2 immunoreactivities were further developed for EM by using immunogold/silver enhancement and immunoperoxidase/diaminobenzidine (DAB) methods, respectively.We showed that conventional immuno-cytochemical staining for TEM was applicable to FIB-SEM. Furthermore, several synaptic contacts, which were thought to exist on the basis of CF-LSM findings, were confirmed with FIB-SEM, revealing the usefulness of the combined method of CF-LSM and FIB-SEM. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Comparison of the prognostic value of liver biopsy and FIB-4 index in patients coinfected with HIV and hepatitis C virus.

PubMed

Berenguer, Juan; Zamora, Francisco X; Aldámiz-Echevarría, Teresa; Von Wichmann, Miguel A; Crespo, Manel; López-Aldeguer, José; Carrero, Ana; Montes, Marisa; Quereda, Carmen; Téllez, María J; Galindo, María J; Sanz, José; Santos, Ignacio; Guardiola, Josep M; Barros, Carlos; Ortega, Enrique; Pulido, Federico; Rubio, Rafael; Mallolas, Josep; Tural, Cristina; Jusdado, Juan J; Pérez, Gloria; Díez, Cristina; Álvarez-Pellicer, Julio; Esteban, Herminia; Bellón, José M; González-García, Juan

2015-03-15

We compared the prognostic value of liver biopsy (LB) and FIB-4 index in patients with human immunodeficiency virus (HIV)/hepatitis C virus (HCV) coinfection. We studied patients from the Grupo de Estudio del SIDA 3603 study cohort, in whom fibrosis was evaluated at baseline using both LB (Metavir score) and FIB-4 index. We assessed overall death (OD) and liver-related events (LREs), defined as decompensation or hepatocellular carcinoma, whichever occurred first. We used receiver operating characteristic (ROC) curves to determine the ability of LB and FIB-4 to predict outcomes. We also assessed the association between advanced fibrosis-LB (F3 or greater) or FIB-4 (≥3.25)-and outcomes using multivariate Cox regression analysis. The study sample comprised 903 patients (328 with sustained virologic response [SVR]). Baseline fibrosis by LB was as follows: F0, n = 71; F1, n = 242; F2, n = 236; F3, n = 236; F4, n = 118. Fibrosis by FIB-4 was as follows: ≤1, n = 148; >1 to <3.25, n = 597; ≥3.25, n = 158. After a median follow-up of 62 months, there were 46 deaths and 71 LREs. The area under the ROC curves for OD/LREs was 0.648 and 0.742 for LB and FIB-4, respectively (P = .006). Similar results were found for patients without SVR and for OD and LREs separately. The adjusted hazard ratios of OD or LRE were 1.740 (95% confidence interval [CI], 1.119-2.7.06; P = .014) for advanced fibrosis assessed by LB and 3.896 (95% CI, 2.463-6.160; P < .001) assessed by FIB-4. FIB-4 outperformed LB as a predictor of OD and LRE. These findings are of relevance for clinical practice and research and call into question the role of LB as a gold standard for assessing prognosis in HIV/HCV coinfection. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Assessing the utility of FIB-SEM images for shale digital rock physics

NASA Astrophysics Data System (ADS)

Kelly, Shaina; El-Sobky, Hesham; Torres-Verdín, Carlos; Balhoff, Matthew T.

2016-09-01

Shales and other unconventional or low permeability (tight) reservoirs house vast quantities of hydrocarbons, often demonstrate considerable water uptake, and are potential repositories for fluid sequestration. The pore-scale topology and fluid transport mechanisms within these nanoporous sedimentary rocks remain to be fully understood. Image-informed pore-scale models are useful tools for studying porous media: a debated question in shale pore-scale petrophysics is whether there is a representative elementary volume (REV) for shale models? Furthermore, if an REV exists, how does it differ among petrophysical properties? We obtain three dimensional (3D) models of the topology of microscale shale volumes from image analysis of focused ion beam-scanning electron microscope (FIB-SEM) image stacks and investigate the utility of these models as a potential REV for shale. The scope of data used in this work includes multiple local groups of neighboring FIB-SEM images of different microscale sizes, corresponding core-scale (milli- and centimeters) laboratory data, and, for comparison, series of two-dimensional (2D) cross sections from broad ion beam SEM images (BIB-SEM), which capture a larger microscale field of view than the FIB-SEM images; this array of data is larger than the majority of investigations with FIB-SEM-derived microscale models of shale. Properties such as porosity, organic matter content, and pore connectivity are extracted from each model. Assessments of permeability with single phase, pressure-driven flow simulations are performed in the connected pore space of the models using the lattice-Boltzmann method. Calculated petrophysical properties are compared to those of neighboring FIB-SEM images and to core-scale measurements of the sample associated with the FIB-SEM sites. Results indicate that FIB-SEM images below ∼5000 μm3 volume (the largest volume analyzed) are not a suitable REV for shale permeability and pore-scale networks; i.e. field of view is compromised at the expense of detailed, but often unconnected, nanopore morphology. Further, we find that it is necessary to acquire several local FIB-SEM or BIB-SEM images and correlate their extracted geometric properties to improve the likelihood of achieving representative values of porosity and organic matter volume. Our work indicates that FIB-SEM images of microscale volumes of shale are a qualitative tool for petrophysical and transport analysis. Finally, we offer alternatives for quantitative pore-scale assessments of shale.

Traditional and Host-Associated Fecal Indicator Bacterial Patterns in Southern California Watersheds: Field Source Identification Studies and Laboratory Microcosms Investigating Presence and Persistence in Water and Sediments

NASA Astrophysics Data System (ADS)

Mika, Kathryn Beth

Overall, recreational beach water quality remains an issue of concern in Southern California and across the globe. Many factors come into play when determining water quality, including physical issues such as the myriad sources that contribute pollution to the site and financial and political issues that control the way water quality is monitored and determined. Current national regulations require the monitoring of fecal indicator bacteria in order to determine recreational water quality. However, it is also important to identify biological and geographical sources of pollution to consistently impaired locations. A commonly applied approach to meet the goals of source identification is to sample sites that have been high in FIB for further study. A tiered approach such as this, however, assumes a correlation between FIB and the sources of interest in the watershed. The research described in this dissertation tests this assumption in two Southern California watersheds, Santa Monica Canyon and Ventura Harbor. In both cases, a tiered approach to sampling using FIB as a first tier to guide sampling would have failed to identify sources of human fecal pollution (as identified by the presence of the human-associated Bacteroides marker HF183). Every watershed is a distinct environment that has different potential sources of bacteria and many factors contributing to the persistence of the bacteria. Rather than attempting to apply an indicator that has worked as a first tier in other watersheds, it would be better to have as a first tier an in-depth study of the watershed using historical data or local experts to provide information on the most likely sources of pollution in the watershed. Using this information it would be possible to design a study using FIB and one or more source-associated parameters to identify specific sources of pollution in the watershed. In addition, sampling FIB and other parameters such as HF183 allow the application of other microbial source tracking tools including indicator ratios and detection frequencies. Source identification studies do not necessarily have to be long-term to identify consistent sources of pollution. For example, within the first four months of sampling at Ventura, the increased frequency of detection of HF183 at the Marina Dock sample location was apparent, and a dry weather influx of HF183 was seen in the Keys channels. In addition to the many sources of FIB to the environment such as storm drains, leaking sewers, and wildlife, there are important environmental reservoirs such as sand and seaweed that can foster FIB growth and persistence in the environment. As such, it is important to understand the effect of different factors on the ability of bacteria to survive and persist in these reservoirs. Microcosm experiments conducted during the course of this dissertation research found that in dry beach sand (0.1% moisture), the addition of moisture was detrimental to the survival of the indicators studied (General Bacteroidales, E. coli, and enterococci). While increased moisture was not always detrimental to bacterial survival, these results point to the ability of bacteria to persist for long periods of time in beach environments under in-situ conditions (including dry sand). These findings point to the importance of understanding the behavior of indicator bacteria populations that have evolved to survive in environmental conditions so that their potential impact on overlying or adjacent water quality can be better understood. In summation, results from this research point to the importance of selecting indicators and sample locations that are most relevant to watershed concerns rather than using a first tier such as FIB to preferentially select sites for further analysis. Measuring a marker for human fecal pollution in both watershed studies provided useful information for potential human inputs that would have been missed if sites were chosen based on high FIB levels. In addition it is very important to understand the contribution of different reservoirs, such as sand, in the study area to the observed microbial pollution. Overall, these results point to the need for further examination of the ability of bacteria to survive under various environmental conditions in both water and sand, using both environmental microbial populations and populations from likely sources such as human sewage.

Assessing Drinking Water Quality and Water Safety Management in Sub-Saharan Africa Using Regulated Monitoring Data.

PubMed

Kumpel, Emily; Peletz, Rachel; Bonham, Mateyo; Khush, Ranjiv

2016-10-18

Universal access to safe drinking water is prioritized in the post-2015 Sustainable Development Goals. Collecting reliable and actionable water quality information in low-resource settings, however, is challenging, and little is known about the correspondence between water quality data collected by local monitoring agencies and global frameworks for water safety. Using 42 926 microbial water quality test results from 32 surveillance agencies and water suppliers in seven sub-Saharan African countries, we determined the degree to which water sources were monitored, how water quality varied by source type, and institutional responses to results. Sixty-four percent of the water samples were collected from piped supplies, although the majority of Africans rely on nonpiped sources. Piped supplies had the lowest levels of fecal indicator bacteria (FIB) compared to any other source type: only 4% of samples of water piped to plots and 2% of samples from water piped to public taps/standpipes were positive for FIB (n = 14 948 and n = 12 278, respectively). Among other types of improved sources, samples from harvested rainwater and boreholes were less often positive for FIB (22%, n = 167 and 31%, n = 3329, respectively) than protected springs or protected dug wells (39%, n = 472 and 65%, n = 505). When data from different settings were aggregated, the FIB levels in different source types broadly reflected the source-type water safety framework used by the Joint Monitoring Programme. However, the insufficient testing of nonpiped sources relative to their use indicates important gaps in current assessments. Our results emphasize the importance of local data collection for water safety management and measurement of progress toward universal safe drinking water access.

Thermal conductivity and nanocrystalline structure of platinum deposited by focused ion beam.

PubMed

Alaie, Seyedhamidreza; Goettler, Drew F; Jiang, Ying-Bing; Abbas, Khawar; Baboly, Mohammadhosein Ghasemi; Anjum, D H; Chaieb, S; Leseman, Zayd C

2015-02-27

Pt deposited by focused ion beam (FIB) is a common material used for attachment of nanosamples, repair of integrated circuits, and synthesis of nanostructures. Despite its common use little information is available on its thermal properties. In this work, Pt deposited by FIB is characterized thermally, structurally, and chemically. Its thermal conductivity is found to be substantially lower than the bulk value of Pt, 7.2 W m(-1) K(-1) versus 71.6 W m(-1) K(-1) at room temperature. The low thermal conductivity is attributed to the nanostructure of the material and its chemical composition. Pt deposited by FIB is shown, via aberration corrected TEM, to be a segregated mix of nanocrystalline Pt and amorphous C with Ga and O impurities. Ga impurities mainly reside in the Pt while O is homogeneously distributed throughout. The Ga impurity, small grain size of the Pt, and the amorphous carbon between grains are the cause for the low thermal conductivity of this material. Since Pt deposited by FIB is a common material for affixing samples, this information can be used to assess systematic errors in thermal characterization of different nanosamples. This application is also demonstrated by thermal characterization of two carbon nanofibers and a correction using the reported thermal properties of the Pt deposited by FIB.

Integral strategy for evaluation of fecal indicator performance in bird-influenced saline inland waters.

PubMed

Kirschner, Alexander K T; Zechmeister, Thomas C; Kavka, Gerhard G; Beiwl, Christian; Herzig, Alois; Mach, Robert L; Farnleitner, Andreas H

2004-12-01

Wild birds are an important nonpoint source of fecal contamination of surface waters, but their contribution to fecal pollution is mostly difficult to estimate. Thus, to evaluate the relation between feces production and input of fecal indicator bacteria (FIB) into aquatic environments by wild waterfowl, we introduced a new holistic approach for evaluating the performance of FIB in six shallow saline habitats. For this, we monitored bird abundance, fecal pellet production, and the abundance of FIB concomitantly with a set of environmental variables over a 9-month period. For estimating fecal pellet production, a new protocol of fecal pellet counting was introduced, which was called fecal taxation (FTX). We could show that, over the whole range of investigated habitats, bird abundance, FTX values, and FIB abundance were highly significantly correlated and could demonstrate the good applicability of the FTX as a meaningful surrogate parameter for recent bird abundances and fecal contamination by birds in shallow aquatic ecosystems. Presumptive enterococci (ENT) were an excellent surrogate parameter of recent fecal contamination in these saline environments for samples collected at biweekly to monthly sampling intervals while presumptive Escherichia coli and fecal coliforms (FC) were often undetectable. Significant negative correlations with salinity indicated that E. coli and FC survival was hampered by osmotic stress. Statistical analyses further revealed that fecal pollution-associated parameters represented one system component independent from other environmental variables and that, besides feces production, rainfall, total suspended solids (direct), and trophy (indirect) had significant positive effects on ENT concentrations. Our holistic approach of linking bird abundance, feces production, and FIB detection with environmental variables may serve as a powerful model for application to other aquatic ecosystems.

Integral Strategy for Evaluation of Fecal Indicator Performance in Bird-Influenced Saline Inland Waters

PubMed Central

Kirschner, Alexander K. T.; Zechmeister, Thomas C.; Kavka, Gerhard G.; Beiwl, Christian; Herzig, Alois; Mach, Robert L.; Farnleitner, Andreas H.

2004-01-01

Wild birds are an important nonpoint source of fecal contamination of surface waters, but their contribution to fecal pollution is mostly difficult to estimate. Thus, to evaluate the relation between feces production and input of fecal indicator bacteria (FIB) into aquatic environments by wild waterfowl, we introduced a new holistic approach for evaluating the performance of FIB in six shallow saline habitats. For this, we monitored bird abundance, fecal pellet production, and the abundance of FIB concomitantly with a set of environmental variables over a 9-month period. For estimating fecal pellet production, a new protocol of fecal pellet counting was introduced, which was called fecal taxation (FTX). We could show that, over the whole range of investigated habitats, bird abundance, FTX values, and FIB abundance were highly significantly correlated and could demonstrate the good applicability of the FTX as a meaningful surrogate parameter for recent bird abundances and fecal contamination by birds in shallow aquatic ecosystems. Presumptive enterococci (ENT) were an excellent surrogate parameter of recent fecal contamination in these saline environments for samples collected at biweekly to monthly sampling intervals while presumptive Escherichia coli and fecal coliforms (FC) were often undetectable. Significant negative correlations with salinity indicated that E. coli and FC survival was hampered by osmotic stress. Statistical analyses further revealed that fecal pollution-associated parameters represented one system component independent from other environmental variables and that, besides feces production, rainfall, total suspended solids (direct), and trophy (indirect) had significant positive effects on ENT concentrations. Our holistic approach of linking bird abundance, feces production, and FIB detection with environmental variables may serve as a powerful model for application to other aquatic ecosystems. PMID:15574941

Thermal etching of silver: Influence of rolling defects

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

Ollivier, M., E-mail: o.maelig@imperial.ac.uk

2016-08-15

Silver is well known to be thermally etched in an oxygen-rich atmosphere and has been extensively studied in the laboratory to understand thermal etching and to limit its effect when this material is used as a catalyst. Yet, in many industrial applications the surface of rolled silver sheets is used without particular surface preparation. Here, it is shown by combining FIB-tomography, FIB-SIMS and analytical SEM that the kinetics of thermal etch pitting are significantly faster on rolled Ag surfaces than on polished surfaces. This occurs due to range of interacting phenomena including (i) the reaction of subsurface carbon-contamination with dissolvedmore » oxygen to form pores that grow to intersect the surface, (ii) surface reconstruction around corrosion pits and surface scratches, and (iii) sublimation at low pressure and high temperature. A method to identify subsurface pores is developed to show that the pores have (111) and (100) internal facets and may be filled with a gas coming from the chemical reaction of oxygen and carbon contamination. - Highlights: Thermal etching of industrial silver sheets vs. polished silver sheets Effect of annealing atmosphere on the thermal etching of silver: surface and subsurface characterization Link between etch pitting and defects induced by rolling. FIB-tomography coupled with EBSD for determining crystal planes of the facets of subsurface pores. FIB-SIMS characterization to probe the gas confined inside subsurface pores.« less

The PROMIS fatigue item bank has good measurement properties in patients with fibromyalgia and severe fatigue.

PubMed

Yost, Kathleen J; Waller, Niels G; Lee, Minji K; Vincent, Ann

2017-06-01

Efficient management of fibromyalgia (FM) requires precise measurement of FM-specific symptoms. Our objective was to assess the measurement properties of the Patient-Reported Outcome Measurement Information System (PROMIS) fatigue item bank (FIB) in people with FM. We applied classical psychometric and item response theory methods to cross-sectional PROMIS-FIB data from two samples. Data on the clinical FM sample were obtained at a tertiary medical center. Data for the U.S. general population sample were obtained from the PROMIS network. The full 95-item bank was administered to both samples. We investigated dimensionality of the item bank in both samples by separately fitting a bifactor model with two group factors; experience and impact. We assessed measurement invariance between samples, and we explored an alternate factor structure with the normative sample and subsequently confirmed that structure in the clinical sample. Finally, we assessed whether reporting FM subdomain scores added value over reporting a single total score. The item bank was dominated by a general fatigue factor. The fit of the initial bifactor model and evidence of measurement invariance indicated that the same constructs were measured across the samples. An alternative bifactor model with three group factors demonstrated slightly improved fit. Subdomain scores add value over a total score. We demonstrated that the PROMIS-FIB is appropriate for measuring fatigue in clinical samples of FM patients. The construct can be presented by a single score; however, subdomain scores for the three group factors identified in the alternative model may also be reported.

Degradation of metallic materials studied by correlative tomography

NASA Astrophysics Data System (ADS)

Burnett, T. L.; Holroyd, N. J. H.; Lewandowski, J. J.; Ogurreck, M.; Rau, C.; Kelley, R.; Pickering, E. J.; Daly, M.; Sherry, A. H.; Pawar, S.; Slater, T. J. A.; Withers, P. J.

2017-07-01

There are a huge array of characterization techniques available today and increasingly powerful computing resources allowing for the effective analysis and modelling of large datasets. However, each experimental and modelling tool only spans limited time and length scales. Correlative tomography can be thought of as the extension of correlative microscopy into three dimensions connecting different techniques, each providing different types of information, or covering different time or length scales. Here the focus is on the linking of time lapse X-ray computed tomography (CT) and serial section electron tomography using the focussed ion beam (FIB)-scanning electron microscope to study the degradation of metals. Correlative tomography can provide new levels of detail by delivering a multiscale 3D picture of key regions of interest. Specifically, the Xe+ Plasma FIB is used as an enabling tool for large-volume high-resolution serial sectioning of materials, and also as a tool for preparation of microscale test samples and samples for nanoscale X-ray CT imaging. The exemplars presented illustrate general aspects relating to correlative workflows, as well as to the time-lapse characterisation of metal microstructures during various failure mechanisms, including ductile fracture of steel and the corrosion of aluminium and magnesium alloys. Correlative tomography is already providing significant insights into materials behaviour, linking together information from different instruments across different scales. Multiscale and multifaceted work flows will become increasingly routine, providing a feed into multiscale materials models as well as illuminating other areas, particularly where hierarchical structures are of interest.

Assessment of sources of human pathogens and fecal contamination in a Florida freshwater lake.

PubMed

Staley, Christopher; Reckhow, Kenneth H; Lukasik, Jerzy; Harwood, Valerie J

2012-11-01

We investigated the potential for a variety of environmental reservoirs to harbor or contribute fecal indicator bacteria (FIB), DNA markers of human fecal contamination, and human pathogens to a freshwater lake. We hypothesized that submerged aquatic vegetation (SAV), sediments, and stormwater act as reservoirs and/or provide inputs of FIB and human pathogens to this inland water. Analysis included microbial source tracking (MST) markers of sewage contamination (Enterococcus faecium esp gene, human-associated Bacteroides HF183, and human polyomaviruses), pathogens (Salmonella, Cryptosporidium, Giardia, and enteric viruses), and FIB (fecal coliforms, Escherichia coli, and enterococci). Bayesian analysis was used to assess relationships among microbial and physicochemical variables. FIB in the water were correlated with concentrations in SAV and sediment. Furthermore, the correlation of antecedent rainfall and major rain events with FIB concentrations and detection of human markers and pathogens points toward multiple reservoirs for microbial contaminants in this system. Although pathogens and human-source markers were detected in 55% and 21% of samples, respectively, markers rarely coincided with pathogen detection. Bayesian analysis revealed that low concentrations (<45 CFU × 100 ml(-1)) of fecal coliforms were associated with 93% probability that pathogens would not be detected; furthermore the Bayes net model showed associations between elevated temperature and rainfall with fecal coliform and enterococci concentrations, but not E. coli. These data indicate that many under-studied matrices (e.g. SAV, sediment, stormwater) are important reservoirs for FIB and potentially human pathogens and demonstrate the usefulness of Bayes net analysis for water quality assessment. Copyright © 2012 Elsevier Ltd. All rights reserved.

Exsolution lamellae in volcanic pyroxene; Single phenocryst thermometry for long-lived magmatic reservoir

NASA Astrophysics Data System (ADS)

I Made, R.; Herrin, J. S.; Tay, Y. Y.; Costa Rodriguez, F.

2017-12-01

Comprehensive understanding of the relevant timescales of thermal and chemical evolution of magma below the active volcanoes can help us to better anticipate volcanic eruptions and their likely precursor signals. In recent years, several lines of thermochronological inquiry have converged on a realization that, within many volcanic systems, magmas experience prolonged periods of relatively low-temperature storage prior to eruption during short duration transient events. This prolonged storage at low magmatic temperatures can result in series of solid state phase transformations within minerals, producing a petrologic record of their thermal history. In this example, we observed pigeonite exsolution lamellae in augite phenocrysts from the 2011 eruption of Cordon Caulle volcano, Chile. The small size of these features ( 70nm width and <1µm spacing), however, presents an analytical challenge. Focused ion beam (FIB) sample preparation has enable us to prepare site and orientation specific samples suitable for transmission electron microscope (TEM) characterization. Compositions of augite hosts (Wo39En38Fs22) were determined by EPMA prior to FIB preparation, while the compositions of pigeonite lamellae (Wo8En51Fs40) were determined by EDS utilizing PENEPMA simulation software for data reduction. These compositions yielded augite-pigeonite equilibrium temperatures of 945°C, in reasonable agreement with augite-liquid and bulk rock-liquidus temperatures. Lamella formation temperature relative to the C2/c → P21/c transition temperature can also be determined from the angle of the exsolution boundary with respect to crystal orientation. Since the C2/c → P21/c transition temperature is compositionally-dependent, however, calibration of this temperature-structure relationship requires us to conduct heating experiments. Toward this aim, we have combined nano beam electron diffraction (NBED) technique with an in-situ TEM heating stage to measure the changing lattice parameters at magmatic temperatures. Through this work we hope to develop two independent temperature determinations from individual augite phenocrysts which bear exsolution textures and apply this knowledge to understanding the thermal conditions of magma storage in long-lived volcanic reservoirs.

SRF niobium characterization using SIMS and FIB-TEM

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

Stevie, F. A.

2015-12-04

Our understanding of superconducting radio frequency (SRF) accelerator cavities has been improved by elemental analysis at high depth resolution and by high magnification microscopy. This paper summarizes the technique development and the results obtained on poly-crystalline, large grain, and single crystal SRF niobium. Focused ion beam made possible sample preparation using transmission electron microscopy and the images obtained showed a very uniform oxide layer for all samples analyzed. Secondary ion mass spectrometry indicated the presence of a high concentration of hydrogen and the hydrogen content exhibited a relationship with improvement in performance. Depth profiles of carbon, nitrogen, and oxygen didmore » not show major differences with heat treatment. Niobium oxide less than 10 nm thick was shown to be an effective hydrogen barrier. Niobium with titanium contamination showed unexpected performance improvement.« less

Factors related to occurrence and distribution of selected bacterial and protozoan pathogens in Pennsylvania streams

USGS Publications Warehouse

Duris, Joseph W.; Reif, Andrew G.; Donna A. Crouse,; Isaacs, Natasha M.

2013-01-01

The occurrence and distribution of fecal indicator bacteria (FIB) and bacterial and protozoan pathogens are controlled by diverse factors. To investigate these factors in Pennsylvania streams, 217 samples were collected quarterly from a 27-station water-quality monitoring network from July 2007 through August 2009. Samples were analyzed for concentrations of Escherichia coli (EC) and enterococci (ENT) indicator bacteria, concentrations of Cryptosporidium oocysts and Giardia cysts, and the presence of four genes related to pathogenic types of EC (eaeA, stx2, stx1, rfbO157) plus three microbial source tracking (MST) gene markers that are also associated with pathogenic ENT and EC (esp, LTIIa, STII). Water samples were concurrently analyzed for basic water chemistry, physical measures of water quality, nutrients, metals, and a suite of 79 organic compounds that included hormones, pharmaceuticals, and antibiotics. For each sample location, stream discharge was measured by using standardized methods at the time of sample collection, and ancillary sample site information, such as land use and geological characteristics, was compiled. Samples exceeding recreational water quality criteria were more likely to contain all measured pathogen genes but notCryptosporidium or Giardia (oo)cysts. FIB and Giardia density and frequency of eaeA gene occurrence were significantly related to season. When discharge at a sampling location was high (>75th percentile of daily mean discharge), there were greater densities of FIB and Giardia, and the stx2, rfbO157, STII, and esp genes were found more frequently than at other discharge conditions. Giardia occurrence was likely related to nonpoint sources, which are highly influential during seasonal overland transport resulting from snowmelt and elevated precipitation in late winter and spring in Pennsylvania. When MST markers of human, swine, or bovine origin were present, samples more frequently carried the eaeA, stx2, stx1, and rfbO157 genes, but no genes were related exclusively to an individual MST marker. The human source pharmaceuticals (HSPs) acetaminophen and caffeine were correlated with Giardia, and the presence of HSPs proved to be more useful than MST markers in distinguishing the occurrence of Giardia. The HSPs caffeine and carbamazepine were correlated with the sum total of pathogen genes detected in a sample, demonstrating the value of using HSPs as an indicator of fecally derived pathogens. Sites influenced by urban land use with less forest were more likely to have greater FIB and Giardia densities and sum of the array of pathogen genes. Sites dominated by shallow carbonate bedrock in the upstream catchment were likely to have greater FIB densities and higher sum totals of pathogen genes but no correlation with Giardia detection. Our study provides a range of specific environmental, chemical, geologic, and land-use variables related to occurrence and distribution of FIB and selected bacterial and protozoan pathogens in Pennsylvania streams. The information presented could be useful for resource managers in understanding bacterial and protozoan pathogen occurrence and their relation to fecal indicator bacteria in similar settings.

Ultrastructurally-smooth thick partitioning and volume stitching for larger-scale connectomics

PubMed Central

Hayworth, Kenneth J.; Xu, C. Shan; Lu, Zhiyuan; Knott, Graham W.; Fetter, Richard D.; Tapia, Juan Carlos; Lichtman, Jeff W.; Hess, Harald F.

2015-01-01

FIB-SEM has become an essential tool for studying neural tissue at resolutions below 10×10×10 nm, producing datasets superior for automatic connectome tracing. We present a technical advance, ultrathick sectioning, which reliably subdivides embedded tissue samples into chunks (20 µm thick) optimally sized and mounted for efficient, parallel FIB-SEM imaging. These chunks are imaged separately and then ‘volume stitched’ back together, producing a final 3D dataset suitable for connectome tracing. PMID:25686390

Organic Aggregates with (delta)D and delta(sup 15)N Anomalies in the Zag Clast Revealed by STXM and NanoSIMS

NASA Technical Reports Server (NTRS)

Kebukawa, Y.; Ito, M.; Zolensky, M. E.; Rahman, Z.; Kilcoyne, A. L. D.; Nakato, A.; Takeichi, Y.; Suga, H.; Miyamoto, C.; Mase, K.;

Three-dimensional multiscale analysis of degradation of nano- and micro-structure in direct methanol fuel cell electrodes after methanol starvation

NASA Astrophysics Data System (ADS)

Netzeband, Christian; Arlt, Tobias; Wippermann, Klaus; Lehnert, Werner; Manke, Ingo

2016-09-01

This study investigates the ageing effects on the microstructure of the anode catalyst layer of direct methanol fuel cells (DMFC) after complete methanol starvation. To this end the samples of two methanol-depleted membrane electrode assemblies (MEA) have been compared with a pristine reference sample. A three-dimensional characterization of the anode catalyst layer (ACL) structure on a nanometer scale has been conducted by focused ion beam (FIB)/scanning electron microscope (SEM) tomography. The FIB/SEM tomography allows for a detailed analysis of statistic parameters of micro-structured materials, such as porosity, tortuosity and pore size distributions. Furthermore, the SEM images displayed a high material contrast between the heavy catalyst metals (Pt/Ru) and the relatively light carbon support, which made it possible to map the catalyst distribution in the acquired FIB/SEM tomographies. Additional synchrotron X-ray tomographies have been conducted in order to obtain an overview of the structural changes of all the components of a section of the MEAs after methanol depletion.

Diagnostic accuracy of APRI, FIB-4 and Forns for the detection of liver cirrhosis in HIV/HCV-coinfected patients.

PubMed

Merli, Marco; Galli, Laura; Castagna, Antonella; Salpietro, Stefania; Gianotti, Nicola; Messina, Emanuela; Poli, Andrea; Morsica, Giulia; Bagaglio, Sabrina; Cernuschi, Massimo; Bigoloni, Alba; Uberti-Foppa, Caterina; Lazzarin, Adriano; Hasson, Hamid

2016-04-01

We determined the diagnostic accuracy and optimal cut off of three indirect fibrosis biomarkers (APRI, FIB-4, Forns) compared with liver stiffness (LS) for the detection of liver cirrhosis in HIV/HCV-coinfected patients. An observational retrospective study on HIV/HCV-coinfected patients with concomitant LS measurement and APRI, FIB-4 and Forns was performed. The presence of liver cirrhosis was defined as a LS ≥13 KPa. The diagnostic accuracy and optimal cut-off values, compared with LS categorization (<13 vs ≥13 KPa), were determined by receiver operating characteristics (ROC) curves. The study sample included 646 patients. The area-under-the ROC curve (95% confidence interval) for the detection of liver cirrhosis were 0.84 (0.81-0.88), 0.87 (0.84-0.91) and 0.87 (0.84-0.90) for APRI, FIB-4 and Forns, respectively. According to the optimal cut off values for liver cirrhosis (≥0.97 for APRI, ≥2.02 for FIB-4 and ≥7.8 for Forns), 80%, 80% and 82% of subjects were correctly classified by the three indirect fibrosis biomarkers, respectively. Misclassifications were mostly due to false positive cases. The study suggests that indirect fibrosis biomarkers can help clinicians to exclude liver cirrhosis in the management of HIV/HCV co-infected patients, reducing the frequency of more expensive or invasive assessments.

Fibrinogen deficiency suppresses the development of early and delayed radiation enteropathy

PubMed Central

Wang, Junru; Pathak, Rupak; Garg, Sarita; Hauer-Jensen, Martin

2017-01-01

AIM To determine the mechanistic role of fibrinogen, a key regulator of inflammation and fibrosis, in early and delayed radiation enteropathy. METHODS Fibrinogen wild-type (Fib+/+), fibrinogen heterozygous (Fib+/-), and fibrinogen knockout (Fib-/-) mice were exposed to localized intestinal irradiation and assessed for early and delayed structural changes in the intestinal tissue. A 5-cm segment of ileum of mice was exteriorized and exposed to 18.5 Gy of x-irradiation. Intestinal tissue injury was assessed by quantitative histology, morphometry, and immunohistochemistry at 2 wk and 26 wk after radiation. Plasma fibrinogen level was measured by enzyme-linked immunosorbent assay. RESULTS There was no difference between sham-irradiated Fib+/+ and Fib+/- mice in terms of fibrinogen concentration in plasma and intestinal tissue, intestinal histology, morphometry, intestinal smooth muscle cell proliferation, and neutrophil infiltration. Therefore, Fib+/- mice were used as littermate controls. Unlike sham-irradiated Fib+/+ and Fib+/- mice, no fibrinogen was detected in the plasma and intestinal tissue of sham-irradiated Fib-/- mice. Moreover, fibrinogen level was not elevated after irradiation in the intestinal tissue of Fib-/- mice, while significant increase in intestinal fibrinogen level was noticed in irradiated Fib+/+ and Fib+/- mice. Importantly, irradiated Fib-/- mice exhibited substantially less overall intestinal structural injury (RIS, P = 0.000002), intestinal wall thickness (P = 0.003), intestinal serosal thickness (P = 0.009), collagen deposition (P = 0.01), TGF-β immunoreactivity (P = 0.03), intestinal smooth muscle proliferation (P = 0.046), neutrophil infiltration (P = 0.01), and intestinal mucosal injury (P = 0.0003), compared to irradiated Fib+/+ and Fib+/- mice at both 2 wk and 26 wk. CONCLUSION These data demonstrate that fibrinogen deficiency directly attenuates development of early and delayed radiation enteropathy. Fibrinogen could be a novel target in treating intestinal damage. PMID:28765691

Quantitative analysis of nano-pore geomaterials and representative sampling for digital rock physics

NASA Astrophysics Data System (ADS)

Yoon, H.; Dewers, T. A.

2014-12-01

Geomaterials containing nano-pores (e.g., shales and carbonate rocks) have become increasingly important for emerging problems such as unconventional gas and oil resources, enhanced oil recovery, and geologic storage of CO2. Accurate prediction of coupled geophysical and chemical processes at the pore scale requires realistic representation of pore structure and topology. This is especially true for chalk materials, where pore networks are small and complex, and require characterization at sub-micron scale. In this work, we apply laser scanning confocal microscopy to characterize pore structures and microlithofacies at micron- and greater scales and dual focused ion beam-scanning electron microscopy (FIB-SEM) for 3D imaging of nanometer-to-micron scale microcracks and pore distributions. With imaging techniques advanced for nano-pore characterization, a problem of scale with FIB-SEM images is how to take nanometer scale information and apply it to the thin-section or larger scale. In this work, several texture characterization techniques including graph-based spectral segmentation, support vector machine, and principal component analysis are applied for segmentation clusters represented by 1-2 FIB-SEM samples per each cluster. Geometric and topological properties are analyzed and lattice-Boltzmann method (LBM) is used to obtain permeability at several different scales. Upscaling of permeability to the Darcy scale (e.g., the thin-section scale) with image dataset will be discussed with emphasis on understanding microfracture-matrix interaction, representative volume for FIB-SEM sampling, and multiphase flow and reactive transport. Funding from the DOE Basic Energy Sciences Geosciences Program is gratefully acknowledged. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Prognostic value of combined preoperative fibrinogen and neutrophil–lymphocyte ratio in patients with hepatocellular carcinoma after liver transplantation

PubMed Central

Chen, Mao-Gen; Wang, Xiao-Ping; Ju, Wei-Qiang; Zhao, Qiang; Wu, Lin-Wei; Ren, Qing-Qi; Guo, Zhi-Yong; Wang, Dong-Ping; Zhu, Xiao-Feng; Ma, Yi; He, Xiao-Shun

2017-01-01

Objectives Elevated plasma fibrinogen (Fib) correlated with patient's prognosis in several solid tumors. However, few studies have illuminated the relationship between preoperative Fib and prognosis of HCC after liver transplantation. We aimed to clarify the prognostic value of Fib and whether the prognostic accuracy can be enhanced by the combination of Fib and neutrophil–lymphocyte ratio (NLR). Results Fib was correlated with Child-pugh stage, alpha-fetoprotein (AFP), size of largest tumor, macro- and micro-vascular invasion. Univariate analysis showed preoperative Fib, AFP, NLR, size of largest tumor, tumor number, macro- and micro- vascular invasion were significantly associated with disease-free survival (DFS) and overall survival (OS) in HCC patients with liver transplantation. After multivariate analysis, only Fib and macro-vascular invasion were independently correlated with DFS and OS. Survival analysis showed that preoperative Fib > 2.345 g/L predicted poor prognosis of patients HCC after liver transplantation. Preoperative Fib showed prognostic value in various subgroups of HCC. Furthermore, the predictive range was expanded by the combination of Fib and NLR. Materials and Methods Data were collected retrospectively from 130 HCC patients who underwent liver transplantation. Preoperative Fib, NLR and clinicopathologic variables were analyzed. The survival analysis was performed by the Kaplan-Meier method, and compared by the log-rank test. Univariate and multivariate analyses were performed to identify the prognostic factors for DFS and OS. Conclusions Preoperative Fib is an independent effective predictor of prognosis for HCC patients, higher levels of Fib predict poorer outcomes and the combination of Fib and NLR enlarges the prognostic accuracy of testing. PMID:27935864

Solar Flare Track Exposure Ages in Regolith Particles: A Calibration for Transmission Electron Microscope Measurements

NASA Technical Reports Server (NTRS)

Berger, Eve L.; Keller, Lindsay P.

2015-01-01

Mineral grains in lunar and asteroidal regolith samples provide a unique record of their interaction with the space environment. Space weathering effects result from multiple processes including: exposure to the solar wind, which results in ion damage and implantation effects that are preserved in the rims of grains (typically the outermost 100 nm); cosmic ray and solar flare activity, which result in track formation; and impact processes that result in the accumulation of vapor-deposited elements, impact melts and adhering grains on particle surfaces. Determining the rate at which these effects accumulate in the grains during their space exposure is critical to studies of the surface evolution of airless bodies. Solar flare energetic particles (mainly Fe-group nuclei) have a penetration depth of a few millimeters and leave a trail of ionization damage in insulating materials that is readily observable by transmission electron microscope (TEM) imaging. The density of solar flare particle tracks is used to infer the length of time an object was at or near the regolith surface (i.e., its exposure age). Track measurements by TEM methods are routine, yet track production rate calibrations have only been determined using chemical etching techniques [e.g., 1, and references therein]. We used focused ion beam-scanning electron microscope (FIB-SEM) sample preparation techniques combined with TEM imaging to determine the track density/exposure age relations for lunar rock 64455. The 64455 sample was used earlier by [2] to determine a track production rate by chemical etching of tracks in anorthite. Here, we show that combined FIB/TEM techniques provide a more accurate determination of a track production rate and also allow us to extend the calibration to solar flare tracks in olivine.

Non-invasive tests in prediction of liver fibrosis in chronic hepatitis B and comparison with post-antiviral treatment results.

PubMed

Başar, Omer; Yimaz, Bariş; Ekiz, Fuat; Giniş, Zeynep; Altinbaş, Akif; Aktaş, Bora; Tuna, Yaşar; Çoban, Sahin; Delibaş, Namik; Yüksel, Osman

2013-04-01

The aim of this study was to assess and compare the performance of a series of non-invasive tests to detect fibrosis in patients with chronic hepatitis B (CHB). Seventy-six patients with CHB, whose blood samples were collected and biopsies were done on the same day, were included in this study. Pre-treatment calculations of aspartate aminotransferase to platelet ratio index (APRI), Forn's index, FIB-4, S-index, Shanghai Liver Fibrosis Group's index (SLFG) and Hepascore(®) were done and relations with mild and advanced fibrosis and cirrhosis were assessed. Post-treatment values of APRI, Forn's index, FIB-4, S-index with oral antiviral agents were also investigated. APRI, S-index, SLFG, FIB-4, Forn's index and Hepascore(®) had 0.669, 0.669, 0.739, 0.741, 0.753, 0.780; retrospectively Area Under the Receiver Operating Characteristic Curve (AUROC) for significant fibrosis. APRI, Forn's index, S-index, FIB-4, SLFG, and Hepascore(®) had 0.681, 0.714, 0.715, 0.738, 0.747, 0.777 retrospectively AUROC for advanced fibrosis. APRI, SLFG, FIB-4, Forn's index, S-index, and Hepascore(®) had 0.741, 0.742, 0.768, 0.779, 0.792, 0.824 retrospectively AUROC for cirrhosis. APRI, Forn's index, FIB-4 and S-index were significantly lower in post-treatment group compared with pre-treatment group (P-values: <0.05, 0.001, 0.003, 0.018; respectively). Hepascore(®) showed the best performance to predict significant fibrosis. Our study also suggests that the use of non-invasive test to predict fibrosis in patients with CHB may reduce the need for liver biopsy and may help to monitor the efficacy of treatment. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

FIB-NanoSIMS-TEM Coordinated Study of a Wark-Lovering Rim in a Vigarano Type A CAI

NASA Technical Reports Server (NTRS)

Cai, A.; Ito, M.; Keller, L. P.; Ross, D. K.; Nakamura-Messenger, K.

2010-01-01

Wark-Lovering (WL) rims are thin multi layered mineral sequences that surround most Ca, Al-rich inclusions (CAIs). Unaltered WL rims are composed of the same primary high temperature minerals as CAIs, such as melilite, spinel, pyroxene, hibonite, perovskite, anorthite and olivine. It is still unclear whether the rim minerals represent a different generation formed by a separate event from their associated CAIs or are a byproduct of CAI formation. Several models have been proposed for the origins of WL rims including condensation, flashheating, reaction of a CAI with a Mg-Si-rich reservoir (nebular gas or solid); on the basis of mineralogy, abundances of trace elements, O and Mg isotopic studies. Detailed mineralogical characterizations of WL rims at micrometer to nanometer scales have been obtained by TEM observations, but so far no coordinated isotopic - mineralogical studies have been performed. Thus, we have applied an O isotopic imaging technique by NanoSIMS 50L to investigate heterogeneous distributions of O isotopic ratios in minerals within a cross section of a WL rim prepared using a focused ion beam (FIB) instrument. After the isotopic measurements, we determine the detailed mineralogy and microstructure of the same WL FIB section to gain insight into its petrogenesis. Here we present preliminary results from O isotopic and elemental maps by NanoSIMS and mineralogical analysis by FE-SEM of a FIB section of a WL rim in the Vigarano reduced CV3 chondrite.

A simple bedside blood test (Fibrofast; FIB-5) is superior to FIB-4 index for the differentiation between non-significant and significant fibrosis in patients with chronic hepatitis C.

PubMed

Shiha, G; Seif, S; Eldesoky, A; Elbasiony, M; Soliman, R; Metwally, A; Zalata, K; Mikhail, N

2017-05-01

A simple non-invasive score (Fibrofast, FIB-5) was developed using five routine laboratory tests (ALT, AST, alkaline phosphatase, albumin and platelets count) for the detection of significant hepatic fibrosis in patients with chronic hepatitis C. The FIB-4 index is a non-invasive test for the assessment of liver fibrosis, and a score of ≤1.45 enables the correct identification of patients who have non-significant (F0-1) from significant fibrosis (F2-4), and could avoid liver biopsy. The aim of this study was to compare the performance characteristics of FIB-5 and FIB-4 to differentiate between non-significant and significant fibrosis. A cross-sectional study included 604 chronic HCV patients. All liver biopsies were scored using the METAVIR system. Both FIB-5 and FIB-4 scores were measured and the performance characteristics were calculated using the ROC curve. The performance characteristics of FIB-5 at ≥7.5 and FIB-4 at ≤1.45 for the differentiation between non-significant fibrosis and significant fibrosis were: specificity 94.4%, PPV 85.7%, and specificity 54.9%, PPV 55.7% respectively. FIB-5 score at the new cutoff is superior to FIB-4 index for the differentiation between non-significant and significant fibrosis.

Use of radon-222 to evaluate the influence of groundwater discharge on fecal indicator bacteria concentrations in the near-shore ocean, Malibu, California

NASA Astrophysics Data System (ADS)

Izbicki, J. A.; Burton, C.; Swarzenski, P. W.

2011-12-01

To protect beach-goers from waterborne disease, California requires water-quality monitoring for fecal indicator bacteria (FIB) at beaches having more than 50,000 visits annually. The source(s) of FIB in ocean beaches in excess of marine recreational water standards is often not known, or may be incorrectly identified. Onsite wastewater treatment systems (OWTS) used to treat residential and commercial sewage have been implicated by regulatory agencies as a possible source of FIB to recreational ocean beaches, near Malibu, California. For this to occur, treated wastewater must first move through groundwater prior to discharge at the ocean. Groundwater discharge to the ocean near Malibu Lagoon (the estuary of Malibu Creek) is complicated by seasonally changing water levels in the lagoon. The lagoon is isolated from the ocean by a sand berm that develops across the mouth of the lagoon during the dry season. Higher water levels in the lagoon during the dry season, and lower water-levels during the wet season, cause seasonal changes in the direction of groundwater flow and the magnitude of discharge from the adjacent small (3,400 hectare), alluvial aquifer. Radon-222, an indicator of groundwater discharge, was measured in Malibu Lagoon, in the near-shore ocean adjacent to the lagoon, and in the near-shore ocean adjacent to unsewered residential development to determine the timing and magnitude of groundwater discharge. During the dry season, when the berm of the lagoon was closed and the lagoon was isolated from the ocean, radon-222 concentrations in the near-shore ocean during low tide increased as water discharged from the lagoon through the berm. Enterococcus concentrations in the near-shore ocean increased to almost 600 Most Probable Number (MPN) per 100 milliliter at this time. Radon-222 concentrations also increased at low tide as groundwater discharged to the ocean from the adjacent alluvial aquifer underlying the unsewered residential development, but there was no corresponding increase in FIB concentrations. In contrast, during the wet season when the berm of the lagoon was open, radon-222 data show groundwater discharge from the alluvial aquifer was primarily into the lagoon at low tide. The water in the lagoon was subsequently discharged directly to the near-shore ocean as a result of tidally driven circulation through the open berm. Radon-222 data showed little, if any, groundwater discharge to the near-shore ocean adjacent to the unsewered residential development at this time, implying that FIB in the near-shore ocean would not be derived from OWTS in the unsewered residential areas. The absence of FIB in recreational beaches adjacent to unsewered residential development at low tide suggests that mechanisms other than groundwater discharge may be responsible for high FIB concentrations in this area. For example, microbial communities sampled in the near-shore ocean were genetically similar to those present in kelp and different from OWTS samples-suggesting that high FIB concentrations, especially at high tide, may result from wave action on the beach releasing FIB entrained in kelp that was derived from birds and other non-human sources.

An assessment of fecal indicator and other bacteria from an urbanized coastal lagoon in the City of Los Angeles, California, USA.

PubMed

Dorsey, John H; Carmona-Galindo, Víctor D; Leary, Christopher; Huh, Julie; Valdez, Jennifer

2013-03-01

A study was performed in Del Rey Lagoon, City of Los Angeles, to determine if the lagoon was as a source or sink for fecal indicator bacteria (FIB: total coliforms, Escherichia coli, enterococci) and to screen for the presence of other potentially pathogenic bacteria. The lagoon receives tidal flows from the adjacent Ballona Estuary whose water usually is contaminated with FIB originating from the highly urbanized Ballona Creek Watershed. During 16 sampling events from February 2008 through March 2009, replicate water samples (n = 3) were collected 1 h prior to the high tide and 1 h prior to the following low tide. FIB concentrations were measured by the defined substrate method (IDEXX, Westbrook, Me) followed by culturing of bacterial isolates sampled from positive IDEXX Quanti-Tray wells and were identified using the Vitek 2 Compact (bioMérieux, Durham, NC). Mean concentrations of FIB often differed by an order of magnitude from flood to ebb flow conditions. The lagoon tended to act as a sink for total coliforms based on the ratio of mean flood to ebb densities (R (F/E)) >1.0 during 56 % of the sampling events and during ebb flows, as a source for E. coli and enterococci (R (F/E) <1.69 % of events). Approximately 54 species were identified from 277 isolates cultured from the IDEXX Quanti-Trays. Of these, 54 % were species known to include pathogenic strains that can be naturally occurring, introduced in runoff, or originated from other sources. Diversity and cluster analyses indicated a dynamic assemblage that changes in species composition with day-to-day fluctuations as well as tidal action. The concept of monitoring the lagoon and estuary as a sentinel habitat for pathogenic assemblages is discussed.

FIB and MIP: understanding nanoscale porosity in molecularly imprinted polymers via 3D FIB/SEM tomography.

PubMed

Neusser, G; Eppler, S; Bowen, J; Allender, C J; Walther, P; Mizaikoff, B; Kranz, C

2017-10-05

We present combined focused ion beam/scanning electron beam (FIB/SEM) tomography as innovative method for differentiating and visualizing the distribution and connectivity of pores within molecularly imprinted polymers (MIPs) and non-imprinted control polymers (NIPs). FIB/SEM tomography is used in cell biology for elucidating three-dimensional structures such as organelles, but has not yet been extensively applied for visualizing the heterogeneity of nanoscopic pore networks, interconnectivity, and tortuosity in polymers. To our best knowledge, the present study is the first application of this strategy for analyzing the nanoscale porosity of MIPs. MIPs imprinted for propranolol - and the corresponding NIPs - were investigated establishing FIB/SEM tomography as a viable future strategy complementing conventional isotherm studies. For visualizing and understanding the properties of pore networks in detail, polymer particles were stained with osmium tetroxide (OsO 4 ) vapor, and embedded in epoxy resin. Staining with OsO 4 provides excellent contrast during high-resolution SEM imaging. After optimizing the threshold to discriminate between the stained polymer matrix, and pores filled with epoxy resin, a 3D model of the sampled volume may be established for deriving not only the pore volume and pore surface area, but also to visualize the interconnectivity and tortuosity of the pores within the sampled polymer volume. Detailed studies using different types of cross-linkers and the effect of hydrolysis on the resulting polymer properties have been investigated. In comparison of MIP and NIP, it could be unambiguously shown that the interconnectivity of the visualized pores in MIPs is significantly higher vs. the non-imprinted polymer, and that the pore volume and pore area is 34% and approx. 35% higher within the MIP matrix. This confirms that the templating process not only induces selective binding sites, but indeed also affects the physical properties of such polymers down to the nanoscale, and that additional chemical modification, e.g., via hydrolysis clearly affects that nature of the polymer.

FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons.

PubMed

Bosch, Carles; Martínez, Albert; Masachs, Nuria; Teixeira, Cátia M; Fernaud, Isabel; Ulloa, Fausto; Pérez-Martínez, Esther; Lois, Carlos; Comella, Joan X; DeFelipe, Javier; Merchán-Pérez, Angel; Soriano, Eduardo

2015-01-01

The fine analysis of synaptic contacts is usually performed using transmission electron microscopy (TEM) and its combination with neuronal labeling techniques. However, the complex 3D architecture of neuronal samples calls for their reconstruction from serial sections. Here we show that focused ion beam/scanning electron microscopy (FIB/SEM) allows efficient, complete, and automatic 3D reconstruction of identified dendrites, including their spines and synapses, from GFP/DAB-labeled neurons, with a resolution comparable to that of TEM. We applied this technology to analyze the synaptogenesis of labeled adult-generated granule cells (GCs) in mice. 3D reconstruction of dendritic spines in GCs aged 3-4 and 8-9 weeks revealed two different stages of dendritic spine development and unexpected features of synapse formation, including vacant and branched dendritic spines and presynaptic terminals establishing synapses with up to 10 dendritic spines. Given the reliability, efficiency, and high resolution of FIB/SEM technology and the wide use of DAB in conventional EM, we consider FIB/SEM fundamental for the detailed characterization of identified synaptic contacts in neurons in a high-throughput manner.

FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons

PubMed Central

Bosch, Carles; Martínez, Albert; Masachs, Nuria; Teixeira, Cátia M.; Fernaud, Isabel; Ulloa, Fausto; Pérez-Martínez, Esther; Lois, Carlos; Comella, Joan X.; DeFelipe, Javier; Merchán-Pérez, Angel; Soriano, Eduardo

2015-01-01

The fine analysis of synaptic contacts is usually performed using transmission electron microscopy (TEM) and its combination with neuronal labeling techniques. However, the complex 3D architecture of neuronal samples calls for their reconstruction from serial sections. Here we show that focused ion beam/scanning electron microscopy (FIB/SEM) allows efficient, complete, and automatic 3D reconstruction of identified dendrites, including their spines and synapses, from GFP/DAB-labeled neurons, with a resolution comparable to that of TEM. We applied this technology to analyze the synaptogenesis of labeled adult-generated granule cells (GCs) in mice. 3D reconstruction of dendritic spines in GCs aged 3–4 and 8–9 weeks revealed two different stages of dendritic spine development and unexpected features of synapse formation, including vacant and branched dendritic spines and presynaptic terminals establishing synapses with up to 10 dendritic spines. Given the reliability, efficiency, and high resolution of FIB/SEM technology and the wide use of DAB in conventional EM, we consider FIB/SEM fundamental for the detailed characterization of identified synaptic contacts in neurons in a high-throughput manner. PMID:26052271

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

Cai, Zhaobing

Ni-Cr-Co-Ti-V-Al high-entropy alloy coating on Ti-6Al-4V was synthesized by laser surface alloying. The coating is composed of a B2 matrix and (Co, Ni)Ti{sub 2} compounds with few β-Ti phases. Focused ion beam technique was utilized to prepare TEM sample and TEM observations agree well with XRD and SEM results. The formation of HEA phases is due to high temperature and rapid cooling rate during laser surface alloying. The thermodynamic parameters, ΔH{sub mix}, ΔS{sub mix}and δ as well as Δχ, should be used to predict the formation of the BCC solid solution, but they are not the strict criteria. Especially whenmore » Δχ reaches a high value (≥ 10%), BCC HEA will be partially decomposed, leading to the formation of (Co, Ni)Ti{sub 2} compound phases. - Highlights: •Preparing HEA coating on Ti-6Al-4V by laser surface alloying is successful. •The synthesized HEA coating mainly consists of BCC HEA and (Co, Ni)Ti{sub 2} compounds. •FIB technology was used to prepare the sample for TEM analysis. • ΔH{sub mix}, ΔS{sub mix}and δ as well as Δχ, should be all used to predict the formation of solid solution.« less

Loading of fecal indicator bacteria in North Carolina tidal creek headwaters: hydrographic patterns and terrestrial runoff relationships.

PubMed

Stumpf, Curtis H; Piehler, Michael F; Thompson, Suzanne; Noble, Rachel T

2010-09-01

In the New River Estuary (NRE) in eastern North Carolina (NC), fecal indicator bacteria (FIB) levels exceed water quality standards, leading to closure of estuarine waters for shellfishing and classification of parts of the estuary as "impaired" per the Clean Water Act section 303(d) list. As a means to investigate fecal contamination and loading of FIB to the NRE, a continuous automated sampler (ISCO) outfitted with flow modules and water quality probes was placed in four first-order tidal creek headwaters. Total storm discharge and bacterial load for Escherichia coli (EC) and Enterococcus spp. (ENT) were calculated using graphical volumetric flow calculations and interpolation of FIB measurements over each storm's duration for 10 storms. Mean total load of 10(9)-10(12) EC and ENT cells (MPN) occurred over the course of each storm. Total storm loading, averaged across all storms, was as much as 30 and 37 times greater than equivalent duration of baseflow loading for EC and ENT, respectively. Within the first 30% of creek storm volume for all storms and all creeks combined, a mean cumulative load of only 37% and 44% of the total EC and ENT cells, respectively, was discharged, indicating these creeks are not demonstrating a 'first flush' scenario for FIB. The median storm Event Mean Concentrations (EMCs) were 6.37 × 10(2) and 2.03 × 10(2) MPN/100 mL, for EC and ENT, respectively, compared with median baseflow concentrations of 1.48 × 10(2) and 4.84 × 10(1) for EC and ENT, respectively, and were significantly different between base and storm flow events. FIB was correlated with TSS (weak), flow rate (strong), and different stages (base, rising, peak, and falling) of the hydrograph (strong). Pollutographs indicate large intra-storm variability of FIB, and the need for more intensive sampling throughout a storm in order to attain accurate FIB contaminant estimates. Instream sediment concentrations ranged from 5 to 478 (MPN/g) and 13 to 776 (MPN/g) for EC and ENT, respectively, indicating sediment as a source, but a minor reservoir. This overall approach for calculating loading in headwater tidal creeks is detailed. Accurate loading characterization of FIB during storms and dry weather conditions, and understanding intra-storm FIB concentrations, is imperative for understanding patterns of water quality impairment, establishing management planning, and developing appropriate mitigation strategies. Copyright © 2010 Elsevier Ltd. All rights reserved.

New advances in scanning microscopy and its application to study parasitic protozoa.

PubMed

de Souza, Wanderley; Attias, Marcia

2018-07-01

Scanning electron microscopy has been used to observe and study parasitic protozoa for at least 40 years. However, field emission electron sources, as well as improvements in lenses and detectors, brought the resolution power of scanning electron microscopes (SEM) to a new level. Parallel to the refinement of instruments, protocols for preservation of the ultrastructure, immunolabeling, exposure of cytoskeleton and inner structures of parasites and host cells were developed. This review is focused on protozoan parasites of medical and veterinary relevance, e.g., Toxoplasma gondii, Tritrichomonas foetus, Giardia intestinalis, and Trypanosoma cruzi, compilating the main achievements in describing the fine ultrastructure of their surface, cytoskeleton and interaction with host cells. Two new resources, namely, Helium Ion Microscopy (HIM) and Slice and View, using either Focused Ion Beam (FIB) abrasion or Microtome Serial Sectioning (MSS) within the microscope chamber, combined to backscattered electron imaging of fixed (chemically or by quick freezing followed by freeze substitution and resin embedded samples is bringing an exponential amount of valuable information. In HIM there is no need of conductive coating and the depth of field is much higher than in any field emission SEM. As for FIB- and MSS-SEM, high resolution 3-D models of areas and volumes larger than any other technique allows can be obtained. The main results achieved with all these technological tools and some protocols for sample preparation are included in this review. In addition, we included some results obtained with environmental/low vacuum scanning microscopy and cryo-scanning electron microscopy, both promising, but not yet largely employed SEM modalities. Copyright © 2018. Published by Elsevier Inc.

Direct observation of dopant distribution in GaAs compound semiconductors using phase-shifting electron holography and Lorentz microscopy.

PubMed

Sasaki, Hirokazu; Otomo, Shinya; Minato, Ryuichiro; Yamamoto, Kazuo; Hirayama, Tsukasa

2014-06-01

Phase-shifting electron holography and Lorentz microscopy were used to map dopant distributions in GaAs compound semiconductors with step-like dopant concentration. Transmission electron microscope specimens were prepared using a triple beam focused ion beam (FIB) system, which combines a Ga ion beam, a scanning electron microscope, and an Ar ion beam to remove the FIB damaged layers. The p-n junctions were clearly observed in both under-focused and over-focused Lorentz microscopy images. A phase image was obtained by using a phase-shifting reconstruction method to simultaneously achieve high sensitivity and high spatial resolution. Differences in dopant concentrations between 1 × 10(19) cm(-3) and 1 × 10(18) cm(-3) regions were clearly observed by using phase-shifting electron holography. We also interpreted phase profiles quantitatively by considering inactive layers induced by ion implantation during the FIB process. The thickness of an inactive layer at different dopant concentration area can be measured from the phase image. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Estimation of plasma fibrinogen levels based on hemoglobin, base excess and Injury Severity Score upon emergency room admission

PubMed Central

2013-01-01

Introduction Fibrinogen plays a key role in hemostasis and is the first coagulation factor to reach critical levels in massively bleeding trauma patients. Consequently, rapid estimation of plasma fibrinogen (FIB) is essential upon emergency room (ER) admission, but is not part of routine coagulation monitoring in many centers. We investigated the predictive ability of the laboratory parameters hemoglobin (Hb) and base excess (BE) upon admission, as well as the Injury Severity Score (ISS), to estimate FIB in major trauma patients. Methods In this retrospective study, major trauma patients (ISS ≥16) with documented FIB analysis upon ER admission were eligible for inclusion. FIB was correlated with Hb, BE and ISS, alone and in combination, using regression analysis. Results A total of 675 patients were enrolled (median ISS 27). FIB upon admission correlated strongly with Hb, BE and ISS. Multiple regression analysis showed that Hb and BE together predicted FIB (adjusted R2 = 0.46; loge(FIB) = 3.567 + 0.223.Hb - 0.007.Hb2 + 0.044.BE), and predictive strength increased when ISS was included (adjusted R2 = 0.51; loge(FIB) = 4.188 + 0.243.Hb - 0.008.Hb2 + 0.036.BE - 0.031.ISS + 0.0003.ISS2). Of all major trauma patients admitted with Hb <12 g/dL, 74% had low (<200 mg/dL) FIB and 54% had critical (<150 mg/dL) FIB. Of patients admitted with Hb <10 g/dL, 89% had low FIB and 73% had critical FIB. These values increased to 93% and 89%, respectively, among patients with an admission Hb <8 g/dL. Sixty-six percent of patients with only a weakly negative BE (<−2 mmol/L) showed low FIB. Of patients with BE <−6 mmol/L upon admission, 81% had low FIB and 63% had critical FIB. The corresponding values for BE <−10 mmol/L were 89% and 78%, respectively. Conclusions Upon ER admission, FIB of major trauma patients shows strong correlation with rapidly obtainable, routine laboratory parameters such as Hb and BE. These two parameters might provide an insightful and rapid tool to identify major trauma patients at risk of acquired hypofibrinogenemia. Early calculation of ISS could further increase the ability to predict FIB in these patients. We propose that FIB can be estimated during the initial phase of trauma care based on bedside tests. PMID:23849249

Analysis of the Relationship Between Physical Environmental Parameters and Beach Water Quality in a Subtropical Setting

NASA Astrophysics Data System (ADS)

Zhu, X.; Wang, J. D.; Elmir, S.; Solo-Gabriele, H. M.; Wright, M. E.; Abdelzaher, A.

2006-12-01

Fecal Indicator Bacteria(FIB) are found in high concentrations in sewage water, and thus are used to indicate whether there is fecal material related pathogen present and to determine whether a beach is safe for recreational use. Studies have shown, however, in subtropical regions, FIB concentrations above EPA standards may be present in the absence of known point sources of human or animal waste, thus reducing the efficacy of FIB beach monitoring programs. An interdisciplinary study is being conducted in Miami, Florida , the goal is to understand the sources and behavior of FIB on a beach without point source loads and also to improve beach health hazard warnings in subtropical regions. This study, examines relationship between enterococci (EPA recommended FIB for use in marine water) and physical environmental parameters such as rain, tide and wind. FIB data employed include Florida Department of Health weekly beach monitoring enterococci (ENT) data during a five year period and a two-day experiment with hourly sampling at Hobie Cat Beach on Virginia Key in the Miami metropolitan area. The environmental data consist of wind from a nearby CMAN tower, and local rain and tide. The analysis also includes data from nearby beaches monitored by the Health Department. Results show the correlation coefficient between ENT and tide at Hobie Cat Beach is positive but not significant(r=0.17). Rain events have a significant influence on ENT at Hobie Cat Beach, with a correlation coefficient of up to 0.7 while at other beaches the correlation is less than 0.2. Reasons for this aberration are being investigated. Although this is the only beach allowing dogs there are other factors of possible importance, such as tidal flats frequented by birds and weaker water circulation and exchange at this beach facing a bay rather than the ocean. Higher ENT levels (> 300CFU/100ml water) are more likely (67% of the time) to be associated with periods of onshore winds, which may affect the circulation of water at the beach or cause waves and wave breaking that stir and resuspend the beach sediment. To help interpret FIB observations and to improve the use of future monitoring results, a coastal circulation model and a bacteria fate model is being constructed to simulate and predict the FIB transport and distribution at Hobie Cat Beach.

FIBRILLIN4 Is Required for Plastoglobule Development and Stress Resistance in Apple and Arabidopsis1[W][OA

PubMed Central

Singh, Dharmendra K.; Maximova, Siela N.; Jensen, Philip J.; Lehman, Brian L.; Ngugi, Henry K.; McNellis, Timothy W.

2010-01-01

The fibrillins are a large family of chloroplast proteins that have been linked with stress tolerance and disease resistance. FIBRILLIN4 (FIB4) is found associated with the photosystem II light-harvesting complex, thylakoids, and plastoglobules, which are chloroplast compartments rich in lipophilic antioxidants. For this study, FIB4 expression was knocked down in apple (Malus 3 domestica) using RNA interference. Plastoglobule osmiophilicity was decreased in fib4 knockdown (fib4 KD) tree chloroplasts compared with the wild type, while total plastoglobule number was unchanged. Compared with the wild type, net photosynthetic CO2 fixation in fib4 KD trees was decreased at high light intensity but was increased at low light intensity. Furthermore, fib4 KD trees produced more anthocyanins than the wild type when transferred from low to high light intensity, indicating greater sensitivity to high light stress. Relative to the wild type, fib4 KD apples were more sensitive to methyl viologen and had higher superoxide levels during methyl viologen treatment. Arabidopsis (Arabidopsis thaliana) fib4 mutants and fib4 KD apples were more susceptible than their wild-type counterparts to the bacterial pathogens Pseudomonas syringae pathovar tomato and Erwinia amylovora, respectively, and were more sensitive to ozone-induced tissue damage. Following ozone stress, plastoglobule osmiophilicity decreased in wild-type apple and remained low in fib4 KD trees; total plastoglobule number increased in fib4 KD apples but not in the wild type. These results indicate that FIB4 is required for plastoglobule development and resistance to multiple stresses. This study suggests that FIB4 is involved in regulating plastoglobule content and that defective regulation of plastoglobule content leads to broad stress sensitivity and altered photosynthetic activity. PMID:20813909

Monitoring and predicting the fecal indicator bacteria concentrations from agricultural, mixed land use and urban stormwater runoff.

PubMed

Paule-Mercado, M A; Ventura, J S; Memon, S A; Jahng, D; Kang, J-H; Lee, C-H

2016-04-15

While the urban runoff are increasingly being studied as a source of fecal indicator bacteria (FIB), less is known about the occurrence of FIB in watershed with mixed land use and ongoing land use and land cover (LULC) change. In this study, Escherichia coli (EC) and fecal streptococcus (FS) were monitored from 2012 to 2013 in agricultural, mixed and urban LULC and analyzed according to the most probable number (MPN). Pearson correlation was used to determine the relationship between FIB and environmental parameters (physicochemical and hydrometeorological). Multiple linear regressions (MLR) were used to identify the significant parameters that affect the FIB concentrations and to predict the response of FIB in LULC change. Overall, the FIB concentrations were higher in urban LULC (EC=3.33-7.39; FS=3.30-7.36log10MPN/100mL) possibly because of runoff from commercial market and 100% impervious cover (IC). Also, during early-summer season; this reflects a greater persistence and growth rate of FIB in a warmer environment. During intra-event, however, the FIB concentrations varied according to site condition. Anthropogenic activities and IC influenced the correlation between the FIB concentrations and environmental parameters. Stormwater temperature (TEMP), turbidity, and TSS positively correlated with the FIB concentrations (p>0.01), since IC increased, implying an accumulation of bacterial sources in urban activities. TEMP, BOD5, turbidity, TSS, and antecedent dry days (ADD) were the most significant explanatory variables for FIB as determined in MLR, possibly because they promoted the FIB growth and survival. The model confirmed the FIB concentrations: EC (R(2)=0.71-0.85; NSE=0.72-0.86) and FS (R(2)=0.65-0.83; NSE=0.66-0.84) are predicted to increase due to urbanization. Therefore, these findings will help in stormwater monitoring strategies, designing the best management practice for FIB removal and as input data for stormwater models. Copyright © 2016 Elsevier B.V. All rights reserved.

A new challenge: in-situ investigation of the elusive nanostructures in wet halite and clay using BIB/FIB-cryo-SEM methods

NASA Astrophysics Data System (ADS)

Desbois, G.; Urai, J. L.

2009-04-01

Mudrocks and saltrocks form seals for hydrocarbon accumulations, aquitards and chemical barriers. The sealing capacity is controlled either by the rock microstructure or by chemical interactions between minerals and the permeating fluid. A detailed knowledge about the sealing characteristics is of particular interest in Petroleum Sciences. Other fields of interest are the storage of anthropogenic carbon dioxide and radioactive waste in geologic formations. A key factor to the understanding of sealing by mudstones and saltrocks is the study of their porosity. However, Halite and clay are so fluids sensitive that investigation on dried samples required by traditional methods of investigations (metal injection methods [6],[3]; magnetic susceptibility measurement [4]; SEM imaging of broken surfaces [5] and CT scanner computing [7]) are critical for robust interpretation. In one hand, none of these methods is able to directly describe the in-situ porosity at the pore scale and on the other hand, most of these methods require dried samples in which the natural structure of pores could be damaged due to the desiccation, dehydration and dissolution-recrystallisation of the fabric. SEM imaging is certainly the most direct approach to investigate the porosity but it is generally limited by the poor quality of the mechanically prepared surfaces. This problem is solved by the recent development of ion milling tools (FIB: Focussed Ion Beam or BIB: Broad Ion Beam, which allows producing in-situ high quality polished cross-sections suitable for high resolution pores SEM imaging at nano-scale. More over, new and innovative developments of the cryo-SEM approach in the Geosciences allow investigating samples under wet natural conditions. Thus, we are developing the combination of FIB/BIB-cryo-SEM methods ([1],[2]), which combine in one machine the vitrification of the pore fluids by very rapid cooling, the excavation of the sample by ion milling tool and SEM imaging. By these, we are able to stabilize the in-situ fluids in grain boundaries or pores, preserve the natural structures at nano scale, produce high quality polished cross-sections for high resolution SEM imaging and reconstruct accurately the grain boundary and the pore space networks in 3D by serial cross sectioning. Our first investigations on wet halite and wet clay materials produced unprecedented high quality images of fully preserved fluid-filled pore space as appear in nature. We have thus validated the use of the FIB/BIB-cryo-SEM technology for the in-situ investigations of the elusive structures in wet geomaterials paving the way towards a fuller understanding of how pore geometry can affect physical properties of rocks. [1] Desbois G. And Urai J.L. (submitted). In-situ morphology of meso-porosity in Boom clay (Mol site, Belgium) inferred by the innovative FIB-cryo-SEM method. E-earth. [2] Desbois G., Urai J.L., Burkhardt C., Drury M., Hayles M. and Humbel B. (2008). Cryogenic vitrification and 3D serial sectioning using high resolution cryo-FIB-SEM technology for brine-filled grain boundaries in halite: first results. Geofluids, 8: 60-72 [3] Esteban L., Géraud Y. And Bouchez J.L. (2006). Pore network geometry in low permeability argillites from magnetic fabric data and oriented mercury injections. Geophysical Research Letters, vol. 33, L18311, doi : 10.1029/2006GL026908. [4] Esteban L., Géraud Y. And Bouchez J.L. (2007). Pore network connectivity anisotropy in Jurassic argillite specimens from eastern Paris Basin (France). Physics and Chemistry of the Earth, 32(1) :161-169. [5] Hildenbrand A., Krooss B. M. and Urai J. L. (2005). Relationship between pore structure and fluid transport in argillaceous rocks. Solid Mechanics and Its Applications, IUTAM Symposium on Physicochemical and Electromechanical Interactions in Porous Media, 125 : 231-237, doi : 10.1007/1-4020-3865-8_26. [6] Hildenbrand A. and Urai J.L. (2003) Investigation of the morphology of pore space in mudstones—first results. Marine and Petroleum Geology, 20(10):1185-1200. [7] H. Taud H., Martinez-Angeles R., Parrot J.F., Hernandez-Escobedo L. (2005). Porosity estimation method by X-ray computed tomography. Journal of Petroleum Science and Engineering, (47), 3-4, 30: 209-217

Evaluation of potential sources and transport mechanisms of fecal indicator bacteria to beach water, Murphy Park Beach, Door County, Wisconsin

USGS Publications Warehouse

Juckem, Paul F.; Corsi, Steven R.; McDermott, Colleen; Kleinheinz, Gregory; Fogarty, Lisa R.; Haack, Sheridan K.; Johnson, Heather E.

2013-01-01

Fecal Indicator Bacteria (FIB) concentrations in beach water have been used for many years as a criterion for closing beaches due to potential health concerns. Yet, current understanding of sources and transport mechanisms that drive FIB occurrence remains insufficient for accurate prediction of closures at many beaches. Murphy Park Beach, a relatively pristine beach on Green Bay in Door County, Wis., was selected for a study to evaluate FIB sources and transport mechanisms. Although the relatively pristine nature of the beach yielded no detection of pathogenic bacterial genes and relatively low FIB concentrations during the study period compared with other Great Lakes Beaches, its selection limited the number of confounding FIB sources and associated transport mechanisms. The primary sources of FIB appear to be internal to the beach rather than external sources such as rivers, storm sewer outfalls, and industrial discharges. Three potential FIB sources were identified: sand, swash-zone groundwater, and Cladophora mats. Modest correlations between FIB concentrations in these potential source reservoirs and FIB concentrations at the beach from the same day illustrate the importance of understanding transport mechanisms between FIB sources and the water column. One likely mechanism for transport and dispersion of FIB from sand and Cladophora sources appears to be agitation of Cladophora mats and erosion of beach sand due to storm activity, as inferred from storm indicators including turbidity, wave height, current speed, wind speed, sky visibility, 24-hour precipitation, and suspended particulate concentration. FIB concentrations in beach water had a statistically significant relation (p-value ‹0.05) with the magnitude of these storm indicators. In addition, transport of FIB in swash-zone groundwater into beach water appears to be driven by groundwater recharge associated with multiday precipitation and corresponding increased swash-zone groundwater discharge at the beach, as indicated by an increase in the specific conductance of beach water. Understanding the dynamics of FIB sources (sand, swash-zone groundwater, and Cladophora) and transport mechanisms (dispersion and erosion from storm energy, and swash-zone groundwater discharge) is important for improving predictions of potential health risks from FIB in beach water.

How item banks and their application can influence measurement practice in rehabilitation medicine: a PROMIS fatigue item bank example.

PubMed

Lai, Jin-Shei; Cella, David; Choi, Seung; Junghaenel, Doerte U; Christodoulou, Christopher; Gershon, Richard; Stone, Arthur

2011-10-01

To illustrate how measurement practices can be advanced by using as an example the fatigue item bank (FIB) and its applications (short forms and computerized adaptive testing [CAT]) that were developed through the National Institutes of Health Patient Reported Outcomes Measurement Information System (PROMIS) Cooperative Group. Psychometric analysis of data collected by an Internet survey company using item response theory-related techniques. A U.S. general population representative sample collected through the Internet. Respondents used for dimensionality evaluation of the PROMIS FIB (N=603) and item calibrations (N=14,931). Not applicable. Fatigue items (112) developed by the PROMIS fatigue domain working group, 13-item Functional Assessment of Chronic Illness Therapy-Fatigue, and 4-item Medical Outcomes Study 36-Item Short Form Health Survey Vitality scale. The PROMIS FIB version 1, which consists of 95 items, showed acceptable psychometric properties. CAT showed consistently better precision than short forms. However, all 3 short forms showed good precision for most participants in that more than 95% of the sample could be measured precisely with reliability greater than 0.9. Measurement practice can be advanced by using a psychometrically sound measurement tool and its applications. This example shows that CAT and short forms derived from the PROMIS FIB can reliably estimate fatigue reported by the U.S. general population. Evaluation in clinical populations is warranted before the item bank can be used for clinical trials. Copyright © 2011 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Efficacy of monitoring and empirical predictive modeling at improving public health protection at Chicago beaches

USGS Publications Warehouse

Nevers, Meredith B.; Whitman, Richard L.

2011-01-01

Efforts to improve public health protection in recreational swimming waters have focused on obtaining real-time estimates of water quality. Current monitoring techniques rely on the time-intensive culturing of fecal indicator bacteria (FIB) from water samples, but rapidly changing FIB concentrations result in management errors that lead to the public being exposed to high FIB concentrations (type II error) or beaches being closed despite acceptable water quality (type I error). Empirical predictive models may provide a rapid solution, but their effectiveness at improving health protection has not been adequately assessed. We sought to determine if emerging monitoring approaches could effectively reduce risk of illness exposure by minimizing management errors. We examined four monitoring approaches (inactive, current protocol, a single predictive model for all beaches, and individual models for each beach) with increasing refinement at 14 Chicago beaches using historical monitoring and hydrometeorological data and compared management outcomes using different standards for decision-making. Predictability (R2) of FIB concentration improved with model refinement at all beaches but one. Predictive models did not always reduce the number of management errors and therefore the overall illness burden. Use of a Chicago-specific single-sample standard-rather than the default 235 E. coli CFU/100 ml widely used-together with predictive modeling resulted in the greatest number of open beach days without any increase in public health risk. These results emphasize that emerging monitoring approaches such as empirical models are not equally applicable at all beaches, and combining monitoring approaches may expand beach access.

Morphology of the pore space in claystones - evidence from BIB/FIB ion beam sectioning and cryo-SEM observations

NASA Astrophysics Data System (ADS)

Desbois, G.; Urai, J. L.; Kukla, P. A.

2009-12-01

Mudrocks and clay-rich fault gouges are important mechanical elements in the Earth’s crust and form seals for crustal fluids such as groundwater and hydrocarbons. Other fields of interest are the storage of anthropogenic carbon dioxide and radioactive waste in geologic formations. In addition, coupled flows, capillary processes, and associated deformation are of importance in many applied fields. A key factor to understanding these processes is a detailed understanding of the morphology of the pore space. Classic studies of porosity in fine grained materials are performed on dried or freeze dried samples and include metal injection methods, magnetic susceptibility measurement, SEM and TEM imaging, neutron scattering, NMR spectroscopy, and ESEM. Confocal microscopy and X-ray tomography are used to image porosity in coarse grained sediments but the resolution of these techniques is not sufficient at present for applications to mudrocks or clay-rich fault gouges. Therefore, observations and interpretations remain difficult because none of these approaches is able to directly describe the in-situ porosity at the pore scale. In addition, some methods require dried samples in which the natural structure of pores may have been damaged to some extent due to desiccation and dehydration of the clay minerals. A recently developed alternative is to study wet samples using a cryo-SEM, which allows stabilization of wet media at cryo-temperature, in-situ sample preparation by ion beam cross-sectioning (BIB, FIB) and observations of the stabilized microstructure at high resolution. We report on a study of Boom clay from a proposed disposal site of radioactive waste (Mol site, Belgium) using cryo-SEM at cryogenic temperature, with ion beam cross-sectioning to prepare smooth, damage free surfaces. Pores commonly have crack-like tips, preferred orientation parallel to bedding and power law size distribution. We define a number of pore types depending on shape and location in the microstructure. 3-D reconstruction by serial cross-sectioning shows 3-D connectivity of the pore space. These findings offer a new insight into the morphology of pores down to nano-scale and provide the basis for microstructure-based models of transport in clays. SEM image (SE) of a Broad Ion Beam polished cross-section performed on dry Boom clay (Mol site, Belgium) showing the 2D apparent porosity (26.3%). The cross-section is perpendicular to the bedding.

Microstructural Study of Micron-Sized Craters Simulating Stardust Impacts in Aluminum 1100 Targets

NASA Technical Reports Server (NTRS)

Leroux, Hugues; Borg, Janet; Troadec, David; Djouadi, Zahia; Horz, Friedrich

2006-01-01

Various microscopic techniques were used to characterize experimental micro- craters in aluminium foils to prepare for the comprehensive analysis of the cometary and interstellar particle impacts in aluminium foils to be returned by the Stardust mission. First, SEM (Scanning Electron Microscopy) and EDS (Energy Dispersive X-ray Spectroscopy) were used to study the morphology of the impact craters and the bulk composition of the residues left by soda-lime glass impactors. A more detailed structural and compositional study of impactor remnants was then performed using TEM (Transmission Electron Microscopy), EDS, and electron diffraction methods. The TEM samples were prepared by Focused Ion Beam (FIB) methods. This technique proved to be especially valuable in studying impact crater residues and impact crater morphology. Finally, we also showed that InfraRed microscopy (IR) can be a quick and reliable tool for such investigations. The combination of all of these tools enables a complete microscopic characterization of the craters.

Multi Length Scale Imaging of Flocculated Estuarine Sediments; Insights into their Complex 3D Structure

NASA Astrophysics Data System (ADS)

Wheatland, Jonathan; Bushby, Andy; Droppo, Ian; Carr, Simon; Spencer, Kate

2015-04-01

Suspended estuarine sediments form flocs that are compositionally complex, fragile and irregularly shaped. The fate and transport of suspended particulate matter (SPM) is determined by the size, shape, density, porosity and stability of these flocs and prediction of SPM transport requires accurate measurements of these three-dimensional (3D) physical properties. However, the multi-scaled nature of flocs in addition to their fragility makes their characterisation in 3D problematic. Correlative microscopy is a strategy involving the spatial registration of information collected at different scales using several imaging modalities. Previously, conventional optical microscopy (COM) and transmission electron microscopy (TEM) have enabled 2-dimensional (2D) floc characterisation at the gross (> 1 µm) and sub-micron scales respectively. Whilst this has proven insightful there remains a critical spatial and dimensional gap preventing the accurate measurement of geometric properties and an understanding of how structures at different scales are related. Within life sciences volumetric imaging techniques such as 3D micro-computed tomography (3D µCT) and focused ion beam scanning electron microscopy [FIB-SEM (or FIB-tomography)] have been combined to characterise materials at the centimetre to micron scale. Combining these techniques with TEM enables an advanced correlative study, allowing material properties across multiple spatial and dimensional scales to be visualised. The aims of this study are; 1) to formulate an advanced correlative imaging strategy combining 3D µCT, FIB-tomography and TEM; 2) to acquire 3D datasets; 3) to produce a model allowing their co-visualisation; 4) to interpret 3D floc structure. To reduce the chance of structural alterations during analysis samples were first 'fixed' in 2.5% glutaraldehyde/2% formaldehyde before being embedding in Durcupan resin. Intermediate steps were implemented to improve contrast and remove pore water, achieved by the addition of heavy metal stains and washing samples in a series of ethanol solutions and acetone. Gross-scale characterisation involved scanning samples using a Nikon Metrology HM X 225 µCT. For micro-scale analysis a working surface was revealed by microtoming the sample. Ultrathin sections were then collected and analysed using a JEOL 1200 Ex II TEM, and FIB-tomography datasets obtained using an FEI Quanta 3D FIB-SEM. Finally, to locate the surface and relate TEM and FIB-tomography datasets to the original floc, samples were rescanned using the µCT. Image processing was initially conducted in ImageJ. Following this datasets were imported into Amira 5.5 where pixel intensity thresholding allowed particle-matrix boundaries to be defined. Using 'landmarks' datasets were then registered to enable their co-visualisation in 3D models. Analysis of registered datasets reveals the complex non-fractal nature of flocs, whose properties span several of orders of magnitude. Primary particles are organised into discrete 'bundles', the arrangement of which directly influences their gross morphology. This strategy, which allows the co-visualisation of spatially registered multi-scale 3D datasets, provides unique insights into the true nature floc which would other have been impossible.

NanoSIMS Imaging Alternation Layers of a Leached SON68 Glass Via A FIB-made Wedged Crater

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

Wang, Yi-Chung; Schreiber, Daniel K.; Neeway, James J.

2014-11-01

Currently, nuclear wastes are commonly immobilized into glasses because of their long-term durability. Exposure to water for long periods of time, however, will eventually corrode the waste form and is the leading potential avenue for radionuclide release into the environment. Because such slow processes cannot be experimentally tested, the prediction of release requires a thorough understanding the mechanisms governing glass corrosion. In addition, due to the exceptional durability of glass, much of the testing must be performed on high-surface-area powders. A technique that can provide accurate compositional profiles with very precise depth resolution for non-flat samples would be a majormore » benefit to the field. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling is an excellent tool that has long been used to examine corrosion layers of glass. The roughness of the buried corrosion layers, however, causes the corresponding SIMS depth profiles to exhibit erroneously wide interfaces. In this study, NanoSIMS was used to image the cross-section of the corrosion layers of a leached SON68 glass sample. A wedged crater was prepared by a focused ion beam (FIB) instrument to obtain a 5× improvement in depth resolution for NanoSIMS measurements. This increase in resolution allowed us to confirm that the breakdown of the silica glass network is further from the pristine glass than a second dissolution front for boron, another glass former. The existence of these two distinct interfaces, separated by only ~20 nm distance in depth, was not apparent by traditional ToF-SIMS depth profiling but has been confirmed also by atom probe tomography. This novel sample geometry will be a major benefit to efficient NanoSIMS sampling of irregular interfaces at the nanometer scale that would otherwise be obscured within ToF-SIMS depth profiles.« less

Transient Elastography is Superior to FIB-4 in Assessing the Risk of Hepatocellular Carcinoma in Patients With Chronic Hepatitis B

PubMed Central

Kim, Seung Up; Kim, Beom Kyung; Park, Jun Yong; Kim, Do Young; Ahn, Sang Hoon; Song, Kijun; Han, Kwang-Hyub

2016-01-01

Abstract Liver stiffness (LS), assessed using transient elastography (TE), and (FIB-4) can both estimate the risk of developing hepatocellular carcinoma (HCC). We compared prognostic performances of LS and FIB-4 to predict HCC development in patients with chronic hepatitis B (CHB). Data from 1308 patients with CHB, who underwent TE, were retrospectively analyzed. FIB-4 was calculated for all patients. The cumulative rate of HCC development was assessed using Kaplan–Meier curves. The predictive performances of LS and FIB-4 were evaluated using time-dependent receiver-operating characteristic (ROC) curves. The mean age (883 men) was 50 years. During follow-up (median 6.1 years), 119 patients developed HCC. The areas under the ROC curves (AUROCs) predicting HCC risk at 3, 5, and 7 years were consistently greater for LS than for FIB-4 (0.791–0.807 vs 0.691–0.725; all P < 0.05). Similarly, when the respective AUROCs for LS and FIB-4 at every time point during the 7-year follow-up were plotted, LS also showed consistently better performance than FIB-4 after 1 year of enrollment. The combined use of LS and FIB-4 significantly enhanced the prognostic performance compared with the use of FIB-4 alone (P < 0.05), but the performance of the combined scores was statistically similar to that of LS alone (P > 0.05). LS showed significantly better performance than FIB-4 in assessing the risk of HCC development, and the combined use of LS and FIB-4 did not provide additional benefit compared with the use of LS alone. Hence, LS assessed using TE might be helpful for optimizing HCC surveillance strategies. PMID:27196449

Transient Elastography is Superior to FIB-4 in Assessing the Risk of Hepatocellular Carcinoma in Patients With Chronic Hepatitis B.

PubMed

Kim, Seung Up; Kim, Beom Kyung; Park, Jun Yong; Kim, Do Young; Ahn, Sang Hoon; Song, Kijun; Han, Kwang-Hyub

2016-05-01

Liver stiffness (LS), assessed using transient elastography (TE), and (FIB-4) can both estimate the risk of developing hepatocellular carcinoma (HCC). We compared prognostic performances of LS and FIB-4 to predict HCC development in patients with chronic hepatitis B (CHB).Data from 1308 patients with CHB, who underwent TE, were retrospectively analyzed. FIB-4 was calculated for all patients. The cumulative rate of HCC development was assessed using Kaplan-Meier curves. The predictive performances of LS and FIB-4 were evaluated using time-dependent receiver-operating characteristic (ROC) curves.The mean age (883 men) was 50 years. During follow-up (median 6.1 years), 119 patients developed HCC. The areas under the ROC curves (AUROCs) predicting HCC risk at 3, 5, and 7 years were consistently greater for LS than for FIB-4 (0.791-0.807 vs 0.691-0.725; all P < 0.05). Similarly, when the respective AUROCs for LS and FIB-4 at every time point during the 7-year follow-up were plotted, LS also showed consistently better performance than FIB-4 after 1 year of enrollment. The combined use of LS and FIB-4 significantly enhanced the prognostic performance compared with the use of FIB-4 alone (P < 0.05), but the performance of the combined scores was statistically similar to that of LS alone (P > 0.05).LS showed significantly better performance than FIB-4 in assessing the risk of HCC development, and the combined use of LS and FIB-4 did not provide additional benefit compared with the use of LS alone. Hence, LS assessed using TE might be helpful for optimizing HCC surveillance strategies.

Reduction of fecal indicator bacteria (FIB) in the Ballona Wetlands saltwater marsh (Los Angeles County, California, USA) with implications for restoration actions.

PubMed

Dorsey, John H; Carter, Patrick M; Bergquist, Sean; Sagarin, Rafe

2010-08-01

A benefit of wetland preservation and restoration is the ecosystem service of improving water quality, typically assessed based on bacterial loading. The Ballona Wetlands, a degraded salt marsh of approximately 100 ac located on the southern border of Marina Del Rey (Los Angeles County, California, USA) are currently the focus of publicly funded restoration planning. The wetlands receive tidal water, usually contaminated with fecal indicator bacteria (FIB: total and fecal coliforms, Escherichia coli, enterococci) from the adjacent Ballona Creek and Estuary. During the summer of 2007, two 24-h studies were conducted to determine FIB tidal dynamics within the wetland. Measurements of water flow and mean FIB concentrations (n = 3) were measured every 1.5 h to determine total FIB load estimates. FIB loading rates (MPN/s) were greatest during flood tides as water entered the wetlands, and then again during spring tide conditions when sediments were resuspended during swifter spring ebb flows. During daylight hours, the wetland acted as a sink for these bacteria as loads diminished, presumably by sunlight and other processes. Conversely, during late afternoon and night, the wetlands shifted to being a source as excess FIB departed on ebb flows. Therefore, the wetlands act as both a source and sink for FIB depending on tidal conditions and exposure to sunlight. Future restoration actions would result in a tradeoff - increased tidal channels offer a greater surface area for FIB inactivation, but also would result in a greater volume of FIB-contaminated resuspended sediments carried out of the wetlands on stronger ebb flows. As levels of FIB in Ballona Creek and Estuary diminish through recently established regulatory actions, the wetlands could shift into a greater sink for FIB. (c) 2010 Elsevier Ltd. All rights reserved.

Molecular dynamics and dynamic Monte-Carlo simulation of irradiation damage with focused ion beams

NASA Astrophysics Data System (ADS)

Ohya, Kaoru

2017-03-01

The focused ion beam (FIB) has become an important tool for micro- and nanostructuring of samples such as milling, deposition and imaging. However, this leads to damage of the surface on the nanometer scale from implanted projectile ions and recoiled material atoms. It is therefore important to investigate each kind of damage quantitatively. We present a dynamic Monte-Carlo (MC) simulation code to simulate the morphological and compositional changes of a multilayered sample under ion irradiation and a molecular dynamics (MD) simulation code to simulate dose-dependent changes in the backscattering-ion (BSI)/secondary-electron (SE) yields of a crystalline sample. Recent progress in the codes for research to simulate the surface morphology and Mo/Si layers intermixing in an EUV lithography mask irradiated with FIBs, and the crystalline orientation effect on BSI and SE yields relating to the channeling contrast in scanning ion microscopes, is also presented.

In vitro effects of 6 % hydroxyethyl starch 130/0.42 solution on feline whole blood coagulation measured by rotational thromboelastometry.

PubMed

Albrecht, Nathalie A; Howard, Judith; Kovacevic, Alan; Adamik, Katja N

2016-07-26

The artificial colloid, hydroxyethyl starch (HES), is recommended for intravascular volume expansion and colloid-osmotic pressure enhancement in dogs and cats. A well-known side effect of HES solutions in humans and dogs is coagulopathy. However, HES-associated coagulopathy has thus far not been investigated in cats. The goal of this study was to assess the in vitro effects of 6 % HES 130/0.42 on feline whole blood samples using rotational thromboelastometry (ROTEM). A further goal was to develop feline reference intervals for ROTEM at our institution. In this in vitro experimental study, blood samples of 24 adult healthy cats were collected by atraumatic jugular phlebotomy following intramuscular sedation. Baseline ROTEM analyses (using ex-tem, in-tem and fib-tem assays) were performed in duplicate. Additionally, ROTEM analyses were performed on blood samples after dilution with either Ringer's acetate (RA) or 6 % HES 130/0.42 (HES) in a 1:6 dilution (i.e. 1 part solution and 6 parts blood). Coefficients of variation of duplicate measures were below 12 % in all ex-tem assays, 3 of 4 in-tem assays but only 1 of 3 fib-tem assays. Reference intervals were similar albeit somewhat narrower than those previously published. Dilution with both solutions lead to significantly prolonged CT (in-tem), CFT (ex-tem and in-tem), and reduced MCF (ex-tem, in-tem, and fib-tem) and alpha (ex-tem and in-tem). Compared to RA, dilution with HES caused a significant prolongation of CT in fib-tem (P = 0.016), CFT in ex-tem (P = 0.017) and in-tem (P = 0.019), as well as a reduction in MCF in in-tem (P = 0.032) and fib-tem (P = 0.020), and alpha in ex-tem (P = 0.014). However, only a single parameter (CFT in ex-tem) was outside of the established reference interval after dilution with HES. In vitro hemodilution of feline blood with RA and HES causes a small but significant impairment of whole blood coagulation, with HES leading to a significantly greater effect on coagulation than RA. Further studies are necessary to evaluate the in vivo effects and the clinical significance of these findings.

Characterizing relationships among fecal indicator bacteria ...

EPA Pesticide Factsheets

Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial source tracking (MST) markers, developed to determine potential sources of fecal contamination, can also be resuspended from bed sediments. The primary objective of this study was to predict occurrence of waterborne pathogens in water and streambed sediments using a simple statistical model that includes traditionally measured FIB, environmental parameters and source allocation, using MST markers as predictor variables. Synoptic sampling events were conducted during baseflow conditions downstream from agricultural (AG), forested (FORS), and wastewater pollution control plant (WPCP) land uses. Concentrations of FIB and MST markers were measured in water and sediments, along with occurrences of the enteric pathogens Campylobacter, Listeria and Salmonella, and the virulence gene that carries Shiga toxin, stx2. Pathogens were detected in water more often than in underlying sediments. Shiga toxin was significantly related to land use, with concentrations of the ruminant marker selected as an independent variable that could correctly classify 76% and 64% of observed Shiga toxin occurrences in water and sediment, respectively. FIB concentrations and water quality parameters were also selected a

Metavir and FIB-4 scores are associated with patient prognosis after curative hepatectomy in hepatitis B virus-related hepatocellular carcinoma: a retrospective cohort study at two centers in China.

PubMed

Liao, Rui; Fu, Yi-Peng; Wang, Ting; Deng, Zhi-Gang; Li, De-Wei; Fan, Jia; Zhou, Jian; Feng, Gen-Sheng; Qiu, Shuang-Jian; Du, Cheng-You

2017-01-03

Although Metavir and Fibrosis-4 (FIB-4) scores are typically used to assess the severity of liver fibrosis, the relationship between these scores and patient outcome in hepatocellular carcinoma (HCC) is unclear. The aim of this study was to evaluate the prognostic value of the severity of hepatic fibrosis in HBV-related HCC patients after curative resection. We examined the prognostic roles of the Metavir and preoperative FIB-4 scores in 432 HBV-HCC patients who underwent curative resection at two different medical centers located in western (Chongqing) and eastern (Shanghai) China. In the testing set (n = 108), the Metavir, FIB-4, and combined Metavir/FIB-4 scores were predictive of overall survival (OS) and recurrence-free survival (RFS). Additionally, they were associated with several clinicopathologic variables. In the validation set (n = 324), the Metavir, FIB-4, and combined Metavir/FIB-4 scores were associated with poor prognosis in HCC patients after curative resection. Importantly, in the negative alpha-fetoprotein subgroup (≤ 20 ng/mL), the FIB-4 index (I vs. II) could discriminate between patient outcomes (high or low OS and RFS). Thus Metavir, preoperative FIB-4, and combined Metavir/FIB-4 scores are prognostic markers in HBV-HCC patients after curative hepatectomy.

Metavir and FIB-4 scores are associated with patient prognosis after curative hepatectomy in hepatitis B virus-related hepatocellular carcinoma: a retrospective cohort study at two centers in China

PubMed Central

Li, De-Wei; Fan, Jia; Zhou, Jian; Feng, Gen-Sheng; Qiu, Shuang-Jian; Du, Cheng-You

2017-01-01

Although Metavir and Fibrosis-4 (FIB-4) scores are typically used to assess the severity of liver fibrosis, the relationship between these scores and patient outcome in hepatocellular carcinoma (HCC) is unclear. The aim of this study was to evaluate the prognostic value of the severity of hepatic fibrosis in HBV-related HCC patients after curative resection. We examined the prognostic roles of the Metavir and preoperative FIB-4 scores in 432 HBV-HCC patients who underwent curative resection at two different medical centers located in western (Chongqing) and eastern (Shanghai) China. In the testing set (n = 108), the Metavir, FIB-4, and combined Metavir/FIB-4 scores were predictive of overall survival (OS) and recurrence-free survival (RFS). Additionally, they were associated with several clinicopathologic variables. In the validation set (n = 324), the Metavir, FIB-4, and combined Metavir/FIB-4 scores were associated with poor prognosis in HCC patients after curative resection. Importantly, in the negative alpha-fetoprotein subgroup (≤ 20 ng/mL), the FIB-4 index (I vs. II) could discriminate between patient outcomes (high or low OS and RFS). Thus Metavir, preoperative FIB-4, and combined Metavir/FIB-4 scores are prognostic markers in HBV-HCC patients after curative hepatectomy. PMID:27662665

Observation of three-dimensional elemental distributions of a Si device using a 360 degrees -tilt FIB and the cold field-emission STEM system.

PubMed

Yaguchi, Toshie; Konno, Mitsuru; Kamino, Takeo; Watanabe, Masashi

2008-11-01

A technique for preparation of a pillar-shaped specimen and its multidirectional observation using a combination of a scanning transmission electron microscope (STEM) and a focused ion beam (FIB) instrument has been developed. The system employs an FIB/STEM compatible holder with a specially designed tilt mechanism, which allows the specimen to be tilted through 360 degrees [T. Yaguchi, M. Konno, T. Kamino, T. Hashimoto, T. Ohnishi, K. Umemura, K. Asayama, Microsc. Microanal. 9 (Suppl. 2) (2003) 118; T. Yaguchi, M. Konno, T. Kamino, T. Hashimoto, T. Ohnishi, M. Watanabe, Microsc. Microanal. 10 (Suppl. 2) (2004) 1030]. This technique was applied to obtain the three-dimensional (3D) elemental distributions around a contact plug of a Si device used in a 90-nm technology. A specimen containing only one contact plug was prepared in the shape of a pillar with a diameter of 200nm and a length of 5mum. Elemental maps were obtained from the pillar specimen using a 200-kV cold-field emission gun (FEG) STEM model HD-2300C equipped with the EDAX genesis X-ray energy-dispersive spectrometry (XEDS) system through a spectrum imaging technique. In this study, elemental distributions of minor elements with weak signals were enhanced by applying principal component analysis (PCA), which is a superior technique to extract weak signals from a large dataset. The distributions of elements, especially the metallization component Ti and minor dopant As in this particular device, were successfully extracted by PCA. Finally, the 3D elemental distributions around the contact plug could be visualized by reconstruction from the tilt series of maps.

Forest statistics for plateau Tennessee counties

Treesearch

Renewable Resources Evaluation Research Work Unit

1982-01-01

These tables were derived from data obtained during a 1980 inventory of 16 counties comprising the Plateau Unit of Tennessee (fib. 1). The data on forest acreage and timber volume were secured by a systematic sampling method involving a forest-nonforest classification on aerial photographs and on-the-ground measurements of trees at sample locations. The sample...

Dynamics of fecal indicator bacteria, bacterial pathogen genes, and organic wastewater contaminants in the Little Calumet River: Portage Burns Waterway, Indiana

USGS Publications Warehouse

Haack, Sheridan K.; Duris, Joseph W.

2013-01-01

Little information exists on the co-occurrence of fecal indicator bacteria (FIB), bacterial pathogens, and organic wastewater-associated chemicals (OWCs) within Great Lakes tributaries. Fifteen watershed sites and one beach site adjacent to the Little Calumet River–Portage Burns Waterway (LCRPBW) on Lake Michigan were tested on four dates for pH, dissolved oxygen, specific conductance, chloride, color, ammonia- and nitrate-nitrogen, soluble phosphorus, sulfate, turbidity, and atrazine; for concentrations of FIB; and for genes indicating the presence of human-pathogenic enterococci (ENT) and of Shiga-toxin producing Escherichia coli (EC) from various animal sources. Nineteen samples were also tested for 60 OWCs. Half of the watershed samples met EC recreational water quality standards; none met ENT standards. Human-wastewater-associated OWC detections were correlated with human-influence indicators such as population/km2, chloride concentrations, and the presence of WWTP effluents, but EC and ENT concentrations were not. Bacterial pathogen genes indicated rural human and several potential animal sources. OWCs of human or ecosystem health concern (musk fragrances AHTN and HHCB, alkylphenols, carbamazepine) and 3 bacterial pathogen genes were detected at the mouth of the LCRPBW, but no such OWCs and only 1 pathogen gene were detected at the beach. The LCRPBW has significant potential to deliver FIB, potential bacterial pathogens, and OWCs of human or ecosystem health concern to the nearshore of Lake Michigan, under conditions enhancing nearshore transport of the river plume. Nearshore mixing of lake and river water, and the lack of relationship between OWCs and FIB or pathogen genes, pose numerous challenges for watershed and nearshore assessment and remediation.

A laboratory marker, FIB-4 index, as a predictor for long-term outcomes of hepatocellular carcinoma patients after curative hepatic resection.

PubMed

Toyoda, Hidenori; Kumada, Takashi; Tada, Toshifumi; Kaneoka, Yuji; Maeda, Atsuyuki

2015-04-01

Liver fibrosis is associated with the prognosis of patients with hepatocellular carcinoma (HCC) after treatment. The laboratory marker for liver fibrosis, the FIB-4 index, is reportedly correlated with the degree of liver fibrosis. We evaluated the predictive value of FIB-4 index on the recurrence and survival of HCC patients who underwent curative hepatectomy. A total of 431 consecutive patients who underwent hepatectomy for primary, nonrecurrent HCC were analyzed. The FIB-4 index was calculated from the patient's age, serum alanine aminotransferase and aspartate aminotransferase levels, and platelet count at the time of HCC diagnosis. Postoperative recurrence and survival rates were compared according to tumor characteristics, tumor markers, Child-Pugh class, and the FIB-4 index. The pretreatment FIB-4 index was associated with recurrence and survival rates, independent of HCC progression or tumor marker levels in a multivariate analysis. Recurrence rates after hepatectomy were higher in patients with a FIB-4 index >3.25 versus ≤3.25 (5-year recurrence rates 69.6% vs 54.8%; P = .0049). Survival was also worse in patients with a FIB-4 index >3.25 than those with a FIB-4 index ≤3.25 (5-year survival rates 67.1% vs 72.2%; P = .0030). The FIB-4 index is a predictive marker for long-term outcomes in patients with HCC treated with curative hepatic resection. Copyright © 2015 Elsevier Inc. All rights reserved.

Disruption of adherens junction and alterations in YAP-related proliferation behavior as part of the underlying cell transformation process of alcohol-induced oral carcinogenesis.

PubMed

Husari, Ayman; Hülter-Hassler, Diana; Steinberg, Thorsten; Schulz, Simon Daniel; Tomakidi, Pascal

2018-01-01

Accumulating evidences indicate that alcohol might play a causative in oral cancer. Unfortunately, in vitro cell systems, uncovering the molecular background of the underlying cell transformation process, are rare. Therefore, this study was conducted, to identify molecular changes and characterize their putative cell behavioral consequences in epitheloid (EPI) and fibroblastoid (FIB) oral keratinocyte phenotypes, arising from chronical alcohol treatment. Concerning adherens junctions (AJs), both EPI and FIB showed membrane-bound β-catenin, but exhibited differences for E-cadherin and zyxin. While EPI revealed E-cadherin/β-catenin membrane co-localization, which in parts also applied for zyxin, FIB membranes were devoid of E-cadherin and exhibited marginal zyxin expression. Fetal calf serum (FCS) administration in starved cells promoted proliferation in both keratinocyte phenotypes, whereat EPI and FIB yielded a strikingly modified FCS sensitivity on the temporal scale. Impedance measurement-based cell index detection yielded proliferation stimulation occurring much earlier in FIB (<20h) compared to EPI (>45h). Nuclear preference of the proliferation-associated YAP co-transcription factor in FIB was FCS independent, while it required FCS in EPI. Taken together, the lack of membrane-inherent E-cadherin/β-catenin co-localization together with low zyxin - reveals perturbation of AJ integrity in FIB. Regarding cell behavior, perturbed AJs in FIB correlate with temporal proliferation sensitivity towards FCS. CYF of 5.6 strongly suggests involvement of chromatin-bound YAP in FIB's proliferation temperosensitivity. These molecular differences detected for EPI and FIB are part of the underlying cell transformation process of alcohol-induced oral carcinogenesis, and indicate FIB being in a more advanced transformation stage. Copyright © 2017 Elsevier B.V. All rights reserved.

HIV mono-infection is associated with FIB-4 - A noninvasive index of liver fibrosis - in women.

PubMed

Blackard, Jason T; Welge, Jeffrey A; Taylor, Lynn E; Mayer, Kenneth H; Klein, Robert S; Celentano, David D; Jamieson, Denise J; Gardner, Lytt; Sherman, Kenneth E

2011-03-01

FIB-4 represents a noninvasive, composite index that is a validated measure of hepatic fibrosis, which is an important indicator of liver disease. To date, there are limited data regarding hepatic fibrosis in women. FIB-4 was evaluated in a cohort of 1227 women, and associations were evaluated in univariate and multivariate regression models among 4 groups of subjects classified by their human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infection status. The median FIB-4 scores were 0.60 in HIV-/HCV- women, 0.83 in HIV-/HCV+ women, 0.86 in HIV+/HCV- women, and 1.30 in HIV+/HCV+ women. In the HIV/HCV co-infected group, multivariate analysis showed that CD4(+) cell count and albumin level were negatively associated with FIB-4 (P <.0001), whereas antiretroviral therapy (ART) was positively associated with FIB-4 score (P =.0008). For the HIV mono-infected group, multivariate analysis showed that CD4(+) cell count (P <.0001) and albumin level (P =.0019) were negatively correlated with FIB-4 score, ART was positively associated with FIB-4 score (P =.0008), and plasma HIV RNA level was marginally associated with FIB-4 score (P =.080). In 72 HIV mono-infected women who were also hepatitis B surface antigen negative, ART naive, and reported no recent alcohol intake, plasma HIV RNA level was associated with increased FIB-4 score (P =.030). HIV RNA level was associated with increased FIB-4 score in the absence of hepatitis B, hepatitis C, ART, or alcohol use, suggesting a potential relationship between HIV infection and hepatic fibrosis in vivo. A better understanding of the various demographic and virologic variables that contribute to hepatic fibrosis may lead to more effective treatment of HIV infection and its co-morbid conditions.

FIB-4 index is associated with hepatocellular carcinoma risk in HIV-infected patients.

PubMed

Park, Lesley S; Tate, Janet P; Justice, Amy C; Lo Re, Vincent; Lim, Joseph K; Bräu, Norbert; Brown, Sheldon T; Butt, Adeel A; Gibert, Cynthia; Goetz, Matthew Bidwell; Rimland, David; Rodriguez-Barradas, Maria C; Dubrow, Robert

2011-12-01

Chronic inflammation caused by hepatitis B virus infection, hepatitis C virus infection, and/or heavy alcohol use can lead to fibrosis, cirrhosis, and eventually hepatocellular carcinoma (HCC). FIB-4 is an index score calculated from platelet count, alanine transaminase, aspartate transaminase, and age that predicts fibrosis and cirrhosis. We hypothesized that high FIB-4 would be associated with development of HCC in HIV-infected persons, who are at high risk due to high prevalence of viral hepatitis and alcohol consumption, and possibly due to HIV infection itself. Using proportional hazards models, we tested this hypothesis among 22,980 HIV-infected men from the Veterans Aging Cohort Study. We identified incident HCC cases from the Veterans Affairs Central Cancer Registry. During follow-up, there were 112 incident HCC diagnoses. The age- and race/ethnic group-adjusted HR was 4.2 [95% confidence interval (CI), 2.4-7.4] for intermediate FIB-4 and 13.0 (95% CI, 7.2-23.4) for high FIB-4, compared with low FIB-4. After further adjustment for enrollment year, CD4 count, HIV-1 RNA level, antiretroviral therapy use, hepatitis B and C virus infection, alcohol abuse/dependency, and diabetes, FIB-4 remained a strong, significant, independent risk factor for HCC. The multivariate-adjusted HR was 3.6 (95% CI, 2.1-6.4) for intermediate FIB-4 and 9.6 (95% CI, 5.2-17.4) for high FIB-4. Calculated from routine, noninvasive laboratory tests, FIB-4 is a strong, independent HCC risk factor in HIV-infected patients. FIB-4 might prove valuable as an easily measured index to identify those at highest risk for HCC, even prior to development of clinical cirrhosis.

FIB-4 Index is a Predictor of Background Liver Fibrosis and Long-Term Outcomes After Curative Resection of Hepatocellular Carcinoma.

PubMed

Okamura, Yukiyasu; Ashida, Ryo; Yamamoto, Yusuke; Ito, Takaaki; Sugiura, Teiichi; Uesaka, Katsuhiko

2016-08-01

The FIB-4 index is a simple formula for predicting the degree of liver fibrosis. This study aimed to examine the relationship between the preoperative FIB-4 index and liver fibrosis in non-tumor regions of surgical specimens and to investigate whether the FIB-4 index is a useful predictor for long-term outcomes experienced by hepatocellular carcinoma (HCC) patients after curative resection. This study retrospectively analyzed 493 HCC patients treated with curative resection. The utility of the FIB-4 index as a predictor of advanced liver fibrosis (F3 or F4) was assessed. The cutoff value for the FIB-4 index was determined using a receiver operating characteristic curve analysis, and the impact of the FIB-4 index on overall and recurrence-free survival after surgery was evaluated. Advanced liver fibrosis was found in 236 patients (47.9 %). The FIB-4 index was significantly higher for the patients with advanced liver fibrosis than for those without this condition (P < 0.001). An FIB-4 index of 2.87 was the optimal cutoff point for predicting advanced liver fibrosis. The multivariate analysis showed the FIB-4 index to be an independent prognostic factor for recurrence-free and overall survival after curative resection only for patients who underwent hepatectomy as initial treatment (hazard ratio, 1.47 and 1.59; 95 % confidence interval, 1.12-1.93 and 1.09-2.32; P = 0.006 and 0.016, respectively). The study showed the FIB4-index to be a predictor of background liver fibrosis and long-term outcomes for HCC patients who underwent hepatectomy as their initial treatment.

Microscale localization and isolation of light emitting imperfections in monocrystalline silicon solar cells

NASA Astrophysics Data System (ADS)

Gajdoš, Adam; Škvarenina, Lubomír.; Škarvada, Pavel; Macků, Robert

2017-12-01

An imperfections or defects may appear in fabricated monocrystalline solar cells. These microstructural imperfections could have impact on the parameters of whole solar cell. The research is divided into two parts, firstly, the detection and localization defects by using several techniques including current-voltage measurement, scanning probe microscopy (SPM), scanning electron microscope (SEM) and electroluminescence. Secondly, the defects isolation by a focused ion beam (FIB) milling and impact of a milling process on solar cells. The defect detection is realized by I-V measurement under reverse biased sample. For purpose of localization, advantage of the fact that defects or imperfections in silicon solar cells emit the visible and near infrared electroluminescence under reverse biased voltage is taken, and CCD camera measurement for macroscopic localization of these spots is applied. After rough macroscopic localization, microscopic localization by scanning probe microscopy combined with a photomultiplier (shadow mapping) is performed. Defect isolation is performed by a SEM equipped with the FIB instrument. FIB uses a beam of gallium ions which modifies crystal structure of a material and may affect parameters of solar cell. As a result, it is interesting that current in reverse biased sample with isolated defect is smaller approximately by 2 orders than current before isolation process.

Presence of Pathogens and Indicator Microbes at a Non-Point Source Subtropical Recreational Marine Beach ▿ †

PubMed Central

Abdelzaher, Amir M.; Wright, Mary E.; Ortega, Cristina; Solo-Gabriele, Helena M.; Miller, Gary; Elmir, Samir; Newman, Xihui; Shih, Peter; Bonilla, J. Alfredo; Bonilla, Tonya D.; Palmer, Carol J.; Scott, Troy; Lukasik, Jerzy; Harwood, Valerie J.; McQuaig, Shannon; Sinigalliano, Chris; Gidley, Maribeth; Plano, Lisa R. W.; Zhu, Xiaofang; Wang, John D.; Fleming, Lora E.

2010-01-01

Swimming in ocean water, including ocean water at beaches not impacted by known point sources of pollution, is an increasing health concern. This study was an initial evaluation of the presence of indicator microbes and pathogens and the association among the indicator microbes, pathogens, and environmental conditions at a subtropical, recreational marine beach in south Florida impacted by non-point sources of pollution. Twelve water and eight sand samples were collected during four sampling events at high or low tide under elevated or reduced solar insolation conditions. The analyses performed included analyses of fecal indicator bacteria (FIB) (fecal coliforms, Escherichia coli, enterococci, and Clostridium perfringens), human-associated microbial source tracking (MST) markers (human polyomaviruses [HPyVs] and Enterococcus faecium esp gene), and pathogens (Vibrio vulnificus, Staphylococcus aureus, enterovirus, norovirus, hepatitis A virus, Cryptosporidium spp., and Giardia spp.). The enterococcus concentrations in water and sand determined by quantitative PCR were greater than the concentrations determined by membrane filtration measurement. The FIB concentrations in water were below the recreational water quality standards for three of the four sampling events, when pathogens and MST markers were also generally undetectable. The FIB levels exceeded regulatory guidelines during one event, and this was accompanied by detection of HPyVs and pathogens, including detection of the autochthonous bacterium V. vulnificus in sand and water, detection of the allochthonous protozoans Giardia spp. in water, and detection of Cryptosporidium spp. in sand samples. The elevated microbial levels were detected at high tide and under low-solar-insolation conditions. Additional sampling should be conducted to further explore the relationships between tidal and solar insolation conditions and between indicator microbes and pathogens in subtropical recreational marine waters impacted by non-point source pollution. PMID:19966020

Diversity in C-Xanes Spectra Obtained from Carbonaceous Solid Inclusions from Monahans Halite

NASA Technical Reports Server (NTRS)

Kebukawa, Y.; Zolensky, M. E.; Fries, M.; Kilcoyne, A. L. D.; Rahman, Z.; Cody, G. D.

2014-01-01

Monahans meteorite (H5) contains fluid inclusion- bearing halite (NaCl) crystals [1]. Microthermometry and Raman spectroscopy showed that the fluid in the inclusions is an aqueous brine and they were trapped near 25degC [1]. Their continued presence in the halite grains requires that their incorporation into the H chondrite asteroid was post metamorphism [2]. Abundant solid inclusions are also present in the halites. The solid inclusions include abundant and widely variable organics [2]. Analyses by Raman microprobe, SEM/EDX, synchrotron X-ray diffraction and TEM reveal that these grains include macromolecular carbon similar in structure to CV3 chondrite matrix carbon, aliphatic carbon compounds, olivine (Fo99-59), high- and low-Ca pyroxene, feldspars, magnetite, sulfides, lepidocrocite, carbonates, diamond, apatite and possibly the zeolite phillipsite [3]. Here we report organic analyses of these carbonaceous residues in Monahans halite using C-, N-, and O- X-ray absorption near edge structure (XANES). Samples and Methods: Approximately 100 nm-thick sections were extracted with a focused ion beam (FIB) at JSC from solid inclusions from Monahans halite. The sections were analyzed using the scanning transmission X-ray microscope (STXM) on beamline 5.3.2.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory for XANES spectroscopy. Results and Discussion: C-XANES spectra of the solid inclusions show micrometer-scale heterogeneity, indicating that the macromolecular carbon in the inclusions have complex chemical variations. C-XANES features include 284.7 eV assigned to aromatic C=C, 288.4-288.8 eV assigned to carboxyl, and 290.6 eV assigned to carbonate. The carbonyl features obtained by CXANES might have been caused by the FIB used in sample preparation. No specific N-XANES features are observed. The CXANES spectra obtained from several areas in the FIB sections include type 1&2 chondritic IOM like, type 3 chondritic IOM like, and none of the above. The natures of the macromolecular carbon in the solid inclusions observed by C-XANES are consistent with the previous studies showing that the carbonaceous solid inclusions have not originated from Monahans parent body [1-3], and have various origins, including various chondritic meteorite parent bodies as well as other unknown source(s).

Simultaneous monitoring of faecal indicators and harmful algae using an in-situ autonomous sensor.

PubMed

Yamahara, K M; Demir-Hilton, E; Preston, C M; Marin, R; Pargett, D; Roman, B; Jensen, S; Birch, J M; Boehm, A B; Scholin, C A

2015-08-01

Faecal indicator bacteria (FIB) and harmful algal blooms (HABs) threaten the health and the economy of coastal communities worldwide. Emerging automated sampling technologies combined with molecular analytical techniques could enable rapid detection of micro-organisms in-situ, thereby improving resource management and public health decision-making. We evaluated this concept using a robotic device, the Environmental Sample Processor (ESP). The ESP automates in-situ sample collection, nucleic acid extraction and molecular analyses. Here, the ESP measured and reported concentrations of FIB (Enterococcus spp.), a microbial source-tracking marker (human-specific Bacteriodales) and a HAB species (Psuedo-nitzschia spp.) over a 45-day deployment on the Santa Cruz Municipal Wharf (Santa Cruz, CA, USA). Both FIB and HABs were enumerated from single in-situ collected water samples. The in-situ qPCR efficiencies ranged from 86% to 105%, while the limit of quantifications during the deployment was 10 copies reaction(-1) . No differences were observed in the concentrations of enterococci, the human-specific marker in Bacteroidales spp., and P. australis between in-situ collected sample and traditional hand sampling methods (P > 0·05). Analytical results were Internet-accessible within hours of sample collection, demonstrating the feasibility of same-day public notification of current water quality conditions. This study presents the first report of in-situ qPCR enumeration of both faecal indicators and harmful algal species in coastal marine waters. We utilize a robotic device for in-situ quantification of enterococci, the human-specific marker in Bacteriodales and Pseudo-nitzschia spp. from the same water samples collected and processed in-situ. The results demonstrate that rapid, in-situ monitoring can be utilized to identify and quantify multiple health-relevant micro-organisms important in water quality monitoring and that this monitoring can be used to inform same-day notifications. © 2015 The Society for Applied Microbiology.

Occurrence of genes coding for MSCRAMM and biofilm-associated protein Bap in Staphylococcus spp. isolated from bovine subclinical mastitis and relationship with somatic cell counts.

PubMed

Zuniga, Eveline; Melville, Priscilla A; Saidenberg, André B S; Laes, Marco A; Gonsales, Fernanda F; Salaberry, Sandra R S; Gregori, Fabio; Brandão, Paulo E; dos Santos, Franklin G B; Lincopan, Nilton E; Benites, Nilson R

2015-12-01

This study aimed to elucidate aspects of the epidemiology of bovine subclinical mastitis through the assessment of genes encoding MSCRAMM (microbial surface components recognizing adhesive matrix molecules - a group of adhesins) and protein Bap (implicated in biofilm formation), in coagulase-positive (CPS) and coagulase-negative (CNS) Staphylococcus isolated from subclinical mastitis. Milk samples were collected for microbiological exams, somatic cell count (SCC) and a survey of the genes coding for MSCRAMM (cna, eno, ebpS, fnbA, fnbB and fib) and biofilm-associated protein Bap (bap) in 106 Staphylococcus spp. isolates using PCR. The frequencies of occurrence of eno (82.1%), fnbA (72.6%), fib (71.7%) and bap (56.6%) were higher (P < 0.0001) compared with the other assessed genes (cna, ebpS and fnbB). The higher frequency of occurrence (P < 0.005) of the bap gene in CNS compared with CPS suggests that in these species biofilm formation is an important mechanism for the persistence of the infection. The medians of the SCCs in the samples where eno, fnbA, fib and bap genes were detected were higher compared with Staphylococcus without the assessed genes (P < 0.05) and negative samples (P < 0.01), which indicated that the presence of these MSCRAMM may be related to a higher intensity of the inflammatory process. Copyright © 2015 Elsevier Ltd. All rights reserved.

Development of new FIB technology for EUVL mask repair

NASA Astrophysics Data System (ADS)

Aramaki, Fumio; Ogawa, Takashi; Matsuda, Osamu; Kozakai, Tomokazu; Sugiyama, Yasuhiko; Oba, Hiroshi; Yasaka, Anto; Amano, Tsuyoshi; Shigemura, Hiroyuki; Suga, Osamu

2011-04-01

The next generation EUVL masks beyond hp15nm are difficult to repair for the current repair technologies including focused ion beam (FIB) and electron beam (EB) in view of the minimum repairable size. We developed a new FIB technology to repair EUVL masks. Conventional FIB use gallium ions (Ga+) generated by a liquid metal ion source (LMIS), but the new FIB uses hydrogen ions (H2+) generated by a gas field ion source (GFIS). The minimum reaction area of H2+ FIB is theoretically much smaller than that of EB. We investigated the repair performance of H2+ FIB. In the concrete, we evaluated image resolution, scan damage, etching rate, material selectivity of etching and actinic image of repaired area. The most important result is that there was no difference between the repaired area and the non-repaired one on actinic images. That result suggests that the H2+ GFIS technology is a promising candidate for the solution to repair the next generation EUVL masks beyond hp15nm.

Multi-signal FIB/SEM tomography

NASA Astrophysics Data System (ADS)

Giannuzzi, Lucille A.

2012-06-01

Focused ion beam (FIB) milling coupled with scanning electron microscopy (SEM) on the same platform enables 3D microstructural analysis of structures using FIB for serial sectioning and SEM for imaging. Since FIB milling is a destructive technique, the acquisition of multiple signals from each slice is desirable. The feasibility of collecting both an inlens backscattered electron (BSE) signal and an inlens secondary electron (SE) simultaneously from a single scan of the electron beam from each FIB slice is demonstrated. The simultaneous acquisition of two different SE signals from two different detectors (inlens vs. Everhart-Thornley (ET) detector) is also possible. Obtaining multiple signals from each FIB slice with one scan increases the acquisition throughput. In addition, optimization of microstructural and morphological information from the target is achieved using multi-signals. Examples of multi-signal FIB/SEM tomography from a dental implant will be provided where both material contrast from the bone/ceramic coating/Ti substrate phases and porosity in the ceramic coating will be characterized.

Controlled motion of domain walls in submicron amorphous wires

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

Ţibu, Mihai; Lostun, Mihaela; Rotărescu, Cristian

Results on the control of the domain wall displacement in cylindrical Fe{sub 77.5}Si{sub 7.5}B{sub 15} amorphous glass-coated submicron wires prepared by rapid quenching from the melt are reported. The control methods have relied on conical notches with various depths, up to a few tens of nm, made in the glass coating and in the metallic nucleus using a focused ion beam (FIB) system, and on the use of small nucleation coils at one of the sample ends in order to apply magnetic field pulses aimed to enhance the nucleation of reverse domains. The notch-based method is used for the firstmore » time in the case of cylindrical ultrathin wires. The results show that the most efficient technique of controlling the domain wall motion in this type of samples is the simultaneous use of notches and nucleation coils. Their effect depends on wire diameter, notch depth, its position on the wire length, and characteristics of the applied pulse.« less

Design and fabrication of single-crystal GaN nano-bridge on homogeneous substrate for nanoindentation

NASA Astrophysics Data System (ADS)

Hung, Shang-Chao

2014-12-01

This study reports a simple method to design and fabricate a freestanding GaN nano-bridge over a homogeneous short column as supporting leg. Test samples were fabricated from MOCVD-grown single-crystal GaN films over sapphire substrate using a FIB milling to leave freestanding short spans. We also investigated the nanoindentation characteristics and the corresponding nanoscopic mechanism of the GaN nano-bridge and its short column with a conical indenter inside transmission electron microscopy. The stress-strain mechanical properties and Young's modulus have also been examined and calculated as 108 GPa ± 4.8 % by the strain energy method. The significant slope switch of the L- D curve corresponds to the transition from the single-point bending indentation to the surface stretching indentation and has been interpreted with the evolution of TEM images. This freestanding fabrication and test have key advantages to characterize nanoscale behavior of one-dimensional bridge structure and greater ease of sample preparation over other micro-fabrication techniques.

Multi-scale characterization by FIB-SEM/TEM/3DAP.

PubMed

Ohkubo, T; Sepehri-Amin, H; Sasaki, T T; Hono, K

2014-11-01

In order to improve properties of functional materials, it is important to understand the relation between the structure and the properties since the structure has large effect to the properties. This can be done by using multi-scale microstructure analysis from macro-scale to nano and atomic scale. Scanning electron microscope (SEM) equipped with focused ion beam (FIB), transmission electron microscope (TEM) and 3D atom probe (3DAP) are complementary analysis tools making it possible to know the structure and the chemistry from micron to atomic resolution. SEM gives us overall microstructural and chemical information by various kinds of detectors such as secondary electron, backscattered electron, EDS and EBSD detectors. Also, it is possible to analyze 3D structure and chemistry via FIB serial sectioning. In addition, using TEM we can focus on desired region to get more complementary information from HRTEM/STEM/Lorentz images, SAED/NBD patterns and EDS/EELS to see the detail micro or nano-structure and chemistry. Especially, combination of probe Cs corrector and split EDS detectors with large detector size enable us to analyze the atomic scale elemental distribution. Furthermore, if the specimen has a complicated 3D nanostructure, or we need to analyze light elements such as hydrogen, lithium or boron, 3DAP can be used as the only technique which can visualize and analyze distribution of all constituent atoms of our materials within a few hundreds nm area. Hence, site-specific sample preparation using FIB/SEM is necessary to get desired information from region of interest. Therefore, this complementary analysis combination works very well to understand the detail of materials.In this presentation, we will show the analysis results obtained from some of functional materials by Carl Zeiss CrossBeam 1540EsB FIB/SEM, FEI Tecnai G(2) F30, Titan G2 80-200 TEMs and locally build laser assisted 3DAP. As the one of the example, result of multi-scale characterization for ultra-fine grain Nd-Fe-B permanent magnet will be shown [1]. In order to improve the magnetic properties, especially to increase the coercivity (resistance against magnetization reversal) of the magnet, decreasing the grain size and isolating each grain by non-ferromagnetic grain boundary phase are quite important since the nucleation of magnetic reversal from grain boundary phase can be suppressed and pinning force of magnetic domain wall at the grain boundary phase can be strengthened. Therefore, micro and nano structure and chemistry analysis can shed a light do grain boundary engineering.Figure 1(a,b) shows SEM BSE images of ultrafine grain Nd-Fe-B sintered magnet and the reconstructed 3D tomography of Nd-rich phases obtained by FIB/SEM serial sectioning. This data can provide us information about the distribution of Nd-rich phase and its volume fraction. Moreover, the HRTEM image from the grain boundary phase, the 3DAP maps and the concentration depth profiles are shown in Fig. 1(c,d,e). This magnet shows high coercivity (1517kA/m), and by comparing these results with the microstructures of low coercivity specimen, importance of grain boundary formation was confirmed and it gives us hint to improve the coercivity further. We will show the detail and results from other materials.jmicro;63/suppl_1/i6/DFU046F1F1DFU046F1Fig. 1.(a) SEM BSE images of ultrafine grain Nd-Fe-B sintered magnet. (b) 3D FIB/SEM tomography of Nd-rich phases. (c) HRTEM image from the grain boundary phase. (d) 3DAP maps of Nd, Cu and Al. (e) Concentration depth profiles for Fe, Nd+Pr, B, Co, Cu and Al, determined from the selected box in (d)[1]. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Does Incorporating Change in APRI or FIB-4 Indices Over Time Improve the Accuracy of a Single Index for Identifying Liver Fibrosis in Persons With Chronic Hepatitis C Virus Infection?

PubMed

Gounder, Prabhu P; Haering, Celia; Bruden, Dana J T; Townshend-Bulson, Lisa; Simons, Brenna C; Spradling, Philip R; McMahon, Brian J

2018-01-01

The aspartate aminotransferase-to-platelet ratio index (APRI) and a fibrosis index calculated using platelets (FIB-4) have been proposed as noninvasive markers of liver fibrosis. To determine APRI/FIB-4 accuracy for predicting histologic liver fibrosis and evaluate whether incorporating change in index improves test accuracy in hepatitis C virus (HCV)-infected Alaska Native persons. Using liver histology as the gold standard, we determined the test characteristics of APRI to predict Metavir ≥F2 fibrosis and FIB-4 to predict Metavir ≥F3 fibrosis. Index discrimination was measured as the area under the receiver operator characteristic curve. We fit a logistic regression model to determine whether incorporating change in APRI/FIB-4 over time improved index discrimination. Among 283 participants, 46% were female, 48% had a body mass index >30, 11% had diabetes mellitus, 8% reported current heavy alcohol use. Participants were infected with HCV genotypes 1 (68%), 2 (17%), or 3 (15%). On liver histology, 30% of study participants had ≥F2 fibrosis and 15% had ≥F3 fibrosis. The positive predictive value of an APRI>1.5/FIB-4>3.25 for identifying fibrosis was 77%/78%. The negative predictive value of an APRI<0.5/FIB-4<1.45 was 91%/87%. The area under the receiver operator characteristic curve of an APRI/FIB-4 for identifying fibrosis was 0.82/0.84. Incorporating change in APRI/FIB-4 did not improve index discrimination. The accuracy of APRI/FIB-4 for identifying liver fibrosis in HCV-infected Alaska Native persons is similar to that reported in other populations and could help prioritize patients for treatment living in areas without access to liver biopsy. Change in APRI/FIB-4 was not predictive of degree of fibrosis.

NEXAFS Study of the Annealing Effect on the Local Structure of FIB-CVD DLC

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

Saikubo, Akihiko; Kato, Yuri; Igaki, Jun-ya

2007-01-19

Annealing effect on the local structure of diamond like carbon (DLC) formed by focused ion beam-chemical vapor deposition (FIB-CVD) was investigated by the measurement of near edge x-ray absorption fine structure (NEXAFS) and energy dispersive x-ray (EDX) spectra. Carbon K edge absorption NEXAFS spectrum of FIB-CVD DLC was measured in the energy range of 275-320 eV. In order to obtain the information on the location of the gallium in the depth direction, incidence angle dependence of NEXAFS spectrum was measured in the incident angle range from 0 deg. to 60 deg. . The peak intensity corresponding to the resonance transitionmore » of 1s{yields}{sigma}* originating from carbon-gallium increased from the FIB-CVD DLC annealed at 200 deg. C to the FIB-CVD DLC annealed at 400 deg. C and decreased from that at 400 deg. C to that at 600 deg. C. Especially, the intensity of this peak remarkably enhanced in the NEXAFS spectrum of the FIB-CVD DLC annealed at 400 deg. C at the incident angle of 60 deg. . On the contrary, the peak intensity corresponding to the resonance transition of 1s{yields}{pi}* originating from carbon double bonding of emission spectrum decreased from the FIB-CVD DLC annealed at 200 deg. C to that at 400 deg. C and increased from that at 400 deg. C to that at 600 deg. C. Gallium concentration in the FIB-CVD DLC decreased from {approx_equal}2.2% of the as-deposited FIB-CVD DLC to {approx_equal}1.5% of the FIB-CVD DLC annealed at 600 deg. C from the elementary analysis using EDX. Both experimental results indicated that gallium atom departed from FIB-CVD DLC by annealing at the temperature of 600 deg. C.« less

HIV Mono-infection Is Associated With FIB-4 – A Noninvasive Index of Liver Fibrosis – in Women

PubMed Central

Welge, Jeffrey A.; Taylor, Lynn E.; Mayer, Kenneth H.; Klein, Robert S.; Celentano, David D.; Jamieson, Denise J.; Gardner, Lytt; Sherman, Kenneth E.

2011-01-01

Background. FIB-4 represents a noninvasive, composite index that is a validated measure of hepatic fibrosis, which is an important indicator of liver disease. To date, there are limited data regarding hepatic fibrosis in women. Methods. FIB-4 was evaluated in a cohort of 1227 women, and associations were evaluated in univariate and multivariate regression models among 4 groups of subjects classified by their human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infection status. Results. The median FIB-4 scores were 0.60 in HIV-/HCV- women, 0.83 in HIV-/HCV+ women, 0.86 in HIV+/HCV- women, and 1.30 in HIV+/HCV+ women. In the HIV/HCV co-infected group, multivariate analysis showed that CD4+ cell count and albumin level were negatively associated with FIB-4 (P <.0001), whereas antiretroviral therapy (ART) was positively associated with FIB-4 score (P =.0008). For the HIV mono-infected group, multivariate analysis showed that CD4+ cell count (P <.0001) and albumin level (P =.0019) were negatively correlated with FIB-4 score, ART was positively associated with FIB-4 score (P =.0008), and plasma HIV RNA level was marginally associated with FIB-4 score (P =.080). In 72 HIV mono-infected women who were also hepatitis B surface antigen negative, ART naive, and reported no recent alcohol intake, plasma HIV RNA level was associated with increased FIB-4 score (P =.030). Conclusions. HIV RNA level was associated with increased FIB-4 score in the absence of hepatitis B, hepatitis C, ART, or alcohol use, suggesting a potential relationship between HIV infection and hepatic fibrosis in vivo. A better understanding of the various demographic and virologic variables that contribute to hepatic fibrosis may lead to more effective treatment of HIV infection and its co-morbid conditions. PMID:21248367

FIB-4 and imaging for measuring fibrosis in hepatitis C virus.

PubMed

Turner, Barbara J; Liang, Yuanyuan; Singal, Amit G

2017-02-01

Noninvasive measures are widely used to assess fibrosis and may be used to prioritize hepatitis C virus (HCV) treatment. We examined risks for likely fibrosis in patients with chronic HCV infection using fibrosis-4 (FIB-4) and imaging. A HCV screening program diagnosed chronic HCV in patients born from 1945 to 1965 admitted in a safety net hospital. Likely fibrosis was based on FIB-4 (≥1.45) alone or combined with imaging interpreted as fibrosis or cirrhosis. Logistic regression was used to calculate adjusted odds ratios (AORs) for demographic, clinical, and insurance factors associated with each outcome. Using multiple linear regression among patients with likely fibrosis, we examined associations with higher Model for End-Stage Liver Disease (MELD) scores. Using FIB-4 alone, 57% (83/146) of patients had likely fibrosis versus 43% (63/148) using FIB-4 plus imaging. Obesity/overweight and Hispanic ethnicity had over three-fold to four-fold higher AORs for fibrosis, respectively, based on FIB-4 plus imaging, but both AORs were only two-fold greater with FIB-4 alone. Being uninsured was significantly associated with fibrosis based on FIB-4 alone [AOR=2.40 (95% confidence interval 1.01-5.70)] but not with imaging. Heavy alcohol use and older age were associated with higher AORs of fibrosis with both measures (all P<0.004). MELD scores were ∼3 points higher for uninsured patients, regardless of measure (both P<0.05). Using FIB-4 plus imaging to identify fibrosis in chronic HCV, higher risks are seen for Hispanics and overweight/obese individuals than using FIB-4 alone. Higher MELD scores at diagnosis for the uninsured indicate delayed access to care.

The FIB-4 score predicts postoperative short-term outcomes of hepatocellular carcinoma fulfilling the milan criteria.

PubMed

Dong, J; Xu, X-h; Ke, M-y; Xiang, J-x; Liu, W-y; Liu, X-m; Wang, B; Zhang, X-f; Lv, Y

2016-05-01

The fibrosis score 4 (FIB-4) score is a useful tool to determine the degree of hepatic fibrosis. Liver fibrosis and cirrhosis are well-known predictors of postoperative complications after hepatectomy. This study examined the impact of FIB-4 on postoperative short-term outcomes of patients with hepatocellular carcinoma (HCC). Three hundred and fifty patients undergoing hepatectomy for HCC between 2008 and 2013 were enrolled. The receiver operating characteristic (ROC) curve analysis was performed to determine the cutoff value of the FIB-4. Univariate and multivariate analysis was performed to identify the risk factors. The correlation of the preoperative FIB-4 value with clinicopathological parameters was examined. Postoperative complications were observed in 202 (57.7%) patients. The optimal cutoff value of the FIB-4 was set at 2.88 and 3.85 for postoperative complications and intraoperative blood loss respectively. It was also an independent prognostic factor for postoperative complications (hazard ratio [HR], 1.202; 95% CI, 1.076-1.344; P = 0.001) and intraoperative blood loss (HR, 1.196; 95% CI, 1.091-1.343; P < 0.001) by multivariate analysis. The FIB-4 was significantly correlated with age, liver function, coagulation function, blood loss, intraoperative blood transfusion (all P < 0.05). Preoperative FIB-4 is a useful index to predict postoperative outcomes in patients with HCC. The FIB-4 should be assessed routinely for hepatocellular carcinoma patients. Copyright © 2016 Elsevier Ltd. All rights reserved.

Potential transfer of aquatic organisms via ballast water with a particular focus on harmful and non-indigenous species: A survey from Adriatic ports.

PubMed

Cabrini, M; Cerino, F; de Olazabal, A; Di Poi, E; Fabbro, C; Fornasaro, D; Goruppi, A; Flander-Putrle, V; Francé, J; Gollasch, S; Hure, M; Lipej, L; Lučić, D; Magaletti, E; Mozetič, P; Tinta, T; Tornambè, A; Turk, V; Uhan, J; David, M

2018-02-14

Ballast water discharges may cause negative impacts to aquatic ecosystems, human health and economic activities by the introduction of potentially harmful species. Fifty untreated ballast water tanks, ten in each port, were sampled in four Adriatic Italian ports and one Slovenian port. Salinity, temperature and fluorescence were measured on board. Faecal indicator bacteria (FIB), phyto- and zooplankton were qualitatively and quantitatively determined to identify the species assemblage arriving in ballast water. FIB exceeded the convention standard limits in 12% of the sampled tanks. Vibrio cholerae was not detected. The number of viable organisms in the size groups (minimum dimension) <50 and ≥10 μm and ≥50 μm resulted above the abundances required from the Ballast Water Management Convention in 55 and 86% of the samples, respectively. This is not surprising as unmanaged ballast waters were sampled. Some potentially toxic and non-indigenous species were observed in both phyto- and zooplankton assemblages. Copyright © 2018 Elsevier Ltd. All rights reserved.

Distribution and sources of surfzone bacteria at Huntington Beach before and after disinfection on an ocean outfall-- a frequency-domain analysis.

PubMed

Noble, M A; Xu, J P; Robertson, G L; Rosenfeld, L K

2006-06-01

Fecal indicator bacteria (FIB) were measured approximately 5 days a week in ankle-depth water at 19 surfzone stations along Huntington Beach and Newport Beach, California, from 1998 to the end of 2003. These sampling periods span the time before and after treated sewage effluent, discharged into the coastal ocean from the local outfall, was disinfected. Bacterial samples were also taken in the vicinity of the outfall during the pre- and post-disinfection periods. Our analysis of the results from both data sets suggest that land-based sources, rather than the local outfall, were the source of the FIB responsible for the frequent closures and postings of local beaches in the summers of 2001 and 2002. Because the annual cycle is the dominant frequency in the fecal and total coliform data sets at most sampling stations, we infer that sources associated with local runoff were responsible for the majority of coliform contamination along wide stretches of the beach. The dominant fortnightly cycle in enterococci at many surfzone sampling stations suggests that the source for these relatively frequent bacteria contamination events in summer is related to the wetting and draining of the land due to the large tidal excursions found during spring tides. Along the most frequently closed section of the beach at stations 3N-15N, the fortnightly cycle is dominant in all FIBs. The strikingly different spatial and spectral patterns found in coliform and in enterococci suggest the presence of different sources, at least for large sections of beach. The presence of a relatively large enterococci fortnightly cycle along the beaches near Newport Harbor indicates that contamination sources similar to those found off Huntington Beach are present, though not at high enough levels to close the Newport beaches.

Detection of multiple potentially pathogenic bacteria in Matang mangrove estuaries, Malaysia.

PubMed

Ghaderpour, Aziz; Mohd Nasori, Khairul Nazrin; Chew, Li Lee; Chong, Ving Ching; Thong, Kwai Lin; Chai, Lay Ching

2014-06-15

The deltaic estuarine system of the Matang Mangrove Forest Reserve of Malaysia is a site where several human settlements and brackish water aquaculture have been established. Here, we evaluated the level of fecal indicator bacteria (FIB) and the presence of potentially pathogenic bacteria in the surface water and sediments. Higher levels of FIB were detected at downstream sampling sites from the fishing village, indicating it as a possible source of anthropogenic pollution to the estuary. Enterococci levels in the estuarine sediments were higher than in the surface water, while total coliforms and E. coli in the estuarine sediments were not detected in all samples. Also, various types of potentially pathogenic bacteria, including Klebsiella pneumoniae, Serratia marcescens and Enterobacter cloacae were isolated. The results indicate that the Matang estuarine system is contaminated with various types of potential human bacterial pathogens which might pose a health risk to the public. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effect of process conditions on the steam reforming of ethanol with a nano-Ni/SiO2 catalyst.

PubMed

Wu, C; Williams, P T

2012-01-01

In this paper, a nano-Ni/SiO2 catalyst was prepared by a sol-gel method and tested for hydrogen production from ethanol steam reforming using a two-stage fixed-bed reaction system. The reaction conditions, such as reaction temperature, water/ethanol ratio and sample feeding rate, were investigated with the prepared nano-Ni/SiO2 catalyst. Brunauer-Emmett-Teller surface area and porosity, temperature-programmed oxidation, X-ray diffraction and focused ion beam (FIB)/scanning electron microscopy were used in this work to analysis the fresh and/or reacted catalysts. An extended catalyst stability test for ethanol steam reforming with the Ni/SiO2 catalyst was carried out at a reaction temperature of 600 degrees C, when the water/ethanol ratio was kept at 3.5 and sample feeding rate was 4.74 g h(-1). The results showed that a stabilized gas and hydrogen production was obtained with a potential H2 production of about 40 wt.%. Increasing the reaction temperature during ethanol steam reforming with the Ni/SiO2 catalyst resulted in an increase of gas and hydrogen production. The gas yield was slightly reduced when the water/ethanol ratio was increased from 2.0 to 3.5. However, the potential H2 production was increased. The investigation of the sample feeding rate showed that the gas production per hour was increased due to the higher sample feeding rate, but the potential H2 production was reduced.

Analysis of FIB-induced damage by electron channelling contrast imaging in the SEM.

PubMed

Gutierrez-Urrutia, Ivan

2017-01-01

We have investigated the Ga + ion-damage effect induced by focused ion beam (FIB) milling in a [001] single crystal of a 316 L stainless steel by the electron channelling contrast imaging (ECCI) technique. The influence of FIB milling on the characteristic electron channelling contrast of surface dislocations was analysed. The ECCI approach provides sound estimation of the damage depth produced by FIB milling. For comparison purposes, we have also studied the same milled surface by a conventional electron backscatter diffraction (EBSD) approach. We observe that the ECCI approach provides further insight into the Ga + ion-damage phenomenon than the EBSD technique by direct imaging of FIB artefacts in the scanning electron microscope. We envisage that the ECCI technique may be a convenient tool to optimize the FIB milling settings in applications where the surface crystal defect content is relevant. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Picosecond laser micromachining prior to FIB milling for electronic microscopy sample preparation

NASA Astrophysics Data System (ADS)

Sikora, Aurélien; Fares, Lahouari; Adrian, Jérôme; Goubier, Vincent; Delobbe, Anne; Corbin, Antoine; Sentis, Marc; Sarnet, Thierry

2017-10-01

In order to check the manufacturing quality of electronic components using electron microscopy, the area of interest must be exposed. This requires the removal of a large quantity of matter without damaging the surrounding area. This step can be accomplished using ion milling but the processing can last a few hours. In order to accelerate the preparation of the samples, picosecond laser micromachining prior to Focused Ion Beam polishing is envisioned. Laser ablation allows the fast removal of matter but induces damages around the ablated area. Therefore the process has to be optimized in order to limit the size of both the heat affected zone and induced dislocation zone. For this purpose, cavities have been engraved in silicon and in electronic components, using a linearly polarized picosecond laser (∼50 ps) at three different wavelengths (343, 515 and 1030 nm). Results showed that the cross sectional shapes and the surface topologies can be tuned by the laser fluence and the number of pulses. Clear cross sections of bumps and cavity openings, exposing multilayer interfaces, are demonstrated. The silicon removal rates, tuned by the applied energy density, have been measured. Removal rates achieved at 200 kHz were typically hundred times higher than those achieved by ion milling and the best efficiency was obtained at 343 nm.

Adenovirus and Norovirus Contaminants in Commercially Distributed Shellfish.

PubMed

Rodriguez-Manzano, Jesus; Hundesa, Ayalkibet; Calgua, Byron; Carratala, Anna; Maluquer de Motes, Carlos; Rusiñol, Marta; Moresco, Vanessa; Ramos, Ana Paula; Martínez-Marca, Fernando; Calvo, Miquel; Monte Barardi, Celia Regina; Girones, Rosina; Bofill-Mas, Sílvia

2014-03-01

Shellfish complying with European Regulations based on quantification of fecal bacterial indicators (FIB) are introduced into markets; however, information on viruses, more stable than FIB, is not available in the literature. To assess the presence of noroviruses (NoVs) GI and GII and human adenoviruses (HAdV) in domestic and imported mussels and clams (n = 151) their presence was analyzed during winter seasons (2004-2008) in north-west Spanish markets through a routine surveillance system. All samples tested negative for NoV GI and 13 % were positive for NoV GII. The role of HAdV as viral indicator was evaluated in 20 negative and 10 positive NoV GII samples showing an estimated sensitivity and specificity of HAdV to predict the presence of NoV GII of 100 and 74 % (cut-off 0.5). The levels of HAdV and NoVs and the efficiency of decontamination in shellfish depuration plants (SDP) were evaluated analyzing pre- and post-depurated mussels collected in May-June 2010 from three different SDP. There were no statistically significant differences in the prevalence and quantification of HAdV between pre- and post-depurated shellfish and between seawater entering and leaving the depuration systems. Moreover, infectious HAdV were detected in depurated mussels. These results confirm previous studies showing that current controls and depuration treatments limiting the number of FIB do not guarantee the absence of viruses in shellfish.

Solid electrolytes for fluoride ion batteries: ionic conductivity in polycrystalline tysonite-type fluorides.

PubMed

Rongeat, Carine; Reddy, M Anji; Witter, Raiker; Fichtner, Maximilian

2014-02-12

Batteries based on a fluoride shuttle (fluoride ion battery, FIB) can theoretically provide high energy densities and can thus be considered as an interesting alternative to Li-ion batteries. Large improvements are still needed regarding their actual performance, in particular for the ionic conductivity of the solid electrolyte. At the current state of the art, two types of fluoride families can be considered for electrolyte applications: alkaline-earth fluorides having a fluorite-type structure and rare-earth fluorides having a tysonite-type structure. As regard to the latter, high ionic conductivities have been reported for doped LaF3 single crystals. However, polycrystalline materials would be easier to implement in a FIB due to practical reasons in the cell manufacturing. Hence, we have analyzed in detail the ionic conductivity of La(1-y)Ba(y)F(3-y) (0 ≤ y ≤ 0.15) solid solutions prepared by ball milling. The combination of DC and AC conductivity analyses provides a better understanding of the conduction mechanism in tysonite-type fluorides with a blocking effect of the grain boundaries. Heat treatment of the electrolyte material was performed and leads to an improvement of the ionic conductivity. This confirms the detrimental effect of grain boundaries and opens new route for the development of solid electrolytes for FIB with high ionic conductivities.

KSC-07pd1494

NASA Image and Video Library

2007-06-13

KENNEDY SPACE CENTER, FLA. -- Another view of the area of orbiter Endeavour's orbital maneuvering system, or OMS, pod where the tear occurred on Atlantis during launch of mission STS-117 on June 8, 2007. Repair is under consideration following testing at KSC and Houston. The test articles each feature three tiles (Low Temperature Reusable Surface Insulation, or LRSI) affixed next to two FIB blankets, simulating the thermal protection system set-up on Atlantis' OMS pod in the vicinity of the in-flight anomaly. These test articles were flown to Texas the morning of June 14. The TPS team at KSC has also provided a total of 22 FIB samples for other testing and analysis. Photo credit: NASA/Kim Shiflett

KSC-07pd1495

NASA Image and Video Library

2007-06-13

KENNEDY SPACE CENTER, FLA. -- Another view of the area of orbiter Endeavour's orbital maneuvering system, or OMS, pod where the tear occurred on Atlantis during launch of mission STS-117 on June 8, 2007. Repair is under consideration following testing at KSC and Houston. The test articles each feature three tiles (Low Temperature Reusable Surface Insulation, or LRSI) affixed next to two FIB blankets, simulating the thermal protection system set-up on Atlantis' OMS pod in the vicinity of the in-flight anomaly. These test articles were flown to Texas the morning of June 14. The TPS team at KSC has also provided a total of 22 FIB samples for other testing and analysis. Photo credit: NASA/Kim Shiflett

Meteorological effects on the levels of fecal indicator bacteria in an urban stream: a modeling approach.

PubMed

Cho, Kyung Hwa; Cha, Sung Min; Kang, Joo-Hyon; Lee, Seung Won; Park, Yongeun; Kim, Jung-Woo; Kim, Joon Ha

2010-04-01

Gwangju Creek (GJC) in Korea, which drains a highly urbanized watershed, has suffered from substantial fecal contamination, thereby limiting the beneficial use of the water in addition to threatening public health. In this study, to quantitatively estimate the sinks and sources of fecal indicator bacteria (FIB) in GJC under varying meteorological conditions, two FIB (i.e., Escherichia coli and enterococci bacteria) were monitored hourly for 24h periods during both wet and dry weather conditions at four sites along GJC, and the collected data was subsequently used to develop a spatiotemporal FIB prediction model. The monitoring data revealed that storm washoff and irradiational die-off by sunlight are the two key processes controlling FIB populations in wet and dry weather, respectively. FIB populations significantly increased during precipitation, with greater concentrations occurring at higher rainfall intensity. During dry weather, FIB populations decreased in the presence of sunlight in daytime but quickly recovered at nighttime due to continuous point-source inputs. In this way, the contributions of the key processes (i.e., irradiational die-off by sunlight, settling, storm washoff, and resuspension) to the FIB levels in GJC under different meteorological conditions were quantitatively estimated using the developed model. The modeling results showed that the die-off by sunlight is the major sink of FIB during the daytime in dry weather with a minor contribution from the settling process. During wet weather, storm washoff and resuspension are equally important processes that are responsible for the substantial increase of FIB populations. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

Synchrotron Radiation X-Ray Fluorescence nanoanalyses of the metallome of a ~3.3 Ga-old microbial biofilm from the Barberton greenstone belt, South Africa.

NASA Astrophysics Data System (ADS)

Hubert, A.; Lemelle, L.; Salome, M.; Cloetens, P.; Westall, F.; Simionovici, A.

2012-04-01

Combining in situ nanometer-scale techniques on the fossilized Josefsdal Chert Microbial Biofilm (JCMB) reveals a distinct vertical structural and compositional organisation: the lower part is calcified as aragonite, while the upper non-calcified kerogenous layer is characterised by up to 1% sulphur [1]. The in situ analysis of all the metals as a group represents a useful microbial fingerprint [2] and we will continue to explore it. Synchrotron Radiation X-Ray Fluorescence maps of high spatial resolution (< 0.3 µm) were recorded on a unique FIB section (15 x 10 x 3 µm3) of the JCMB. A 300 nm resolution was reached at 2500 eV on the ID21 scanning X-ray microscope (SXM) and a 120x165 (horizontal x vertical) nm at 17450 eV on ID22NI at the European Synchrotron Radiation Facility (ESRF). All maps reveal chemical heterogeneities not previously discernible by scanning the same FIB cut using micron resolution. The feasibility of high-resolution analyses with high flux on rock samples was first shown for samples that had in this respect an ideal hotspot geometry in a uniform silica matrix [3, 4]. Our FIB sample preparation ensures negligible thickness variations so quantitation of all the metals in the JCMB is presently only limited by the important intrinsic heterogeneity of the sample. Methods to deal with micrometer bulk heterogeneity have just been developed by performing redundant volumetric scans in fluorescence tomography to counterbalance the complex sample geometry [5]. An alternative methodology more adapted to the thin slice geometry is tested here. A relationship between the ratio of the Compton to Rayleigh (C-R) scatterings and the average atomic number (Zave), only established with unpolarized X-rays [6], was measured using fully polarized synchrotron beams [7]. C-R peaks measured on thick Astimex standards (1 mm) and those calculated from Monte-Carlo simulations of thick and thin (100 µm and 1 µm) samples having the same compositions were analyzed using a version of the PyMCA software [8] specially optimised for this purpose. The empirical relations of the type Zave = a•(C/R)b obtained for the three analyses sets provide a comprehensive set of calibrations suitable for any sample of any thickness. On the basis of these calibrations, we inferred positions and concentrations of undetected low-Z phases in the JCMB and further corrected the concentrations of the detected metals in the organic phases. 1. Westall F., et al., 2011. Earth & Planet. Sci. Lett., 310, 468-479. 2. Zerkle A L., et al., 2005. Am. J. Science, 305, 467-502. 3. Westphal A. J., et al., 2010. AIP Conference Proceedings, 1221, 131-138. 4. Bleuet P., et al., 2008. App. Phys. Lett., 92, 213111-1-3. 5. Golosio B., et al., 2003. Appl. Phys., 94, 145-157. 6. M. Haschke, 2003. PhD dissertation, T.U. Berlin. 7. Simionovici A. S., et al., 2010. Proceedings of the Meteoritical Society Conference, N.Y., USA. 8. Solé V.A., et al., 2006, Elsevier, 62, 63-68.

Distribution of Fecal Indicator Bacteria along the Malibu, California, Coastline

USGS Publications Warehouse

Izbicki, John

2011-01-01

Each year, over 550 million people visit California's public beaches. To protect beach-goers from exposure to waterborne disease, California state law requires water-quality monitoring for fecal indicator bacteria (FIB), such as enterococci and Escherichia coli (E. coli), at beaches having more than 50,000 yearly visitors. FIB are used to assess the microbiological quality of water because, although not typically disease causing, they are correlated with the occurrence of certain waterborne diseases. Tests show that FIB concentrations occasionally exceed U.S. Environmental Protection Agency (USEPA) public health standards for recreational water in Malibu Lagoon and at several Malibu beaches (Regional Water Quality Control Board, 2009). Scientists from the U.S. Geological Survey's (USGS) California Water Science Center are doing a study to identify the distribution and sources of FIB in coastal Malibu waters (fig. 1). The study methods were similar to those used in a study of FIB contamination on beaches in the Santa Barbara, California, area (Izbicki and others, 2009). This report describes the study approach and presents preliminary results used to evaluate the distribution and source of FIB in the Malibu area. Results of this study will help decision-makers address human health issues associated with FIB contamination in Malibu, and the methods used in this study can be used in other coastal areas affected by FIB contamination.

Microbial source tracking in shellfish harvesting waters in the Gulf of Nicoya, Costa Rica.

PubMed

Symonds, E M; Young, S; Verbyla, M E; McQuaig-Ulrich, S M; Ross, E; Jiménez, J A; Harwood, V J; Breitbart, M

2017-03-15

Current microbial water quality monitoring is generally limited to culture-based measurements of fecal indicator bacteria (FIB). Given the many possible sources of fecal pollution within a watershed and extra-intestinal FIB reservoirs, it is important to determine source(s) of fecal pollution as a means to improve water quality and protect public health. The principal objective of this investigation was to characterize the microbial water quality of shellfish harvesting areas in the Gulf of Nicoya, Costa Rica during 2015. In order to achieve this objective, the specificity and sensitivity of 11 existing microbial source tracking (MST) PCR assays, associated with cows (BacCow), dogs (BacCan, DogBac), domestic wastewater (PMMoV), general avian (GFD), gulls (Gull2), horses (HorseBac, HoF), humans (HF183, HPyV), and pigs (PF), were evaluated using domestic wastewater and animal fecal samples collected from the region. The sensitivity of animal-associated assays ranged from 13 to 100%, while assay specificity ranged from 38 to 100%. The specificity of pepper mild mottle virus (PMMoV) and human polyomavirus (HPyV) was 100% for domestic wastewater, as compared to 94% specificity of the HF183 Bacteroidales marker. PMMoV was identified as a useful domestic wastewater-associated marker, with concentrations as high as 1.1 × 10 5 copies/ml and 100% sensitivity and specificity. Monthly surface water samples collected from four shellfish harvesting areas were analyzed using culture-based methods for Escherichia coli as well as molecular methods for FIB and a suite of MST markers, which were selected for their specificity in the region. While culturable E. coli results suggested possible fecal pollution during the monitoring period, the absence of human/domestic wastewater-associated markers and low FIB concentrations determined using molecular methods indicated sufficient microbial water quality for shellfish harvesting. This is the first study to our knowledge to test the performance of MST markers in Costa Rica as well as in Central America. Given the lack of wastewater treatment and the presence of secondary sources of FIB, this study highlights the importance of an MST toolbox approach to characterize water quality in tropical regions. Furthermore, it confirms and extends the geographic range of PMMoV as an effective tool for monitoring domestic wastewater pollution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Associations between fecal indicator bacteria prevalence and demographic data in private water supplies in Virginia.

PubMed

Smith, Tamara; Krometis, Leigh-Anne H; Hagedorn, Charles; Lawrence, Annie H; Benham, Brian; Ling, Erin; Ziegler, Peter; Marmagas, Susan West

2014-12-01

Over 1.7 million Virginians rely on private water sources to provide household water. The heaviest reliance on these systems occurs in rural areas, which are often underserved with respect to available financial resources and access to environmental health education. This study aimed to identify potential associations between concentrations of fecal indicator bacteria (FIB) (coliforms, Escherichia coli) in over 800 samples collected at the point-of-use from homes with private water supply systems and homeowner-provided demographic data (household income and education). Of the 828 samples tested, 349 (42%) of samples tested positive for total coliform and 55 (6.6%) tested positive for E. coli. Source tracking efforts targeting optical brightener concentrations via fluorometry and the presence of a human-specific Bacteroides marker via quantitative real-time polymerase chain reaction (qPCR) suggest possible contamination from human septage in over 20 samples. Statistical methods implied that household income has an association with the proportion of samples positive for total coliform, though the relationship between education level and FIB is less clear. Further exploration of links between demographic data and private water quality will be helpful in building effective strategies to improve rural drinking water quality.

In situ probing the interior of single bacterial cells at nanometer scale

NASA Astrophysics Data System (ADS)

Liu, Boyin; Hemayet Uddin, Md; Ng, Tuck Wah; Paterson, David L.; Velkov, Tony; Li, Jian; Fu, Jing

2014-10-01

We report a novel approach to probe the interior of single bacterial cells at nanometre resolution by combining focused ion beam (FIB) and atomic force microscopy (AFM). After removing layers of pre-defined thickness in the order of 100 nm on the target bacterial cells with FIB milling, AFM of different modes can be employed to probe the cellular interior under both ambient and aqueous environments. Our initial investigations focused on the surface topology induced by FIB milling and the hydration effects on AFM measurements, followed by assessment of the sample protocols. With fine-tuning of the process parameters, in situ AFM probing beneath the bacterial cell wall was achieved for the first time. We further demonstrate the proposed method by performing a spatial mapping of intracellular elasticity and chemistry of the multi-drug resistant strain Klebsiella pneumoniae cells prior to and after it was exposed to the ‘last-line’ antibiotic polymyxin B. Our results revealed increased stiffness occurring in both surface and interior regions of the treated cells, suggesting loss of integrity of the outer membrane from polymyxin treatments. In addition, the hydrophobicity measurement using a functionalized AFM tip was able to highlight the evident hydrophobic portion of the cell such as the regions containing cell membrane. We expect that the proposed FIB-AFM platform will help in gaining deeper insights of bacteria-drug interactions to develop potential strategies for combating multi-drug resistance.

Differences in the Spectrum of Anti-Citrullinated Protein Antibody Fine Specificities Between Malaysian and Swedish Patients With Rheumatoid Arthritis: Implications for Disease Pathogenesis.

PubMed

Too, Chun Lai; Murad, Shahnaz; Hansson, Monika; Alm, Linda Mathsson; Dhaliwal, Jasbir Singh; Holmdahl, Rikard; Jakobsson, Per-Johan; Alfredsson, Lars; Klareskog, Lars; Rönnelid, Johan; Padyukov, Leonid

2017-01-01

Antibodies to the citrullinated protein antigens (ACPAs) are important in the diagnosis and pathogenesis of rheumatoid arthritis (RA). However, the prevalence of ACPAs with different fine specificities in different populations is unclear. This study sought to examine the fine specificity of the antibody responses toward citrullinated proteins in RA patients from Malaysia, an area where genetic and environmental determinants of RA are different from those in more frequently studied cohorts of Caucasian subjects. A multiplex analytic microarray system was used to analyze the occurrence of antibodies to 10 different citrullinated peptides (filaggrin [fil307-324], vimentin [Vim2-17, Vim60-75], fibrinogen [Fibα563-583, Fibα580-600, Fibβ36-52, Fibβ62-81a, Fibβ62-81b], enolase [Eno5-21], and type II collagen [CitCII355-378]) in serum samples from 4,089 RA patients (1,231 Malaysian and 2,858 Swedish) and 827 healthy control subjects (249 Malaysian and 578 Swedish). The positive reaction threshold for each peptide was set separately for each population based on a specificity of 98%. Distinct differences in the frequencies of 5 ACPA fine specificities (Vim60-75, Vim2-17, Fibβ62-81b, Eno5-21, and CitCII355-378) were found between the Malaysian and Swedish RA populations, despite a nearly identical percentage of patients in each population who were positive for anti-cyclic citrullinated peptide 2 antibodies. In Malaysian RA patients compared with Swedish RA patients, the frequencies of antibodies to Vim60-75 (54% versus 44%, corrected P [P corr ] = 1.06 × 10 -8 ) and CitCII355-378 (17% versus 13%, P corr  = 0.02) were significantly higher, while the frequencies of antibodies to Vim2-17 (25% versus 32%, P corr  = 1.91 × 10 -4 ), Fibβ62-81b (15% versus 30%, P corr  = 2.47 × 10 -22 ), and Eno5-21 (23% versus 50%, P corr  = 3.64 × 10 -57 ) were significantly lower. Serum ACPA fine specificities differ between RA patients in different populations, although the total proportions of individuals positive for ACPAs are similar. Differing patterns of ACPA fine specificity could be attributed to variations in genetic and/or environmental factors. © 2016 The Authors. Arthritis & Rheumatology published by Wiley Periodicals, Inc. on behalf of the American College of Rheumatology.

Long-term prognosis of patients with chronic hepatitis C who did not receive interferon-based therapy: causes of death and analysis based on the FIB-4 index.

PubMed

Tada, Toshifumi; Kumada, Takashi; Toyoda, Hidenori; Kiriyama, Seiki; Tanikawa, Makoto; Hisanaga, Yasuhiro; Kanamori, Akira; Kitabatake, Shusuke; Yama, Tsuyoki; Tanaka, Junko

2016-04-01

Interferon (IFN)-based therapy has been reported to reduce the liver-related mortality rate in patients with chronic hepatitis C virus (HCV) infection. However, predictors of survival and causes of death, including non-liver-related causes, have not been sufficiently investigated in chronic HCV patients who have not received IFN-based therapy. A total of 1723 patients with chronic HCV infection who were not treated with IFN-based therapy were enrolled. Survival from liver-related diseases and non-liver-related diseases and causes of death were analyzed on the basis of the fibrosis-4 (FIB-4) index, an index of liver fibrosis. The median follow-up duration was 10.3 years. Of 465 patients who died during the follow-up period, 48.4 % died of liver-related diseases; of the remainder, 51.6 % died of non-liver-related diseases. On the basis of FIB-4 index, the liver-related mortality rate increased as the FIB-4 index increased: 16.1 % in the FIB-4 index < 1.45 group, 36.7 % in the 1.45 ≤ FIB-4 index ≤ 3.25 group, and 58.7 % in the FIB-4 index > 3.25 group (p < 0.001). Conversely, the non-liver-related mortality rate decreased as the FIB-4 index increased: 83.9, 63.3, and 41.3 %, respectively (p = 0.001). In the multivariate analysis, a FIB-4 index greater than 3.25 was identified as a risk factor independently associated with both liver-related death (hazard ratio 13.020; 95 % confidence interval 4.155-40.770) and non-liver-related death (hazard ratio 1.667; 95 % confidence interval 1.188-2.340). Patients with chronic HCV infection and an elevated FIB-4 index may benefit from monitoring not only for the development of liver-related diseases but also for the development of non-liver-related diseases.

High liver fibrosis index FIB-4 is highly predictive of hepatocellular carcinoma in chronic hepatitis B carriers.

PubMed

Suh, Beomseok; Park, Sehhoon; Shin, Dong Wook; Yun, Jae Moon; Yang, Hyung-Kook; Yu, Su Jong; Shin, Cheong-Il; Kim, Jin-Soo; Ahn, Eunmi; Lee, Hyejin; Park, Jin Ho; Cho, BeLong

2015-04-01

Screening for hepatocellular carcinoma (HCC) is clinically important given that its early detection has remarkable survival benefits. We investigated the possible role of FIB-4, a recently developed noninvasive marker for liver fibrosis based on routine laboratory tests, as a clinical indicator for predicting future HCC among hepatitis B surface antigen (HBsAg) carriers. Our retrospective cohort study involved 986 Korean HBsAg carriers 40 years of age or older who visited Seoul National University Hospital for a health checkup. National medical service claims data were used to determine HCC incidence. Median follow-up time was 5.4 years (interquartile range: 4.4 years). Adjusted for age, sex, body mass index, smoking, alcohol, and antiviral medication for hepatitis B, compared to subjects with FIB-4 <1.25, subjects with 1.7≤ FIB-4 <2.4 showed an adjusted hazard ratio (aHR) of 4.57 (95% confidence interval [CI]: 1.50-13.92) and subjects with FIB-4 ≥2.4 showed an aHR of 21.34 (95% CI: 7.73-58.92) for HCC incidence. FIB-4 was shown to have incremental predictive value to ultrasonographic liver cirrhosis for HCC incidence (C-index: 0.701 vs. 0.831; P = 0.001). FIB-4 was also better predictive of HCC incidence, compared to that of ultrasonographic liver cirrhosis (C-index: 0.775 vs. 0.701; P = 0.040). High FIB-4 is a highly predictive risk factor for HCC incidence among Korean HBsAg carriers. FIB-4 is a promising, easily applicable, and cost-effective clinical tool in identifying a subpopulation of HBsAg carriers who are at heightened risk. Our study needs to be replicated in larger future studies on various ethnic groups; nonetheless, our study suggests that FIB-4 may play a valuable role in HCC screening among HBsAg carriers. © 2014 by the American Association for the Study of Liver Diseases.

Comparative genomic analysis and characterization of incompatibility group FIB plasmid encoded virulence factors of Salmonella enterica isolated from food sources.

PubMed

Khajanchi, Bijay K; Hasan, Nur A; Choi, Seon Young; Han, Jing; Zhao, Shaohua; Colwell, Rita R; Cerniglia, Carl E; Foley, Steven L

2017-08-02

The degree to which the chromosomal mediated iron acquisition system contributes to virulence of many bacterial pathogens is well defined. However, the functional roles of plasmid encoded iron acquisition systems, specifically Sit and aerobactin, have yet to be determined for Salmonella spp. In a recent study, Salmonella enterica strains isolated from different food sources were sequenced on the Illumina MiSeq platform and found to harbor the incompatibility group (Inc) FIB plasmid. In this study, we examined sequence diversity and the contribution of factors encoded on the IncFIB plasmid to the virulence of S. enterica. Whole genome sequences of seven S. enterica isolates were compared to genomes of serovars of S. enterica isolated from food, animal, and human sources. SeqSero analysis predicted that six strains were serovar Typhimurium and one was Heidelberg. Among the S. Typhimurium strains, single nucleotide polymorphism (SNP)-based phylogenetic analyses revealed that five of the isolates clustered as a single monophyletic S. Typhimurium subclade, while one of the other strains branched with S. Typhimurium from a bovine source. DNA sequence based phylogenetic diversity analyses showed that the IncFIB plasmid-encoded Sit and aerobactin iron acquisition systems are conserved among bacterial species including S. enterica. The IncFIB plasmid was transferred to an IncFIB plasmid deficient strain of S. enterica by conjugation. The transconjugant SE819::IncFIB persisted in human intestinal epithelial (Caco-2) cells at a higher rate than the recipient SE819. Genes of the Sit and aerobactin operons in the IncFIB plasmid were differentially expressed in iron-rich and iron-depleted growth media. Minimal sequence diversity was detected in the Sit and aerobactin operons in the IncFIB plasmids present among different bacterial species, including foodborne Salmonella strains. IncFIB plasmid encoded factors play a role during infection under low-iron conditions in host cells.

TEM Observation of the Ti Interlayer Between SiC Substrates During Diffusion Bonding

NASA Technical Reports Server (NTRS)

Tsuda, Hiroshi; Mori, Shigeo; Halbig, Michael C.; Singh, Mori

2012-01-01

Diffusion bonding was carried out to join SiC to SiC substrates using titanium interlayers. In this study, 10 m and 20 m thick physical vapor deposited (PVD) Ti surface coatings, and 10 and 20 m thick Ti foils were used. Diffusion bonding was performed at 1250 C for PVD Ti coatings and 1200 C for Ti foil. This study investigates the microstructures of the phases formed during diffusion bonding through TEM and selected-area diffraction analysis of a sample prepared with an FIB, which allows samples to be taken from the reacted area. In all samples, Ti3SiC2, Ti5Si3Cx and TiSi2 phases were identified. In addition, TiC and unknown phases also appeared in the samples in which Ti foils were used as interlayers. Furthermore, Ti3SiC2 phases show high concentration and Ti5Si3Cx formed less when samples were processed at a higher temperature and thinner interlayer samples were used. It appears that the formation of microcracks is caused by the presence of intermediate phase Ti5Si3Cx, which has anisotropic thermal expansion, and by the presence of an unidentified Ti-Si-C ternary phase with relatively low Si content.

Background of the FIB-4 index in Japanese non-alcoholic fatty liver disease.

PubMed

Wada, Takashi; Zeniya, Mikio

2015-01-01

We investigated the distribution and characteristics of the FIB-4 index of liver fibrosis in 1,441 Japanese men (age 50.7±10.2 years) and 304 women (age 53.9±10.3 years) who underwent comprehensive general health checkups and were identified as having non-alcoholic fatty liver disease. With respect to the FIB-4 index, differences according to sex, metabolic indices, and ultrasonic findings were investigated. Among 9,255 individuals who underwent comprehensive general health checkups, 2,750 (29.8%) were found to have mild fatty liver or fatty liver based on ultrasound findings. After excluding patients who consumed ≥150 g alcohol/week (818 individuals), those testing positive for hepatitis B surface antigens or hepatitis C virus antibody (184 individuals), and those for whom data were insufficient (three individuals), we investigated the FIB-4 indices in the remaining 1,745 subjects. There were no sex differences in the FIB-4 index. A total of 1,370 patients (78.5%) exhibited a low cut-off index (COI) (<1.30), 357 (20.5%), exhibited an indeterminate COI (1.30-2.67), and 18 (1.0%) exhibited a high COI (>2.67). There were no associations between the FIB-4 index and the constituent factors of metabolic syndrome. In contrast, there was a significant difference in the ln FIB-4 index between the patients with and without mild fatty liver or fatty liver on ultrasound among men (0.006±0.43 and -0.092±0.39, p<0.001), but not women. The FIB-4 index was is significantly lower in men, but not women, with fatty liver. The FIB-4 index must be calculated separately during medical checkups and evaluated in conjunction with ultrasound findings.

Utility of the FIB-4 Index for hepatocarcinogenesis in hepatitis C virus carriers with normal alanine aminotransferase levels.

PubMed

Ito, T; Kumada, T; Toyoda, H; Tada, T; Kiriyama, S; Tanikawa, M; Hisanaga, Y; Kanamori, A; Kitabatake, S

2015-10-01

The FIB-4 index is a simple formula using age, aspartate aminotransferase, alanine aminotransferase (ALT) and platelet count to evaluate liver fibrosis. We investigated the ability of the FIB-4 index for hepatocarcinogenesis in hepatitis C virus (HCV) carriers with normal ALT levels. A total of 516 patients with ALT levels persistently at or below 40 IU/L during an observation period of over 3 years were included. Factors associated with the development of HCC were determined. Hepatocellular carcinoma (HCC) developed in 60 of 516 patients (11.6%). The incidence rate of HCC at 5 and 10 years was 2.6% and 17.6%, respectively. When patients were categorized according to the FIB-4 index as ≤ 2.0 (n = 226), >2.0 and ≤ 4.0 (n = 169), and > 4.0 (n = 121), the cumulative incidence of HCC at 5 years was 0.5%, 1.3% and 8.0%, respectively, and 2.8%, 25.6% and 37.1% at 10 years, respectively. Patients with FIB-4 index >4.0 were at the highest risk (P < 0.001). Factors that were significantly associated with HCC in the multivariate analysis were FIB-4 index >2.0 (hazard ratio (HR), 7.690), FIB-4 index >4.0 (HR, 8.991), α-fetoprotein (AFP) >5 ng/mL (HR, 2.742), AFP >10 ng/mL (HR, 4.915) and total bilirubin >1.2 mg/dL (HR, 2.142). A scoring system for hepatocarcinogenesis that combines the FIB-4 index and AFP predicted patient outcomes with excellent discriminative ability. The FIB-4 index is strongly associated with the risk of HCC in HCV carriers with normal ALT levels. © 2015 John Wiley & Sons Ltd.

The FIB-4 index is a significant prognostic factor in patients with non-B non-C hepatocellular carcinoma after curative surgery.

PubMed

Okamura, Yukiyasu; Ashida, Ryo; Yamamoto, Yusuke; Ito, Takaaki; Sugiura, Teiichi; Bekku, Emima; Aramaki, Takeshi; Uesaka, Katsuhiko

2016-03-01

The aspartate aminotransferase to platelet ratio index (APRI) and fibrosis-4 (FIB-4) index were developed as a non-invasive parameter for predicting liver fibrosis. This study aimed to validate the APRI and FIB-4 indexes in patients treated with curative therapy for non-B non-C (NBNC) hepatocellular carcinoma (HCC). Accumulated database comprising 399 patients who underwent hepatectomy was reviewed retrospectively. Analyses were performed to evaluate whether the APRI and FIB-4 indexes are predictors of liver cirrhosis and/or the prognosis in patients with NBNC-HCC. Forty-seven patients with NBNC-HCC who underwent curative radiofrequency ablation therapy (RFA) in the same period were enrolled as the validation set. The APRI and FIB-4 indexes were significantly higher in the cirrhosis group than in the no-cirrhosis group (P = 0.001 and P < 0.001, respectively). A receiver operating characteristic curve analysis showed that the FIB-4 index was more accurate in predicting background liver cirrhosis than the APRI. According to a multivariate analysis, an FIB-4 index larger than 2.7 (hazard ratio 2.11 and 2.21, 95 % confidence interval 1.06-4.18 and 1.38-3.54, P = 0.033 and P = 0.001) remained significant independent predictors of overall and recurrence-free survival, respectively. The present findings showed that the FIB-4 index is a significant predictor of background liver cirrhosis and the prognosis after curative resection for NBNB-HCC.

Porosity and permeability determination of organic-rich Posidonia shales based on 3-D analyses by FIB-SEM microscopy

NASA Astrophysics Data System (ADS)

Grathoff, Georg H.; Peltz, Markus; Enzmann, Frieder; Kaufhold, Stephan

2016-07-01

The goal of this study is to better understand the porosity and permeability in shales to improve modelling fluid and gas flow related to shale diagenesis. Two samples (WIC and HAD) were investigated, both mid-Jurassic organic-rich Posidonia shales from Hils area, central Germany of different maturity (WIC R0 0.53 % and HAD R0 1.45 %). The method for image collection was focused ion beam (FIB) microscopy coupled with scanning electron microscopy (SEM). For image and data analysis Avizo and GeoDict was used. Porosity was calculated from segmented 3-D FIB based images and permeability was simulated by a Navier Stokes-Brinkman solver in the segmented images. Results show that the quantity and distribution of pore clusters and pores (≥ 40 nm) are similar. The largest pores are located within carbonates and clay minerals, whereas the smallest pores are within the matured organic matter. Orientation of the pores calculated as pore paths showed minor directional differences between the samples. Both samples have no continuous connectivity of pore clusters along the axes in the x, y, and z direction on the scale of 10 to 20 of micrometer, but do show connectivity on the micrometer scale. The volume of organic matter in the studied volume is representative of the total organic carbon (TOC) in the samples. Organic matter does show axis connectivity in the x, y, and z directions. With increasing maturity the porosity in organic matter increases from close to 0 to more than 5 %. These pores are small and in the large organic particles have little connection to the mineral matrix. Continuous pore size distributions are compared with mercury intrusion porosimetry (MIP) data. Differences between both methods are caused by resolution limits of the FIB-SEM and by the development of small pores during the maturation of the organic matter. Calculations show no permeability when only considering visible pores due to the lack of axis connectivity. Adding the organic matter with a background permeability of 1 × 10-21 m2 to the calculations, the total permeability increased by up to 1 order of magnitude for the low mature and decreases slightly for the overmature sample from the gas window. Anisotropy of permeability was observed. Permeability coefficients increase by 1 order of magnitude if simulations are performed parallel to the bedding. Our results compare well with experimental data from the literature suggesting that upscaling may be possible in the future as soon as maturity dependent organic matter permeability coefficients can be determined.

Surface effects on exciton diffusion in non polar ZnO/ZnMgO heterostructures

NASA Astrophysics Data System (ADS)

Sakr, G.; Sartel, C.; Sallet, V.; Lusson, A.; Patriarche, G.; Galtier, P.; Barjon, J.

2017-12-01

The diffusion of excitons injected in ZnO/Zn0.92Mg0.08O quantum well heterostructures grown by metal-organic-vapor-phase-epitaxy on non-polar ZnO substrates is investigated at room temperature. Cathodoluminescence linescans in a field-emission-gun scanning-electron-microscope are performed across cleaved cross-sections. A 55 nm diffusion length is assessed for excitons in bulk ZnMgO. When prepared as small angle bevels using focused ion beam (FIB), the effective diffusion length of excitons is shown to decrease down to 8 nm in the thinner part of the slab. This effect is attributed to non-radiative surface recombinations, with a 7  ×  104 cm s-1 recombination velocity estimated at the FIB-machined ZnMgO surface. The strong reduction of the diffusion extent in such thin lamellae usually used for transmission electron microscopy could be use improve the spatial resolution of cathodoluminescence images, often limited by diffusion processes.

Polymerization of room-temperature ionic liquid monomers by electron beam irradiation with the aim of fabricating three-dimensional micropolymer/nanopolymer structures.

PubMed

Minamimoto, H; Irie, H; Uematsu, T; Tsuda, T; Imanishi, A; Seki, S; Kuwabata, S

2015-04-14

A novel method for fabricating microsized and nanosized polymer structures from a room-temperature ionic liquid (RTIL) on a Si substrate was developed by the patterned irradiation of an electron beam (EB). An extremely low vapor pressure of the RTIL, 1-allyl-3-ethylimidazolium bis((trifluoromethane)sulfonyl)amide, allows it to be introduced into the high-vacuum chamber of an electron beam apparatus to conduct a radiation-induced polymerization in the nanoregion. We prepared various three-dimensional (3D) micro/nanopolymer structures having high aspect ratios of up to 5 with a resolution of sub-100 nm. In addition, the effects of the irradiation dose and beam current on the physicochemical properties of the deposited polymers were investigated by recording the FT-IR spectra and Young's modulus. Interestingly, the overall shapes of the obtained structures were different from those prepared in our recent study using a focused ion beam (FIB) even if the samples were irradiated in a similar manner. This may be due to the different transmission between the two types of beams as discussed on the basis of the theoretical calculations of the quantum beam trajectories. Perceptions obtained in this study provide facile preparation procedures for the micro/nanostructures.

Epitaxial graphene growth on FIB patterned 3C-SiC nanostructures on Si (111): reducing milling damage.

PubMed

Amjadipour, Mojtaba; MacLeod, Jennifer; Lipton-Duffin, Josh; Iacopi, Francesca; Motta, Nunzio

2017-08-25

Epitaxial growth of graphene on SiC is a scalable procedure that does not require any further transfer step, making this an ideal platform for graphene nanostructure fabrication. Focused ion beam (FIB) is a very promising tool for exploring the reduction of the lateral dimension of graphene on SiC to the nanometre scale. However, exposure of graphene to the Ga + beam causes significant surface damage through amorphisation and contamination, preventing epitaxial graphene growth. In this paper we demonstrate that combining a protective silicon layer with FIB patterning implemented prior to graphene growth can significantly reduce the damage associated with FIB milling. Using this approach, we successfully achieved graphene growth over 3C-SiC/Si FIB patterned nanostructures.

Nanoscale Pore Imaging and Pore Scale Fluid Flow Modeling in Chalk

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

Tomutsa, Liviu; Silin, Dmitriy

2004-08-19

For many rocks of high economic interest such as chalk, diatomite, tight gas sands or coal, nanometer scale resolution is needed to resolve the 3D-pore structure, which controls the flow and trapping of fluids in the rocks. Such resolutions cannot be achieved with existing tomographic technologies. A new 3D imaging method, based on serial sectioning and using the Focused Ion Beam (FIB) technology has been developed. FIB allows for the milling of layers as thin as 10 nanometers by using accelerated Ga+ ions to sputter atoms from the sample surface. After each milling step, as a new surface is exposed,more » a 2D image of this surface is generated. Next, the 2D images are stacked to reconstruct the 3D pore or grain structure. Resolutions as high as 10 nm are achievable using such a technique. A new robust method of pore-scale fluid flow modeling has been developed and applied to sandstone and chalk samples. The method uses direct morphological analysis of the pore space to characterize the petrophysical properties of diverse formations. Not only petrophysical properties (porosity, permeability, relative permeability and capillary pressures) can be computed but also flow processes, such as those encountered in various IOR approaches, can be simulated. Petrophysical properties computed with the new method using the new FIB data will be presented. Present study is a part of the development of an Electronic Core Laboratory at LBNL/UCB.« less

3D-characterization of the veneer-zirconia interface using FIB nano-tomography.

PubMed

Mainjot, Amélie K; Douillard, Thierry; Gremillard, Laurent; Sadoun, Michaël J; Chevalier, Jérôme

2013-02-01

The phenomena occurring during zirconia frameworks veneering process are not yet fully understood. In particular the study of zirconia behavior at the interface with the veneer remains a challenge. However this interface has been reported to act on residual stress in the veneering ceramic, which plays a significant role in clinical failures such as chipping. The objective of this study was thus to investigate the veneer-zirconia interface using a recent 3D-analysis tool and to confront these observations to residual stress measurements in the veneering ceramic. Two cross-sectioned bilayered disc samples (veneer on zirconia), exhibiting different residual stress profiles in the veneering ceramic, were investigated using 2D and 3D imaging (respectively Scanning Electron Microscopy (SEM) and Focused Ion Beam nanotomography (FIB-nt), associated with chemical analysis by Energy Dispersive X-ray Spectroscopy (EDS). The observations did not reveal any structural change in the bulk of zirconia layer of both samples. However the presence of structural alterations and sub-surface microcracks were highlighted in the first micrometer of zirconia surface, exclusively for the sample exhibiting interior tensile stress in the veneering ceramic. No interdiffusion phenomena were observed. FIB nanotomography was proven to be a powerful technique to study the veneer-zirconia interface. The determination of the origin and the nature of zirconia alterations need to be further studied. The results of the present study support the hypothesis that zirconia surface property changes could be involved in the development of tensile stress in the veneering ceramic, increasing the risk of chipping. Copyright © 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Simulation of the planetary interior differentiation processes in the laboratory.

PubMed

Fei, Yingwei

2013-11-15

A planetary interior is under high-pressure and high-temperature conditions and it has a layered structure. There are two important processes that led to that layered structure, (1) percolation of liquid metal in a solid silicate matrix by planet differentiation, and (2) inner core crystallization by subsequent planet cooling. We conduct high-pressure and high-temperature experiments to simulate both processes in the laboratory. Formation of percolative planetary core depends on the efficiency of melt percolation, which is controlled by the dihedral (wetting) angle. The percolation simulation includes heating the sample at high pressure to a target temperature at which iron-sulfur alloy is molten while the silicate remains solid, and then determining the true dihedral angle to evaluate the style of liquid migration in a crystalline matrix by 3D visualization. The 3D volume rendering is achieved by slicing the recovered sample with a focused ion beam (FIB) and taking SEM image of each slice with a FIB/SEM crossbeam instrument. The second set of experiments is designed to understand the inner core crystallization and element distribution between the liquid outer core and solid inner core by determining the melting temperature and element partitioning at high pressure. The melting experiments are conducted in the multi-anvil apparatus up to 27 GPa and extended to higher pressure in the diamond-anvil cell with laser-heating. We have developed techniques to recover small heated samples by precision FIB milling and obtain high-resolution images of the laser-heated spot that show melting texture at high pressure. By analyzing the chemical compositions of the coexisting liquid and solid phases, we precisely determine the liquidus curve, providing necessary data to understand the inner core crystallization process.

Simulation of the Planetary Interior Differentiation Processes in the Laboratory

PubMed Central

Fei, Yingwei

2013-01-01

A planetary interior is under high-pressure and high-temperature conditions and it has a layered structure. There are two important processes that led to that layered structure, (1) percolation of liquid metal in a solid silicate matrix by planet differentiation, and (2) inner core crystallization by subsequent planet cooling. We conduct high-pressure and high-temperature experiments to simulate both processes in the laboratory. Formation of percolative planetary core depends on the efficiency of melt percolation, which is controlled by the dihedral (wetting) angle. The percolation simulation includes heating the sample at high pressure to a target temperature at which iron-sulfur alloy is molten while the silicate remains solid, and then determining the true dihedral angle to evaluate the style of liquid migration in a crystalline matrix by 3D visualization. The 3D volume rendering is achieved by slicing the recovered sample with a focused ion beam (FIB) and taking SEM image of each slice with a FIB/SEM crossbeam instrument. The second set of experiments is designed to understand the inner core crystallization and element distribution between the liquid outer core and solid inner core by determining the melting temperature and element partitioning at high pressure. The melting experiments are conducted in the multi-anvil apparatus up to 27 GPa and extended to higher pressure in the diamond-anvil cell with laser-heating. We have developed techniques to recover small heated samples by precision FIB milling and obtain high-resolution images of the laser-heated spot that show melting texture at high pressure. By analyzing the chemical compositions of the coexisting liquid and solid phases, we precisely determine the liquidus curve, providing necessary data to understand the inner core crystallization process. PMID:24326245

Fibrinogen, Riboflavin, and UVA to Immobilize a Corneal Flap—Conditions for Tissue Adhesion

PubMed Central

Littlechild, Stacy L.; Brummer, Gage; Zhang, Yuntao; Conrad, Gary W.

2012-01-01

Purpose. Laser-assisted in situ keratomileus (LASIK) creates a permanent flap that remains non-attached to the underlying laser-modified stroma. This lack of permanent adhesion is a liability. To immobilize a corneal flap, a protocol using fibrinogen (FIB), riboflavin (RF), and ultraviolet (UVA) light (FIB+RF+UVA) was devised to re-adhere the flap to the stroma. Methods. A model flap was created using rabbit (Oryctolagus cuniculus) and shark (Squalus acanthias) corneas. Solutions containing FIB and RF were applied between corneal strips as glue. Experimental corneas were irradiated with long wavelength (365 nm) UVA. To quantify adhesive strength between corneal strips, the glue-tissue interface was subjected to a constant force while a digital force gauge recorded peak tension. Results. In the presence of FIB, substantive non-covalent interactions occurred between rabbit corneal strips. Adhesiveness was augmented if RF and UVA also were applied, suggesting formation of covalent bonds. Additionally, exposing both sides of rabbit corneas to UVA generated more adhesion than exposure from one side, suggesting that RF in the FIB solution catalyzes formation of covalent bonds at only the interface between stromal molecules and FIB closest to the UVA. In contrast, in the presence of FIB, shark corneal strips interacted non-covalently more substantively than those of rabbits, and adhesion was not augmented by applying RF+UVA, from either or both sides. Residual RF could be rinsed away within 1 hour. Conclusions. Glue solution containing FIB and RF, together with UVA treatment, may aid immobilization of a corneal flap, potentially reducing risk of flap dislodgement. PMID:22589434

Validation of APRI and FIB-4 score in an Antwerp cohort of chronic hepatitis C patients.

PubMed

Verlinden, Wim; Bourgeois, Stefan; De Maeyer, Marc; Vonghia, Luisa; Vanwolleghem, Thomas; Michielsen, Peter; Francque, Sven

2015-12-01

Evaluation of liver fibrosis in chronic hepatitis C patients guides clinical decision-making. The aim of this study is to validate APRI and FIB-4, two easily calculated noninvasive tests to predict fibrosis, in chronic HCV patients using biopsy as a gold standard and to compare accuracy between HCV monoinfected and HIV/HCV coinfected patients. We retrospectively studied HCV patients of two centres who underwent liver biopsy. Liver fibrosis was staged according to METAVIR. 136 patients were included. The AUROC of FIB-4 (0.896) to discriminate F0-F2 vs. F3-F4 was significantly higher (p=0.0186) than the AUROC of APRI (0.842). The difference in AUROC between HIV-negative and positive patients was not significant for APRI (p=0.471), nor for FIB-4 (p=0.495). Performance status was lower in HIV-positive patients with 46.7% and 69.0% of patients correctly classified using APRI and FIB-4, compared to 56.6% and 73.6% in HIV-negative patients, respectively. Conversion of transaminase values from one hospital to the other did not significantly change the AUROC of FIB-4 (p=0.928). APRI and FIB-4 have a better performance status in HCV monoinfected patients compared to HIV/HCV coinfected patients. FIB-4 has a better AUROC compared to APRI and is the preferred noninvasive fibrosis score to discriminate between F0-F2 and F3-F4. Different hospitals should use their local absolute serum transaminase values without conversion. © Acta Gastro-Enterologica Belgica.

An integrated evaluation of some faecal indicator bacteria (FIB) and chemical markers as potential tools for monitoring sewage contamination in subtropical estuaries.

PubMed

Cabral, Ana Caroline; Stark, Jonathan S; Kolm, Hedda E; Martins, César C

2018-04-01

Sewage input and the relationship between chemical markers (linear alkylbenzenes and coprostanol) and fecal indicator bacteria (FIB, Escherichia coli and enterococci), were evaluated in order to establish thresholds values for chemical markers in suspended particulate matter (SPM) as indicators of sewage contamination in two subtropical estuaries in South Atlantic Brazil. Both chemical markers presented no linear relationship with FIB due to high spatial microbiological variability, however, microbiological water quality was related to coprostanol values when analyzed by logistic regression, indicating that linear models may not be the best representation of the relationship between both classes of indicators. Logistic regression was performed with all data and separately for two sampling seasons, using 800 and 100 MPN 100 mL -1 of E. coli and enterococci, respectively, as the microbiological limits of sewage contamination. Threshold values of coprostanol varied depending on the FIB and season, ranging between 1.00 and 2.23 μg g -1 SPM. The range of threshold values of coprostanol for SPM are relatively higher and more variable than those suggested in literature for sediments (0.10-0.50 μg g -1 ), probably due to higher concentration of coprostanol in SPM than in sediment. Temperature may affect the relationship between microbiological indicators and coprostanol, since the threshold value of coprostanol found here was similar to tropical areas, but lower than those found during winter in temperate areas, reinforcing the idea that threshold values should be calibrated for different climatic conditions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Three-dimensional patterning in polymer optical waveguides using focused ion beam milling

NASA Astrophysics Data System (ADS)

Kruse, Kevin; Burrell, Derek; Middlebrook, Christopher

2016-07-01

Waveguide (WG) photonic-bridge taper modules are designed for symmetric planar coupling between silicon WGs and single-mode fibers (SMFs) to minimize photonic chip and packaging footprint requirements with improving broadband functionality. Micromachined fabrication and evaluation of polymer WG tapers utilizing high-resolution focused ion beam (FIB) milling is performed and presented. Polymer etch rates utilizing the FIB and optimal methods for milling polymer tapers are identified for three-dimensional patterning. Polymer WG tapers with low sidewall roughness are manufactured utilizing FIB milling and optically tested for fabrication loss. FIB platforms utilize a focused beam of ions (Ga+) to etch submicron patterns into substrates. Fabricating low-loss polymer WG taper prototypes with the FIB before moving on to mass-production techniques provides theoretical understanding of the polymer taper and its feasibility for connectorization devices between silicon WGs and SMFs.

A drug-like antagonist inhibits thyrotropin receptor-mediated stimulation of cAMP production in Graves' orbital fibroblasts.

PubMed

Neumann, Susanne; Pope, Arthur; Geras-Raaka, Elizabeth; Raaka, Bruce M; Bahn, Rebecca S; Gershengorn, Marvin C

2012-08-01

Fibroblasts (FIBs) within the retro-orbital space of patients with Graves' disease (GOFs) express thyrotropin receptors (TSHRs) and are thought to be an orbital target of TSHR-stimulating autoantibodies in Graves' ophthalmopathy (GO). Recently, we developed a low molecular weight, drug-like TSHR antagonist (NCGC00229600) that inhibited TSHR activation in a model cell system overexpressing TSHRs and in normal human thyrocytes expressing endogenous TSHRs. Herein, we test the hypothesis that NCGC00229600 will inhibit activation of TSHRs endogenously expressed in GOFs. Three strains of GOFs, previously obtained from patients with GO, were studied as undifferentiated FIBs and after differentiation into adipocytes (ADIPs), and another seven strains were studied only as FIBs. ADIP differentiation was monitored by morphology and measurement of adiponectin mRNA. FIBs and ADIPs were treated with the TSH- or TSHR-stimulating antibody M22 in the absence or presence of NCGC00229600 and TSHR activation was monitored by cAMP production. FIBs contained few if any lipid vesicles and undetectable levels of adiponectin mRNA, whereas ADIPs exhibited abundant lipid vesicles and levels of adiponectin mRNA more than 250,000 times greater than FIBs; TSHR mRNA levels were 10-fold higher in ADIPs than FIBs. FIBs exhibited higher absolute levels of basal and forskolin-stimulated cAMP production than ADIPs. Consistent with previous findings, TSH stimulated cAMP production in the majority of ADIP strains and less consistently in FIBs. Most importantly, NCGC00229600 reduced both TSH- and M22-stimulated cAMP production in GOFs. These data confirm previous findings that TSHR activation may cause increased cAMP production in GOFs and show that NCGC00229600 can inhibit TSHR activation in GOFs. These findings suggest that drug-like TSHR antagonists may have a role in treatment of GO.

Validation of the FIB-4 index for evaluation of fibrosis in patients with recurrent hepatitis C after living donor liver transplantation: A single center experience.

PubMed

Kitajima, Toshihiro; Kaido, Toshimi; Hamaguchi, Yuhei; Yagi, Shintaro; Taura, Kojiro; Fujimoto, Yasuhiro; Hatano, Etsuro; Okajima, Hideaki; Haga, Hironori; Uemoto, Shinji

2016-07-01

The FIB-4 index has been proposed as a simple, non-invasive surrogate marker of liver fibrosis in patients with hepatitis C virus (HCV). However, the utility of FIB-4 in HCV positive patients after living donor liver transplantation (LDLT) has not been assessed. The aim of this study was to evaluate the efficacy of FIB-4 in the detection of significant liver graft fibrosis caused by recurrent HCV infection after LDLT compared with other simple fibrosis markers. A total of 259 liver biopsies (LB) with evidence of recurrent HCV were taken from 110 HCV positive LDLT patients who had undergone concomitant splenectomy before administration of antiviral therapy. In LB performed at 3 months or later after LT (n = 202, subject group), FIB-4 was compared between fibrosis stages and the accuracy of FIB-4 in predicting significant fibrosis (METAVIR, F ≥ 2) was assessed compared with aspartate aminotransferase (AST) to alanine aminotransferase (ALT) ratio, age-platelet index, and AST to platelet ratio index (APRI). FIB-4 was significantly different between all fibrosis stages (F0 and F1-F4, P = 0.022; F0/1 and F2-F4, P < 0.0005; and F0-F2 and F3F4, P = 0.034) and provided the best area under the receiver-operator curve (AUROC) compared with other markers (FIB-4, 0.711; APRI, 0.693; age-platelet index, 0.663; and AST to ALT ratio, 0.562). The optimal cut-off value to identify significant fibrosis was 2.20 with 65% sensitivity and 69% specificity. FIB-4 is a more reliable marker for diagnosing significant liver fibrosis than APRI, age-platelet index, and AST to ALT ratio in LDLT patients with HCV. © 2015 The Japan Society of Hepatology.

Comparing the efficiency of Fib-4, Egy-score, APRI, and GUCI in liver fibrosis staging in Egyptians with chronic hepatitis C.

PubMed

Cordie, Ahmed; Salama, Ahmed; El-Sharkawy, Marwa; El-Nahaas, Saeed M; Khairy, Marwa; Elsharkawy, Aisha; Hassany, Mohamed; Esmat, Gamal

2018-06-01

Assessment of hepatic fibrosis in chronic hepatitis C virus patients by liver biopsy is not widely accepted despite its accuracy, being invasive, carrying complications, and adding cost. This paved the way to development and use of non-invasive markers of fibrosis in diagnosis of hepatic fibrosis. We aimed at evaluating the efficiency of Fib-4, Egy-score, Aspartate-to-platelet ratio index (APRI), and Göteborg University Cirrhosis Index (GUCI) in comparison to liver biopsy, in the assessment of hepatic fibrosis in chronic hepatitis C patients. This was a cross sectional study including 200 chronic HCV patients were divided into two groups according to stage of fibrosis (Metavir score) into non-significant fibrosis (1.27, APRI >0.48, Egy-score >0.73, and GUCI >0.57 significantly predict significant fibrosis (P < 0.01). Fib-4 carries the best performance and significant reliability with AUROC 0.783, sensitivity 74%, specificity 69%, PPV 0.55, and NPV 0.86. The addition of BMI to Fib-4 improved the significant fibrosis AUROC curve performance but did not reach statistical significant improvement. We concluded that age and BMI are good predictors of hepatic fibrosis. Fib-4 (>1.27) is the best method of prediction of significant fibrosis compared to Egy-score, APRI, and GUCI. Addition of BMI to Fib-4 did not improve diagnostic value of Fib-4. © 2018 Wiley Periodicals, Inc.

Reducing Router Forwarding Table Size Using Aggregation and Caching

ERIC Educational Resources Information Center

Liu, Yaoqing

2013-01-01

The fast growth of global routing table size has been causing concerns that the Forwarding Information Base (FIB) will not be able to fit in existing routers' expensive line-card memory, and upgrades will lead to a higher cost for network operators and customers. FIB Aggregation, a technique that merges multiple FIB entries into one, is probably…

Superconducting properties of NbN film, bridge and meanders

NASA Astrophysics Data System (ADS)

Joshi, Lalit M.; Verma, Apoorva; Gupta, Anurag; Rout, P. K.; Husale, Sudhir; Budhani, R. C.

2018-05-01

The transport properties of superconducting NbN nanostructures in the form of thin film, bridge of width (w) = 50 μm and three meanders of w = 500, 250 and 100 nm have been investigated by resistance (R) measurements in temperature (T) range = 2 -300 K and magnetic field (B) range = 0 - 7 Tesla. The nanostructuring was carried out using Focused Ion Beam (FIB) milling. Reduction of sample width results in significant changes in the normal and superconducting state properties. For instance, the observed metallic behavior in the thin film sample is lost and the normal state resistance increases drastically from 2.4 Ω to 418 kΩ for the 100 nm meander. In the superconducting state, the value of critical temperature Tc (upper critical field Bc2 at T = 0 K) reduces gradually with width reduction, it changes from 13.15 K (42.8 Tesla) in the case of thin film sample to 5.7 K (12.7 Tesla) for the 100 nm meander sample. The superconducting transitions are found to get broader for the bridge sample and the meanders additionally show low-temperature resistive tails. In case of all the samples with reduced width, the transition onsets are found to be rounded at surprisingly high values of T ˜ 25 K >> Tc. These results are discussed in terms of the possible effects of FIB processing and weak localization in our samples.

Prognostic Value of the Fibrosis-4 Index in Human Immunodeficiency Virus Type-1 Infected Patients Initiating Antiretroviral Therapy with or without Hepatitis C Virus

PubMed Central

Mussini, Cristina; Lorenzini, Patrizia; Puoti, Massimo; Lichtner, Miriam; Lapadula, Giuseppe; Di Giambenedetto, Simona; Antinori, Andrea; Madeddu, Giordano; Cozzi-Lepri, Alessandro; d’Arminio Monforte, Antonella; De Luca, Andrea

2015-01-01

Objective To evaluate the Fibrosis (FIB)-4 index as a predictor of major liver-related events (LRE) and liver-related death (LRD) in human immunodeficiency virus (HIV) type-1 patients initiating combination antiretroviral therapy (cART). Design Retrospective analysis of a prospective cohort study. Setting Italian HIV care centers participating to the ICONA Foundation cohort. Participants Treatment-naive patients enrolled in ICONA were selected who: initiated cART, had hepatitis C virus (HCV) serology results, were HBsAg negative, had an available FIB-4 index at cART start and during follow up. Methods Cox regression models were used to determine the association of FIB4 with the risk of major LRE (gastrointestinal bleeding, ascites, hepatic encephalopathy, hepato-renal syndrome or hepatocellular carcinoma) or LRD. Results Three-thousand four-hundred seventy-five patients were enrolled: 73.3% were males, 27.2% HCV seropositive. At baseline (time of cART initiation) their median age was 39 years, had a median CD4+ T cell count of 260 cells/uL, and median HIV RNA 4.9 log copies/mL, 65.9% had a FIB-4 <1.45, 26.4% 1.45–3.25 and 7.7% >3.25. Over a follow up of 18,662 person-years, 41 events were observed: 25 major LRE and 16 LRD (incidence rate, IR, 2.2 per 1,000 PYFU [95% confidence interval, CI 1.6–3.0]). IR was higher in HCV seropositives as compared to negatives (5.9 vs 0.5 per 1,000 PYFU). Higher baseline FIB-4 category as compared to <1.45 (FIB-4 1.45–3.25: HR 3.55, 95% CI 1.09–11.58; FIB-4>3.25: HR 4.25, 1.21–14.92) and time-updated FIB-4 (FIB-4 1.45–3.25: HR 3.40, 1.02–11.40; FIB-4>3.25: HR 21.24, 6.75–66.84) were independently predictive of major LRE/LRD, after adjusting for HIV- and HCV-related variables, alcohol consumption and type of cART. Conclusions The FIB-4 index at cART initiation, and its modification over time are risk factors for major LRE or LRD, independently of infection with HCV and could be used to monitor patients on cART. PMID:26640953

SPECT imaging of fibrin using fibrin-binding peptides.

PubMed

Starmans, Lucas W E; van Duijnhoven, Sander M J; Rossin, Raffaella; Aime, Silvio; Daemen, Mat J A P; Nicolay, Klaas; Grüll, Holger

2013-01-01

Noninvasive detection of fibrin in vivo using diagnostic imaging modalities may improve clinical decision-making on possible therapeutic options in atherosclerosis, cancer and thrombus-related pathologies such as pulmonary embolism and deep venous thrombosis. The aim of this study was to assess the potential of a novel (111)In-labeled fibrin-binding peptide (FibPep) to visualize thrombi in mice noninvasively using single-photon emission computed tomography (SPECT). FibPep and a negative control peptide (NCFibPep) were synthesized and their fibrin-binding properties were assessed in vitro. FibPep showed enhanced binding compared with NCFibPep to both fibrin and blood clots. FibPep bound to fibrin with a dissociation constant (K(d)) of 0.8 μ m, whereas NCFibPep displayed at least a 100-fold lower affinity towards fibrin. A FeCl3 -injury carotid artery thrombosis mouse model was used to evaluate the peptides in vivo. FibPep and NCFibPep displayed rapid blood clearance and were eliminated via the renal pathway. In vivo SPECT imaging using FibPep allowed clear visualization of thrombi. Ex vivo biodistribution showed significantly increased uptake of FibPep in the thrombus-containing carotid in comparison to the noninjured carotid (5.7 ± 0.7 and 0.6 ± 0.4% injected dose per gram (%ID g(-1)), respectively; p < 0.01; n = 4), whereas nonspecific NCFibPep did not (0.4 ± 0.2 and 0.3 ± 0.0%ID g(-1), respectively; n = 4). In conclusion, FibPep displayed high affinity towards fibrin in vitro and rapid blood clearance in vivo, and allowed sensitive detection of thrombi using SPECT imaging. Therefore, this particular imaging approach may provide a new tool to diagnose and monitor diseases such as atherosclerosis and cancer. Copyright © 2013 John Wiley & Sons, Ltd.

Biotic Interactions and Sunlight Affect Persistence of Fecal Indicator Bacteria and Microbial Source Tracking Genetic Markers in the Upper Mississippi River

PubMed Central

McMinn, Brian R.; Shanks, Orin C.; Sivaganesan, Mano; Fout, G. Shay; Ashbolt, Nicholas J.

2014-01-01

The sanitary quality of recreational waters that may be impacted by sewage is assessed by enumerating fecal indicator bacteria (FIB) (Escherichia coli and enterococci); these organisms are found in the gastrointestinal tracts of humans and many other animals, and hence their presence provides no information about the pollution source. Microbial source tracking (MST) methods can discriminate between different pollution sources, providing critical information to water quality managers, but relatively little is known about factors influencing the decay of FIB and MST genetic markers following release into aquatic environments. An in situ mesocosm was deployed at a temperate recreational beach in the Mississippi River to evaluate the effects of ambient sunlight and biotic interactions (predation, competition, and viral lysis) on the decay of culture-based FIB, as well as molecularly based FIB (Entero1a and GenBac3) and human-associated MST genetic markers (HF183 and HumM2) measured by quantitative real-time PCR (qPCR). In general, culturable FIB decayed the fastest, while molecularly based FIB and human-associated genetic markers decayed more slowly. There was a strong correlation between the decay of molecularly based FIB and that of human-associated genetic markers (r2, 0.96 to 0.98; P < 0.0001) but not between culturable FIB and any qPCR measurement. Overall, exposure to ambient sunlight may be an important factor in the early-stage decay dynamics but generally was not after continued exposure (i.e., after 120 h), when biotic interactions tended to be the only/major influential determinant of persistence. PMID:24747902

Non-alcoholic fatty liver disease fibrosis score and FIB-4 scoring system could identify patients at risk of systemic complications.

PubMed

Takahashi, Yuka; Kurosaki, Masayuki; Tamaki, Nobuharu; Yasui, Yutaka; Hosokawa, Takanori; Tsuchiya, Kaoru; Nakanishi, Hiroyuki; Itakura, Jun; Izumi, Namiki

2015-06-01

To investigate the relation between systemic complications of non-alcoholic fatty liver disease (NAFLD) and non-invasive fibrosis scores. The NAFLD fibrosis score (NFS) and FIB-4 were measured in 1559 people who underwent a complete medical checkup at our hospital and were followed for more than 3 years. Correlation between these scores and prevalence and new incidence rates of diabetes or cerebral-cardiovascular diseases were analyzed. The 1559 cases were classified into two groups using the low cut-off values of NFS and FIB-4: group 1 (≥low cut-off score with fatty liver) and group 2 (the others). In group 1, the prevalence of diabetes and cerebral-cardiovascular diseases at baseline and additional incidences during the observation period was higher compared with group 2. Diabetes at baseline in group 1 versus group 2 were 31.5% versus 3.1% (NFS, P < 0.0001), 17.0% versus 4.7% (FIB-4, P < 0.0001), and cerebral-cardiovascular diseases at baseline were 7.7% versus 2.3% (NFS, P = 0.002) and 9.0% versus 2.3% (FIB-4, P = 0.0012). New incidences of diabetes were 4.5% versus 1.2% (NFS, P = 0.034) and 3.6% versus 1.2% (FIB-4, P = 0.11), and of cerebral-cardiovascular diseases were 5.0% versus 0.9% (NFS, P = 0.0019) and 5.4% versus 0.9% (FIB-4, P = 0.0034). NFS and FIB-4 are useful to extract cases with high risk of systemic complications of NAFLD in the public. © 2014 The Japan Society of Hepatology.

[Relationship between reference values of fibrinogen and geographical factors based on neural network analysis].

PubMed

Li, Meng-Jiao; Ge, Miao; Wang, Cong-Xia; Cen, Min-Yi; Jiang, Ji-Lin; He, Jin-Wei; Lin, Qian-Yi; Liu, Xin

2016-08-20

To analyze the relationship between the reference values of fibrinogen (FIB) in healthy Chinese adults and geographical factors to provide scientific evidences for establishing the uniform standard. The reference values of FIB of 10701 Chinese healthy adults from 103 cities were collected to investigate their relationship with 18 geographical factors including spatial index, terrain index, climate index, and soil index. Geographical factors that significantly correlated with the reference values were selected for constructing the BP neural network model. The spatial distribution map of the reference value of FIB of healthy Chinese adults was fitted by disjunctive kriging interpolation. We used the 5-layer neural network and selected 2000 times of training covering 11 hidden layers to build the simulation rule for simulating the relationship between FIB and geographical environmental factors using the MATLAB software. s The reference value of FIB in healthy Chinese adults was significantly correlated with the latitude, sunshine duration, annual average temperature, annual average relative humidity, annual precipitation, annual range of air temperature, average annual soil gravel content, and soil cation exchange capacity (silt). The artificial neural networks were created to analyze the simulation of the selected indicators of geographical factors. The spatial distribution map of the reference values of FIB in healthy Chinese adults showed a distribution pattern that FIB levels were higher in the South and lower in the North, and higher in the East and lower in the West. When the geographical factors of a certain area are known, the reference values of FIB in healthy Chinese adults can be obtained by establishing the neural network mode or plotting the spatial distribution map.

Fecal indicator bacteria and Salmonella in ponds managed as bird habitat, San Francisco Bay, California, USA

USGS Publications Warehouse

Shellenbarger, G.G.; Athearn, N.D.; Takekawa, John Y.; Boehm, A.B.

2008-01-01

Throughout the world, coastal resource managers are encouraging the restoration of previously modified coastal habitats back into wetlands and managed ponds for their ecosystem value. Because many coastal wetlands are adjacent to urban centers and waters used for human recreation, it is important to understand how wildlife can affect water quality. We measured fecal indicator bacteria (FIB) concentrations, presence/absence of Salmonella, bird abundance, and physico-chemical parameters in two coastal, managed ponds and adjacent sloughs for 4 weeks during the summer and winter in 2006. We characterized the microbial water quality in these waters relative to state water-quality standards and examined the relationship between FIB, bird abundance, and physico-chemical parameters. A box model approach was utilized to determine the net source or sink of FIB in the ponds during the study periods. FIB concentrations often exceeded state standards, particularly in the summer, and microbial water quality in the sloughs was generally lower than in ponds during both seasons. Specifically, the inflow of water from the sloughs to the ponds during the summer, more so than waterfowl use, appeared to increase the FIB concentrations in the ponds. The box model results suggested that the ponds served as net wetland sources and sinks for FIB, and high bird abundances in the winter likely contributed to net winter source terms for two of the three FIB in both ponds. Eight serovars of the human pathogen Salmonella were isolated from slough and pond waters, although the source of the pathogen to these wetlands was not identified. Thus, it appeared that factors other than bird abundance were most important in modulating FIB concentrations in these ponds.

Diagnostic Usefulness of APRI and FIB-4 for the Prediction of Liver Fibrosis After Liver Transplantation in Patients Infected with Hepatitis C Virus.

PubMed

Imai, H; Kamei, H; Onishi, Y; Ishizu, Y; Ishigami, M; Goto, H; Ogura, Y

2018-06-01

Aspartate transaminase-to-platelet ratio index (APRI) and fibrosis-4 (FIB-4) are well known as representative indirect serum biomarkers related to liver fibrosis. The usefulness of these markers for the diagnosis of liver fibrosis after liver transplantation (LT) in hepatitis C virus (HCV)-infected patients and the influence of splenectomy were investigated. From June 2003 to May 2014, 31 HCV-infected patients who underwent LT and postoperative follow-up liver biopsies were included in this study. The association between liver fibrosis and serum biomarkers and the influence of splenectomy on APRI and FIB-4 were also investigated. A total of 195 biopsy specimens were collected, and liver fibrosis was identified as: F0, 59.7%; F1, 34.1%; and F2, 6.3%. Both APRI and FIB-4 were significantly higher in patients who showed F1 and F2 in liver biopsy specimen than F0 (P values, .009 and .022, respectively); sensitivity and specificity of APRI were, respectively, 63.4% and 66.7%, and those of FIB-4 were 57.7% and 69.6%. In 11 patients (35.5%) who underwent splenectomy at the time of LT, the cutoff values for APRI and FIB-4 were 0.61 and 1.41, which were significantly lower than the corresponding values (1.00 and 3.64) of patients without splenectomy. APRI and FIB-4 could effectively estimate liver fibrosis after LT for HCV-related liver disease. For LT patients with splenectomy, APRI and FIB-4 were also useful to estimate liver fibrosis, but the standard values should be adjusted lower than those for patients without splenectomy. Copyright © 2018 Elsevier Inc. All rights reserved.

FIB-4 index for assessing the prognosis of hepatocellular carcinoma in patients with Child-Pugh class A liver function.

PubMed

Ito, Takanori; Kumada, Takashi; Toyoda, Hidenori; Tada, Toshifumi

2015-07-01

We evaluated the prognosis of hepatocellular carcinoma (HCC) patients with Child-Pugh (C-P) class A based on FIB-4 index, which is a liver fibrosis marker. A total of 915 HCC patients with C-P class A were investigated. We assessed the prognosis using FIB-4 index, and factors associated with survival rates were analyzed in these patients. When patients were categorized according to FIB-4 index as <2.0 (n = 93), ≥ 2.0 and <4.0 (n = 311), and ≥ 4.0 (n = 511), survival rates at 5 years were 70.5% [95% confidence interval (CI) 59.0-79.9], 56.4% (95% CI 50.1-62.5), and 47.1% (95% CI 42.2-52.1), respectively. Patients with FIB-4 index <2.0 had a higher survival rate than the other groups (≥ 4.0 vs ≥ 2.0 and <4.0, p = 0.010; ≥ 2.0 and <4.0 vs <2.0, p = 0.028). We were able to predict prognosis in patients with C-P score 5 by FIB-4 index, but survival rate did not significantly differ in patients with C-P score 6. Multivariate analysis identified C-P score, FIB-4 index [≥ 2.0 and <4.0; hazard ratios (HRs) 1.638 (95% CI 1.084-2.474); p = 0.019/≥ 4.0; HR 1.828 (95% CI 1.217-2.744); p = 0.004], Lens culinaris agglutinin-reactive α-fetoprotein, tumor size, number, vascular invasion, antiviral therapy, and hepatectomy as independent predictive factors for survival. The FIB-4 index is useful for assessing prognosis in HCC patients with C-P class A, especially those with C-P score 5.

Distribution and sources of surfzone bacteria at Huntington Beach before and after disinfection on an ocean outfall - A frequency-domain analysis

USGS Publications Warehouse

Noble, M.A.; Xu, J. P.; Robertson, G.L.; Rosenfeld, L.K.

2006-01-01

Fecal indicator bacteria (FIB) were measured approximately 5 days a week in ankle-depth water at 19 surfzone stations along Huntington Beach and Newport Beach, California, from 1998 to the end of 2003. These sampling periods span the time before and after treated sewage effluent, discharged into the coastal ocean from the local outfall, was disinfected. Bacterial samples were also taken in the vicinity of the outfall during the pre- and post-disinfection periods. Our analysis of the results from both data sets suggest that land-based sources, rather than the local outfall, were the source of the FIB responsible for the frequent closures and postings of local beaches in the summers of 2001 and 2002. Because the annual cycle is the dominant frequency in the fecal and total coliform data sets at most sampling stations, we infer that sources associated with local runoff were responsible for the majority of coliform contamination along wide stretches of the beach. The dominant fortnightly cycle in enterococci at many surfzone sampling stations suggests that the source for these relatively frequent bacteria contamination events in summer is related to the wetting and draining of the land due to the large tidal excursions found during spring tides. Along the most frequently closed section of the beach at stations 3N-15N, the fortnightly cycle is dominant in all FIBs. The strikingly different spatial and spectral patterns found in coliform and in enterococci suggest the presence of different sources, at least for large sections of beach. The presence of a relatively large enterococci fortnightly cycle along the beaches near Newport Harbor indicates that contamination sources similar to those found off Huntington Beach are present, though not at high enough levels to close the Newport beaches. ?? 2006 Elsevier Ltd. All rights reserved.

Simulation of FIB-SEM images for analysis of porous microstructures.

PubMed

Prill, Torben; Schladitz, Katja

2013-01-01

Focused ion beam nanotomography-scanning electron microscopy tomography yields high-quality three-dimensional images of materials microstructures at the nanometer scale combining serial sectioning using a focused ion beam with SEM. However, FIB-SEM tomography of highly porous media leads to shine-through artifacts preventing automatic segmentation of the solid component. We simulate the SEM process in order to generate synthetic FIB-SEM image data for developing and validating segmentation methods. Monte-Carlo techniques yield accurate results, but are too slow for the simulation of FIB-SEM tomography requiring hundreds of SEM images for one dataset alone. Nevertheless, a quasi-analytic description of the specimen and various acceleration techniques, including a track compression algorithm and an acceleration for the simulation of secondary electrons, cut down the computing time by orders of magnitude, allowing for the first time to simulate FIB-SEM tomography. © Wiley Periodicals, Inc.

Real-time observation of FIB-created dots and ripples on GaAs

NASA Astrophysics Data System (ADS)

Rose, F.; Fujita, H.; Kawakatsu, H.

2008-01-01

We report a phenomenological study of Ga dots and ripples created by a focused ion beam (FIB) on the GaAs(001) surface. Real-time observation of dot diffusion and ripple formation was made possible by recording FIB movies. In the case of FIB irradiation with a 40 nA current of Ga+ ions accelerated under 40 kV with an incidence angle of θ = 30°, increasing ion dose gives rise to three different regimes. In Regime 1, dots with lateral sizes in the range 50-460 nm are formed. Dots diffuse under continuous sputtering. In Regime 2, dots self-assemble into Bradley and Harper (BH) type ripples with a pseudo-period of λ = 1150 ± 25 nm. In Regime 3, ripples are eroded and the surface topology evolves into microplanes. In the case of normal incidence, FIB sputtering leads only to the formation of dots, without surface rippling.

Time resolved impedance spectroscopy analysis of lithium phosphorous oxynitride - LiPON layers under mechanical stress

NASA Astrophysics Data System (ADS)

Glenneberg, Jens; Bardenhagen, Ingo; Langer, Frederieke; Busse, Matthias; Kun, Robert

2017-08-01

In this paper we present investigations on the morphological and electrochemical changes of lithium phosphorous oxynitride (LiPON) under mechanically bent conditions. Therefore, two types of electrochemical cells with LiPON thin films were prepared by physical vapor deposition. First, symmetrical cells with two blocking electrodes (Cu/LiPON/Cu) were fabricated. Second, to simulate a more application-related scenario cells with one blocking and one non-blocking electrode (Cu/LiPON/Li/Cu) were analyzed. In order to investigate mechanical distortion induced transport property changes in LiPON layers the cells were deposited on a flexible polyimide substrate. Morphology of the as-prepared samples and deviations from the initial state after applying external stress by bending the cells over different radii were investigated by Focused Ion Beam- Scanning Electron Microscopy (FIB-SEM) cross-section and surface images. Mechanical stress induced changes in the impedance were evaluated by time-resolved electrochemical impedance spectroscopy (EIS). Due to the formation of a stable, ion-conducting solid electrolyte interphase (SEI), cells with lithium show decreased impedance values. Furthermore, applying mechanical stress to the cells results in a further reduction of the electrolyte resistance. These results are supported by finite element analysis (FEA) simulations.

Formation and evolution of ripples on ion-irradiated semiconductor surfaces

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

Kang, M.; Wu, J. H.; Ye, W.

We have examined the formation and evolution of ripples on focused-ion-beam (FIB) irradiated compound semiconductor surfaces. Using initially normal-incidence Ga{sup +} FIB irradiation of InSb, we tuned the local beam incidence angle (θ{sub eff}) by varying the pitch and/or dwell time. For single-pass FIB irradiation, increasing θ{sub eff} induces morphological evolution from pits and islands to ripples to featureless surfaces. Multiple-pass FIB irradiation of the rippled surfaces at a fixed θ{sub eff} leads to island formation on the ripple crests, followed by nanorod (NR) growth. This ripple-NR transition provides an alternative approach for achieving dense arrays of NRs.

Evaluation of 111In-labeled EPep and FibPep as tracers for fibrin SPECT imaging.

PubMed

Starmans, Lucas W E; van Duijnhoven, Sander M J; Rossin, Raffaella; Berben, Monique; Aime, Silvio; Daemen, Mat J A P; Nicolay, Klaas; Grüll, Holger

2013-11-04

Fibrin targeting is an attractive strategy for nuclear imaging of thrombosis, atherosclerosis and cancer. Recently, FibPep, an (111)In-labeled fibrin-binding peptide, was established as a tracer for fibrin SPECT imaging and was reported to allow sensitive detection of minute thrombi in mice using SPECT. In this study, we developed EPep, a novel (111)In-labeled fibrin-binding peptide containing the fibrin-binding domain of the clinically verified EP-2104R peptide, and sought to compare the potential of EPep and FibPep as tracers for fibrin SPECT imaging. In vitro, both EPep and FibPep showed high stability in serum, but were less stable in liver and kidney homogenate assays. Both peptide probes displayed comparable affinities toward human and mouse derived fibrin (Kd ≈ 1 μM), and similarly to FibPep, EPep showed fast blood clearance, low nontarget uptake and high thrombus uptake (6.8 ± 1.2% ID g(-1)) in a mouse carotid artery thrombosis model. Furthermore, EPep showed a similar affinity toward rat derived fibrin (Kd ≈ 1 μM), displayed high thrombus uptake in a rat carotid artery thrombosis model (0.74 ± 0.39% ID g(-1)), and allowed sensitive detection of thrombosis in rats using SPECT. In contrast, FibPep displayed a significantly lower affinity toward rat derived fibrin (Kd ≈ 14 μM) and low uptake in rat thrombi (0.06 ± 0.02% ID g(-1)) and did not allow clear visualization of carotid artery thrombosis in rats using SPECT. These results were confirmed ex vivo by autoradiography, which showed a 7-fold higher ratio of activity in the thrombus over the contralateral carotid artery for EPep in comparison to FibPep. These findings suggest that the FibPep binding fibrin epitope is not fully homologous between humans and rats, and that preclinical rat models of disease should not be employed to gauge the clinical potential of FibPep. In conclusion, both peptides showed approximately similar metabolic stability and affinity toward human and mouse derived fibrin, and displayed high thrombus uptake in a mouse carotid artery thrombosis model. Therefore, both EPep and FibPep are promising fibrin targeted tracers for translation into clinical settings to serve as novel tools for molecular imaging of fibrin.

Pathogenic bacteria and microbial-source tracking markers in Brandywine Creek Basin, Pennsylvania and Delaware, 2009-10

USGS Publications Warehouse

Duris, Joseph W.; Reif, Andrew G.; Olson, Leif E.; Johnson, Heather E.

2011-01-01

The City of Wilmington, Delaware, is in the downstream part of the Brandywine Creek Basin, on the main stem of Brandywine Creek. Wilmington uses this stream, which drains a mixed-land-use area upstream, for its main drinking-water supply. Because the stream is used for drinking water, Wilmington is in need of information about the occurrence and distribution of specific fecally derived pathogenic bacteria (disease-causing bacteria) and their relations to commonly measured fecal-indicator bacteria (FIB), as well as information regarding the potential sources of the fecal pollution and pathogens in the basin. This study focused on five routinely sampled sites within the basin, one each on the West Branch and the East Branch of Brandywine Creek and at three on the main stem below the confluence of the West and East Branches. These sites were sampled monthly for 1 year. Targeted event samples were collected on two occasions during high flow and two occasions during normal flow. On the basis of this study, high flows in the Brandywine Creek Basin were related to increases in FIB densities, and in the frequency of selected pathogen and source markers, in the West Branch and main stem of Brandywine Creek, but not in the East Branch. Water exceeding the moderate fullbody-contact single-sample recreational water-quality criteria (RWQC) for Escherichia coli (E. coli) was more likely to contain selected markers for pathogenic E. coli (eaeA,stx1, and rfbO157 gene markers) and bovine fecal sources (E. hirae and LTIIa gene markers), whereas samples exceeding the enterococci RWQC were more likely to contain the same pathogenic markers but also were more likely to carry a marker indicative of human source (esp gene marker). On four sample dates, during high flow between October and March, the West Branch was the only observed potential contributor of selected pathogen and bovine source markers to the main stem of Brandywine Creek. Indeed, the stx2 marker, which indicates a highly virulent type of pathogenic E. coli, was found only in the West Branch and main stem at high flow but was not found in the East Branch under similar conditions. However, it must be noted that throughout the entire year of sampling there were occasions, during both high and normal flows, when both the East and West Branches were potential contributors of pathogen and microbial-source tracking markers to the main stem. Therefore, this study indicates that under selected conditions (high flow, October through March), West Branch Brandywine Creek Basin was the most likely source of elevated FIB densities in the main stem. These elevated densities are associated with more frequent detection of selected pathogenic E. coli markers (rfbO157 stx1) and are associated with MST markers of bovine source. However, during other times of the year, both the West Branch and East Branch Basins are acting as potential sources of FIB and fecally derived pathogens.

Diagnostic accuracy of APRI and FIB-4 for predicting hepatitis B virus-related liver fibrosis accompanied with hepatocellular carcinoma.

PubMed

Xiao, Guangqin; Zhu, Feng; Wang, Min; Zhang, Hang; Ye, Dawei; Yang, Jiayin; Jiang, Li; Liu, Chang; Yan, Lunan; Qin, Renyi

2016-10-01

Aspartate aminotransferase to platelet ratio index (APRI) and the fibrosis index based on four factors (FIB-4) are the two most focused non-invasive models to assess liver fibrosis. We aimed to examine the validity of these two models for predicting hepatitis B virus (HBV)-related liver fibrosis accompanied with hepatocellular carcinoma (HCC). We enrolled HBV-infected patients with liver cancer who had received hepatectomy. The accuracy of APRI and FIB-4 for diagnosing liver fibrosis was assessed based on their sensitivity, specificity, diagnostic efficiency, positive predictive value (PPV), negative predictive value (NPV), kappa (κ) value and area under the receiver-operating characteristic curve (AUC). Finally 2176 patients were included, with 1682 retrospective subjects and 494 prospective subjects. APRI (rs=0.310) and FIB-4 (rs=0.278) were positively correlated with liver fibrosis. And χ(2) analysis demonstrated that APRI and FIB-4 values correlated with different levels of liver fibrosis with all P values less than 0.01. The AUC values for APRI and FIB-4 were 0.685 and 0.626 (P=0.73) for predicting significant fibrosis, 0.681 and 0.648 (P=0.81) for differentiation of advanced fibrosis and 0.676 and 0.652 (P=0.77) for diagnosing cirrhosis. APRI and FIB-4 correlate with liver fibrosis. However these two models have low accuracy for predicting HBV-related liver fibrosis in HCC patients. Copyright © 2016. Published by Elsevier Ltd.

Toxicological Responses of Fischer Rats to Naturally Occurring Asbestos Samples from the United States and Canada

EPA Science Inventory

To support risk assessment efforts, a comparative study was designed to provide understanding of the toxicity of different types of fibers encountered in EPA clean-up efforts. Physico-chemical properties, and consequentially toxicity, are likely to be different among various fib...

Prediction of future hepatocellular carcinoma incidence in moderate to heavy alcohol drinkers with the FIB-4 liver fibrosis index.

PubMed

Suh, Beomseok; Yun, Jae Moon; Park, Sehhoon; Shin, Dong Wook; Lee, Tae Hoon; Yang, Hyung-Kook; Ahn, Eunmi; Lee, Hyejin; Park, Jin Ho; Cho, BeLong

2015-11-01

Although heavy alcoholics are at heightened risk for hepatocellular carcinoma (HCC), there are no guidelines that recommend HCC screening for heavy alcoholics. This study investigated FIB-4, a noninvasive and easily applicable liver fibrosis index, as a risk factor for HCC incidence among alcohol drinkers without viral hepatitis. This retrospective cohort study included 6661 generally healthy adults who were 30 years old or older, did not have chronic viral hepatitis, and visited Seoul National University Hospital for a general, routine health evaluation. The future HCC incidence was determined from National Health Insurance medical service claims data (median follow-up, 6.2 years). With adjustments for age, sex, body mass index, smoking, and alcohol, compared with subjects with FIB-4 values less 1.00, subjects with FIB-4 values greater than or equal to 1.75 and less than 2.10 and subjects with FIB-4 values greater than or equal to 2.10 had adjusted hazard ratios (aHRs) of 5.18 (95% confidence interval [CI], 1.12-24.00) and 13.63 (95% CI, 3.77-49.33), respectively, for HCC incidence. This was heightened in subjects who drank more 30 g of alcohol per day: the aHRs were 8.39 (95% CI, 1.28-54.87) and 16.58 (95% CI, 3.87-71.04), respectively. FIB-4 was shown to have a higher predictive value for HCC incidence than ultrasonographically detected liver cirrhosis (C-index, 0.665 vs 0.527; P = .044). High FIB-4 is a risk factor with a high predictive value for HCC incidence, especially among moderate to heavy alcoholics (>30 g/d). FIB-4 is a readily available and probably cost-effective clinical tool with potential value for identifying subpopulations of alcoholics at particularly high risk who would benefit from regular HCC screening. Further investigations are warranted to validate our results; nonetheless, our study suggests that FIB-4 may be useful in HCC screening among alcoholics. © 2015 American Cancer Society.

Applicability of universal Bacteroidales genetic marker for microbial monitoring of drinking water sources in comparison to conventional indicators.

PubMed

Shahryari, A; Nikaeen, M; Khiadani Hajian, M; Nabavi, F; Hatamzadeh, M; Hassanzadeh, A

2014-11-01

Water quality monitoring is essential for the provision of safe drinking water. In this study, we compared a selection of fecal indicators with universal Bacteroidales genetic marker to identify fecal pollution of a variety of drinking water sources. A total of 60 samples were collected from water sources. The microbiological parameters included total coliforms, fecal coliforms, Escherichia coli and fecal streptococci as the fecal indicator bacteria (FIB), Clostridium perfringens and H2S bacteria as alternative indicators, universal Bacteroidales genetic marker as a promising alternative fecal indicator, and Salmonella spp., Shigella spp., and E. coli O157 as pathogenic bacteria. From 60 samples analyzed, Bacteroidales was the most frequently detected indicator followed by total coliforms. However, the Bacteroidales assay failed to detect the marker in nine samples positive for FIB and other alternative indicators. The results of our study showed that the absence of Bacteroidales is not necessarily an evidence of fecal and pathogenic bacteria absence and may be unable to ensure the safety of the water. Further research, however, is required for a better understanding of the use of a Bacteroidales genetic marker as an indicator in water quality monitoring programs.

A two scale analysis of tight sandstones

NASA Astrophysics Data System (ADS)

Adler, P. M.; Davy, C. A.; Song, Y.; Troadec, D.; Hauss, G.; Skoczylas, F.

2015-12-01

Tight sandstones have a low porosity and a very small permeability K. Available models for K do not compare well with measurements. These sandstones are made of SiO_2 grains, with a typical size of several hundreds of micron. These grains are separated by a network of micro-cracks, with sizes ranging between microns down to tens of nm. Therefore, the structure can be schematized by Voronoi polyhedra separated by plane and permeable polygonal micro-cracks. Our goal is to estimate K based on a two scale analysis and to compare the results to measurements. For a particular sample [2], local measurements on several scales include FIB/SEM [3], CMT and 2D SEM. FIB/SEM is selected because the peak pore size given by Mercury Intrusion Porosimetry is of 350nm. FIB/SEM imaging (with 50 nm voxel size) identifies an individual crack of 180nm average opening, whereas CMT provides a connected porosity (individual crack) for 60 nm voxel size, of 4 micron average opening. Numerical modelling is performed by combining the micro-crack network scale (given by 2D SEM) and the 3D micro-crack scale (given by either FIB/SEM or CMT). Estimates of the micro-crack density are derived from 2D SEM trace maps by counting the intersections with scanlines, the surface density of traces, and the number of fracture intersections. K is deduced by using a semi empirical formula valid for identical, isotropic and uniformly distributed fractures [1]. This value is proportional to the micro-crack transmissivity sigma. Sigma is determined by solving the Stokes equation in the micro-cracks measured by FIB/SEM or CMT. K is obtained by combining the two previous results. Good correlation with measured values on centimetric plugs is found when using sigma from CMT data. The results are discussed and further research is proposed. [1] Adler et al, Fractured porous media, Oxford Univ. Press, 2012. [2] Duan et al, Int. J. Rock Mech. Mining Sci., 65, p75, 2014. [3] Song et al, Marine and Petroleum Eng., 65, p63, 2015.

Microbiological quality assessment of sand and water from three selected beaches of South Coast, São Paulo State, Brazil.

PubMed

Pinto, K C; Hachich, E M; Sato, M I Z; Di Bari, M; Coelho, M C L S; Matté, M H; Lamparelli, C C; Razzolini, M T P

2012-01-01

This study aimed to assess the sanitary quality of water, and wet and dry sand from three beaches located in the South Coast region of São Paulo State, Brazil, selected taking into account the frequency of tourists and the water quality (good, fair and poor). Thirty-six water samples each of wet and dry sand and seawater were collected monthly over a period of one year and analyzed for fecal indicator bacteria (FIB: thermotolerant coliforms, Escherichia coli, and enterococci), presumptive Staphylococcus aureus, Pseudomonas aeruginosa, Candida albicans and dermatophytes. The results revealed FIB concentrations more elevated in dry sand followed by wet sand and water. P. aeruginosa and presumptive S. aureus were detected with a similar frequency in water and sand samples, but maximum concentrations and geometric means were higher in dry sand. C. albicans was detected only in water samples whereas the dermatophyte Microsporum sp. was isolated exclusively from dry and wet sand samples. This evaluation showed also that the environment had a significant influence on P. aeruginosa but not on presumptive S. aureus concentrations. According to threshold values proposed in the literature for E. coli and enterococci dry sand densities, none of the beaches would be considered of sufficient quality for recreational activities.

Experimental Hypervelocity Dust Impact in Olivine: FIB/TEM Characterization of Micron-Scale Craters with Comparison to Natural and Laser-Simulated Small-Scale Impact Effects

NASA Technical Reports Server (NTRS)

Christoffersen, R.; Loeffler, M. J.; Rahman, Z.; Dukes, C.; IMPACT Team

2017-01-01

The space weathering of regoliths on airless bodies and the formation of their exospheres is driven to a large extent by hypervelocity impacts from the high relative flux of micron to sub-micron meteoroids that comprise approximately 90 percent of the solar system meteoroid population. Laboratory hypervelocity impact experiments are crucial for quantifying how these small impact events drive space weathering through target shock, melting and vaporization. Simulating these small scale impacts experimentally is challenging because the natural impactors are both very small and many have velocities above the approximately 8 kilometers-per-second limit attainable by conventional chemical/light gas accelerator technology. Electrostatic "dust" accelerators, such as the one recently developed at the Colorado Center for Lunar Dust and Atmospheric Studies (CCLDAS), allow the experimental velocity regime to be extended up to tens of kilometers-per-second. Even at these velocities the region of latent target damage created by each impact, in the form of microcraters or pits, is still only about 0.1 to 10 micrometers in size. Both field-emission analytical scanning electron microscopy (FE-SEM) and advanced field-emission scanning transmission electron microscopy (FE-STEM) are uniquely suited for characterizing the individual dust impact sites in these experiments. In this study, we have used both techniques, along with focused ion beam (FIB) sample preparation, to characterize the micrometer to nanometer scale effects created by accelerated dust impacts into olivine single crystals. To our knowledge this work presents the first TEM-scale characterization of dust impacts into a key solar system silicate mineral using the CCLDAS facility. Our overarching goal for this work is to establish a basis to compare with our previous results on natural dust-impacted lunar olivine and laser-irradiated olivine.

Characterization of the multilayered shell of a limpet, Lottia kogamogai (Mollusca: Patellogastropoda), using SEM-EBSD and FIB-TEM techniques.

PubMed

Suzuki, Michio; Kameda, Jun; Sasaki, Takenori; Saruwatari, Kazuko; Nagasawa, Hiromichi; Kogure, Toshihiro

2010-08-01

The microstructure and its crystallographic aspect of the shell of a limpet, Lottiakogamogai, have been investigated, as the first step to clarify the mechanism of shell formation in limpet. The shell consists of five distinct layers stacked along the shell thickness direction. Transmission electron microscopy (TEM) with the focused ion beam (FIB) sample preparation technique was primarily adopted, as well as scanning electron microscopy (SEM) with electron back-scattered diffraction (EBSD). The five layers were termed as M+3, M+2, M+1, M, M-1 from the outside to the inside in previous works, where M means myostracum. The outmost M+3 layer consists of calcite with a "mosaic" structure; granular submicron sub-grains with small-angle grain boundaries often accompanying dislocation arrays. M+2 layer consists of flat prismatic aragonite crystals with a leaf-like cross section, stacked obliquely to the shell surface. It looks that the prismatic crystals are surrounded by organic sheets, forming a compartment structure. M+1 and M-1 layers adopt a crossed lamellar structure consisting of aragonite flat prisms with rectangular cross section. M layer has a prismatic structure of aragonite perpendicular to the shell surface and with irregular shaped cross sections. Distinct organic sheets were not observed between the crystals in M+1, M and M-1 layers. The {110} twins are common in all aragonite M+2, M+1, M and M-1 layers, with the twin boundaries parallel to the prisms. These results for the microstructure of each layer should be considered in the discussion of the formation mechanism of the limpet shell structure. Copyright 2010 Elsevier Inc. All rights reserved.

Status of faecal pollution in ports: A basin-wide investigation in the Adriatic Sea.

PubMed

Luna, Gian Marco; Manini, Elena; Turk, Valentina; Tinta, Tinkara; D'Errico, Giuseppe; Baldrighi, Elisa; Baljak, Vanja; Buda, Donatella; Cabrini, Marina; Campanelli, Alessandra; Cenov, Arijana; Del Negro, Paola; Drakulović, Dragana; Fabbro, Cinzia; Glad, Marin; Grilec, Dolores; Grilli, Federica; Jokanović, Sandra; Jozić, Slaven; Kauzlarić, Vesna; Kraus, Romina; Marini, Mauro; Mikuš, Josip; Milandri, Stefania; Pećarević, Marijana; Perini, Laura; Quero, Grazia Marina; Šolić, Mladen; Lušić, Darija Vukić; Zoffoli, Silvia

2018-04-07

Ports are subject to a variety of anthropogenic impacts, and there is mounting evidence of faecal contamination through several routes. Yet, little is known about pollution in ports by faecal indicator bacteria (FIB). FIB spatio-temporal dynamics were assessed in 12 ports of the Adriatic Sea, a semi-enclosed basin under strong anthropogenic pressure, and their relationships with environmental variables were explored to gain insight into pollution sources. FIB were abundant in ports, often more so than in adjacent areas; their abundance patterns were related to salinity, oxygen, and nutrient levels. In addition, a molecular method, quantitative (q)PCR, was used to quantify FIB. qPCR enabled faster FIB determination and water quality monitoring that culture-based methods. These data provide robust baseline evidence of faecal contamination in ports and can be used to improve the management of routine port activities (dredging and ballast water exchange), having potential to spread pathogens in the sea. Copyright © 2018 Elsevier Ltd. All rights reserved.

Human cardiac telocytes: 3D imaging by FIB-SEM tomography

PubMed Central

Cretoiu, D; Hummel, E; Zimmermann, H; Gherghiceanu, M; Popescu, L M

2014-01-01

Telocyte (TC) is a newly identified type of cell in the cardiac interstitium (www.telocytes.com). TCs are described by classical transmission electron microscopy as cells with very thin and long telopodes (Tps; cellular prolongations) having podoms (dilations) and podomers (very thin segments). TCs’ three-dimensional (3D) morphology is still unknown. Cardiac TCs seem to be particularly involved in long and short distance intercellular signalling and, therefore, their 3D architecture is important for understanding their spatial connections. Using focused ion beam scanning electron microscopy (FIB-SEM) we show, for the first time, the whole ultrastructural anatomy of cardiac TCs. 3D reconstruction of cardiac TCs by FIB-SEM tomography confirms that they have long, narrow but flattened (ribbon-like) telopodes, with humps generated by the podoms. FIB-SEM tomography also confirms the network made by TCs in the cardiac interstitium through adherens junctions. This study provides the first FIB-SEM tomography of a human cell type. PMID:25327290

An improved cryo-FIB method for fabrication of frozen hydrated lamella.

PubMed

Zhang, Jianguo; Ji, Gang; Huang, Xiaojun; Xu, Wei; Sun, Fei

2016-05-01

Cryo-electron tomography (cryo-ET) provides great insights into the ultrastructure of cells and tissues in their native state and provides a promising way to study the in situ 3D structures of macromolecular complexes. However, this technique has been limited on the very thin specimen, which is not applicable for most cells and tissues. Besides cryo-sectioning approach, cryo focused ion beam (cryo-FIB) appeared recently to achieve 'artifact-free' thin frozen hydrated lamella via fabrication. Considering that the current cryo-FIB methods need modified holders or cartridges, here, with a "D-shaped" molybdenum grid and a specific shutter system, we developed a simple cryo-FIB approach for thin frozen hydrated lamella fabrication, which fits both standard transmission cryo-electron microscopes with side-entry cryo-holders and state-of-the-art ones with AutoGrids. Our approach will expand the usage of cryo-FIB approach in many labs. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Origin and spatial-temporal distribution of faecal bacteria in a bay of Lake Geneva, Switzerland.

PubMed

Poté, John; Goldscheider, Nico; Haller, Laurence; Zopfi, Jakob; Khajehnouri, Fereidoun; Wildi, Walter

2009-07-01

The origin and distribution of microbial contamination in Lake Geneva's most polluted bay were assessed using faecal indicator bacteria (FIB). The lake is used as drinking water, for recreation and fishing. During 1 year, water samples were taken at 23 points in the bay and three contamination sources: a wastewater treatment plant (WWTP), a river and a storm water outlet. Analyses included Escherichia coli, enterococci (ENT), total coliforms (TC), and heterotrophic plate counts (HPC). E. coli input flux rates from the WWTP can reach 2.5 x 10(10) CFU/s; those from the river are one to three orders of magnitude lower. Different pathogenic Salmonella serotypes were identified in water from these sources. FIB levels in the bay are highly variable. Results demonstrate that (1) the WWTP outlet at 30 m depth impacts near-surface water quality during holomixis in winter; (2) when the lake is stratified, the effluent water is generally trapped below the thermocline; (3) during major floods, upwelling across the thermocline may occur; (4) the river permanently contributes to contamination, mainly near the river mouth and during floods, when the storm water outlet contributes additionally; (5) the lowest FIB levels in the near-surface water occur during low-flow periods in the bathing season.

Nanometer-scale imaging and pore-scale fluid flow modeling inchalk

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

Tomutsa, Liviu; Silin, Dmitriy; Radmilovich, Velimir

2005-08-23

For many rocks of high economic interest such as chalk,diatomite, tight gas sands or coal, nanometer scale resolution is neededto resolve the 3D-pore structure, which controls the flow and trapping offluids in the rocks. Such resolutions cannot be achieved with existingtomographic technologies. A new 3D imaging method, based on serialsectioning and using the Focused Ion Beam (FIB) technology has beendeveloped. FIB allows for the milling of layers as thin as 10 nanometersby using accelerated Ga+ ions to sputter atoms from the sample surface.After each milling step, as a new surface is exposed, a 2D image of thissurface is generated. Next,more » the 2D images are stacked to reconstruct the3D pore or grain structure. Resolutions as high as 10 nm are achievableusing this technique. A new image processing method uses directmorphological analysis of the pore space to characterize thepetrophysical properties of diverse formations. In addition to estimationof the petrophysical properties (porosity, permeability, relativepermeability and capillary pressures), the method is used for simulationof fluid displacement processes, such as those encountered in variousimproved oil recovery (IOR) approaches. Computed with the new methodcapillary pressure curves are in good agreement with laboratory data. Themethod has also been applied for visualization of the fluid distributionat various saturations from the new FIB data.« less

Ion irradiation effects on a magnetic Si/Ni/Si trilayer and lateral magnetic-nonmagnetic multistrip patterning by focused ion beam

NASA Astrophysics Data System (ADS)

Dev, B. N.; Banu, Nasrin; Fassbender, J.; Grenzer, J.; Schell, N.; Bischoff, L.; Groetzschel, R.; McCord, J.

2017-10-01

Fabrication of a multistrip magnetic/nonmagnetic structure in a thin sandwiched Ni layer [Si(5 nm)/Ni(15 nm)/Si] by a focused ion beam (FIB) irradiation has been attempted. A control experiment was initially performed by irradiation with a standard 30 keV Ga ion beam at various fluences. Analyses were carried out by Rutherford backscattering spectrometry, X-ray reflectivity, magnetooptical Kerr effect (MOKE) measurements and MOKE microscopy. With increasing ion fluence, the coercivity as well as Kerr rotation decreases. A threshold ion fluence has been identified, where ferromagnetism of the Ni layer is lost at room temperature and due to Si incorporation into the Ni layer, a Ni0.68Si0.32 alloy layer is formed. This fluence was used in FIB irradiation of parallel 50 nm wide stripes, leaving 1 µm wide unirradiated stripes in between. MOKE microscopy on this FIB-patterned sample has revealed interacting magnetic domains across several stripes. Considering shape anisotropy effects, which would favour an alignment of magnetization parallel to the stripe axis, the opposite behaviour is observed. Magneto-elastic effects introducing a stress-induced anisotropy component oriented perpendicular to the stripe axis are the most plausible explanation for the observed behaviour.

Transmission Kikuchi diffraction and transmission electron forescatter imaging of electropolished and FIB manufactured TEM specimens

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

Zieliński, W., E-mail: wiziel@inmat.pw.edu.pl; Płociński, T.; Kurzydłowski, K.J.

2015-06-15

We present a study of the efficiency of the utility of scanning electron microscope (SEM)-based transmission methods for characterizing grain structure in thinned bulk metals. Foils of type 316 stainless steel were prepared by two methods commonly used for transmission electron microscopy — double-jet electropolishing and focused ion beam milling. A customized holder allowed positioning of the foils in a configuration appropriate for both transmission electron forward scatter diffraction, and for transmission imaging by the use of a forescatter detector with two diodes. We found that both crystallographic orientation maps and dark-field transmitted images could be obtained for specimens preparedmore » by either method. However, for both methods, preparation-induced artifacts may affect the quality or accuracy of transmission SEM data, especially those acquired by the use of transmission Kikuchi diffraction. Generally, the quality of orientation data was better for specimens prepared by electropolishing, due to the absence of ion-induced damage. - Highlights: • The transmission imaging and diffraction techniques are emerging in scanning electron microscopy (SEM) as promising new field of materials characterization. • The manuscript titled: “Transmission Kikuchi Diffraction and Transmission Electron Forescatter Imaging of Electropolished and FIB Manufactured TEM Specimens” documents how different specimen thinning procedures can effect efficiency of transmission Kikuchi diffraction and transmission electron forescatter imaging. • The abilities to make precision crystallographic orientation maps and dark-field images in transmission was studied on electropolished versus focus ion beam manufactured TEM specimens. • Depending on the need, electropolished and focused ion beam technique may produce suitable specimens for transmission imaging and diffraction in SEM.« less

Elevated liver fibrosis index FIB-4 is not reliable for HCC risk stratification in predominantly non-Asian CHB patients

PubMed Central

Demir, Münevver; Grünewald, Friederike; Lang, Sonja; Schramm, Christoph; Bowe, Andrea; Mück, Vera; Kütting, Fabian; Goeser, Tobias; Steffen, Hans-Michael

2016-01-01

Abstract We aimed to validate the liver fibrosis index FIB-4 as a model for risk stratification of hepatocellular carcinoma development in predominantly non-Asian patients with chronic hepatitis B infection seen at a tertiary referral center in Germany. We retrospectively analyzed 373 adult patients with chronic hepatitis B infection. Patient demographics, hepatitis B markers, antiviral treatment, laboratory parameters, results from liver imaging and histology were recorded. Patients were divided into 2 groups according to their FIB-4 levels and their hazard ratios for developing hepatocellular carcinoma were analyzed adjusted for age, sex, body mass index, alcohol consumption, and antiviral medication. Median follow-up was 8.7 years (range 1–21.3 years), 93% of patients were of non-Asian origin, and 64% were male. Compared with patients with a low FIB-4 (<1.25) patients with FIB-4 ≥1.25 showed a hazard ratio for incidence of hepatocellular carcinoma of 3.03 (95% confidence interval (CI): 1.24–7.41) and an adjusted hazard ratio of 1.75 (95% CI: 0.64–4.74). Notably, 68% of patients with liver cirrhosis and 68% of those who developed HCC during observation had a low FIB-4 (<1.25). We could not confirm that a FIB-4 value ≥1.25 is a reliable clinical indicator for incidence of hepatocellular carcinoma in predominantly non-Asian patients with chronic hepatitis B. Further studies in geographically and ethnically diverse populations are needed to prove its utility as a predictive tool. PMID:27661015

Fibrinogen, Riboflavin, and UVA to Immobilize a Corneal Flap – Molecular Mechanisms

PubMed Central

Littlechild, Stacy L.; Zhang, Yuntao; Tomich, John M.; Conrad, Gary W.

2012-01-01

Purpose. Tissue glue containing fibrinogen (FIB) and riboflavin (RF), upon exposure to long wavelength ultraviolet light (UVA, 365 nM) has been proposed potentially to solve long-standing problems presented by corneal wound and epithelial ingrowth side-effects from laser-assisted in situ keratomileuis (LASIK). Data presented in a previous study demonstrated an ability of FIB + RF + UVA to adhere two stromal surfaces; however, to our knowledge no molecular mechanisms have been proposed to account for interactions occurring between corneal extracellular matrix (ECM) and tissue glue molecules. Here, we document several covalent and noncovalent interactions between these classes of macromolecules. Methods. SDS-PAGE and Western blot techniques were used to identify covalent interactions between tissue glue molecules and corneal ECM molecules in either the presence or absence of RF and UVA, in vitro and ex vivo. Surface plasmon resonance (SPR) was used to characterize noncovalent interactions, and obtain ka, kd, and KD binding affinity values. Results. SDS-PAGE and Western blot analyses indicated that covalent interactions occurred between neighboring FIB molecules, as well as between FIB and collagen type I (Coll-I) proteins (in vitro and ex vivo). These interactions occurred only in the presence of RF and UVA. SPR data demonstrated the ability of FIB to bind noncovalently to corneal stroma molecules, Coll-I, decorin, dermatan sulfate, and corneal basement membrane molecules, laminin and heparan sulfate – only in the presence of Zn2+. Conclusions. Covalent and (zinc-mediated) noncovalent mechanisms involving FIB and stromal ECM molecules contribute to the adhesion created by FIB + RF + UVA. PMID:22879413

Elevated liver fibrosis index FIB-4 is not reliable for HCC risk stratification in predominantly non-Asian CHB patients.

PubMed

Demir, Münevver; Grünewald, Friederike; Lang, Sonja; Schramm, Christoph; Bowe, Andrea; Mück, Vera; Kütting, Fabian; Goeser, Tobias; Steffen, Hans-Michael

2016-09-01

We aimed to validate the liver fibrosis index FIB-4 as a model for risk stratification of hepatocellular carcinoma development in predominantly non-Asian patients with chronic hepatitis B infection seen at a tertiary referral center in Germany.We retrospectively analyzed 373 adult patients with chronic hepatitis B infection. Patient demographics, hepatitis B markers, antiviral treatment, laboratory parameters, results from liver imaging and histology were recorded. Patients were divided into 2 groups according to their FIB-4 levels and their hazard ratios for developing hepatocellular carcinoma were analyzed adjusted for age, sex, body mass index, alcohol consumption, and antiviral medication.Median follow-up was 8.7 years (range 1-21.3 years), 93% of patients were of non-Asian origin, and 64% were male. Compared with patients with a low FIB-4 (<1.25) patients with FIB-4 ≥1.25 showed a hazard ratio for incidence of hepatocellular carcinoma of 3.03 (95% confidence interval (CI): 1.24-7.41) and an adjusted hazard ratio of 1.75 (95% CI: 0.64-4.74). Notably, 68% of patients with liver cirrhosis and 68% of those who developed HCC during observation had a low FIB-4 (<1.25).We could not confirm that a FIB-4 value ≥1.25 is a reliable clinical indicator for incidence of hepatocellular carcinoma in predominantly non-Asian patients with chronic hepatitis B. Further studies in geographically and ethnically diverse populations are needed to prove its utility as a predictive tool.

The monomeric, tetrameric, and fibrillar organization of Fib: the dynamic building block of the bacterial linear motor of Spiroplasma melliferum BC3.

PubMed

Cohen-Krausz, Sara; Cabahug, Pamela C; Trachtenberg, Shlomo

2011-07-08

Spiroplasmas belong to the class Mollicutes, representing the minimal, free-living, and self-replicating forms of life. Spiroplasmas are helical wall-less bacteria and the only ones known to swim by means of a linear motor (rather than the near-universal rotary bacterial motor). The linear motor follows the shortest path along the cell's helical membranal tube. The motor is composed of a flat monolayered ribbon of seven parallel fibrils and is believed to function in controlling cell helicity and motility through dynamic, coordinated, differential length changes in the fibrils. The latter cause local perturbations of helical symmetry, which are essential for net directional displacement in environments with a low Reynolds number. The underlying fibrils' core building block is a circular tetramer of the 59-kDa protein Fib. The fibrils' differential length changes are believed to be driven by molecular switching of Fib, leading consequently to axial ratio and length changes in tetrameric rings. Using cryo electron microscopy, diffractometry, single-particle analysis of isolated ribbons, and sequence analyses of Fib, we determined the overall molecular organization of the Fib monomer, tetramer, fibril, and linear motor of Spiroplasma melliferum BC3 that underlies cell geometry and motility. Fib appears to be a bidomained molecule, of which the N-terminal half is apparently a globular phosphorylase. By a combination of reversible rotation and diagonal shift of Fib monomers, the tetramer adopts either a cross-like nonhanded conformation or a ring-like handed conformation. The sense of Fib rotation may determine the handedness of the linear motor and, eventually, of the cell. A further change in the axial ratio of the ring-like tetramers controls fibril lengths and the consequent helical geometry. Analysis of tetramer quadrants from adjacent fibrils clearly demonstrates local differential fibril lengths. Copyright © 2011 Elsevier Ltd. All rights reserved.

AST-platelet ratio index, Forns index and FIB-4 in the prediction of significant fibrosis and cirrhosis in patients with chronic hepatitis C.

PubMed

Güzelbulut, Fatih; Çetınkaya, Züleyha Akkan; Sezıklı, Mesut; Yaşar, Bülent; Ozkara, Selvinaz; Övünç, Ayşe Oya Kurdaş

2011-06-01

The aim of this study was to evaluate the diagnostic accuracy of aspartate aminotransferase-platelet ratio index, the Forns index and FIB-4 for the assessment of hepatic fibrosis in chronic hepatitis C patients by comparison with liver biopsy. We retrospectively reviewed our computerized data of chronic hepatitis C patients who admitted to the Gastroenterology Clinic between 2004 and 2008. Treatment-naive chronic hepatitis C patients who had undergone liver biopsy and had laboratory test results allowing the calculation of aspartate aminotransferase-platelet ratio index, the Forns index and FIB-4 were included in this study. The degree of fibrosis was scored according to the METAVIR staging system. Significant fibrosis was defined as F2-4 and cirrhosis as F4. Aspartate aminotransferase-platelet ratio index, the Forns index and FIB-4 were calculated based on the original studies. Tests results were compared between groups F0-1 (no or mild fibrosis) versus F2-4 (significant fibrosis) and F03 (no cirrhosis) versus F4 (cirrhosis). One hundred and fifty patients with chronic hepatitis C were included in this study. The areas under the ROC curves of the Forns index, aspartate aminotransferase-platelet ratio index and FIB-4 to predict significant fibrosis were 0.795, 0.774 and 0.764, respectively. The area under the ROC curves of the Forns index, aspartate aminotransferase-platelet ratio index and FIB-4 to predict cirrhosis were 0.879, 0.839 and 0.874, respectively. The Forns index, aspartate aminotransferase-platelet ratio index and FIB-4 were accurate noninvasive blood tests to predict the presence or absence of significant fibrosis and cirrhosis in half of the chronic hepatitis C patients. The Forns index was slightly better than the aspartate aminotransferase-platelet ratio index and FIB-4 in the prediction of significant fibrosis and cirrhosis.

Predictive value of FIB-4 and APRI versus METAVIR on sustained virologic response in genotype 1 hepatitis C patients.

PubMed

Ferenci, Peter; Aires, Rodrigo; Beavers, Kimberly L; Curescu, Manuela; Abrão Ferreira, Paulo R; Gschwantler, Michael; Ion, Stefan; Larrey, Dominique; Maticic, Mojca; Puoti, Massimo; Schuller, János; Tornai, Istvan; Tusnádi, Anna; Messinger, Diethelm; Tatsch, Fernando; Horban, Andrzej

2014-01-01

Advanced liver fibrosis is a negative predictor of virologic response in genotype 1 chronic hepatitis C (CHC) patients. Biopsy, however, is invasive, costly, and carries some risk of complications. Using data from the prospective, international cohort study PROPHESYS, we assessed two alternative noninvasive measures of fibrosis, the FIB-4 and AST-to-platelet ratio index (APRI), to predict virologic response in CHC patients. CHC genotype 1, monoinfected, treatment-naive patients prescribed peginterferon alfa-2a (40 KD)/ribavirin in accordance with country-specific legal and regulatory requirements and who had baseline METAVIR, FIB-4, and APRI scores (N = 1,592) were included in this analysis. Patients were stratified according to the baseline METAVIR, FIB-4, or APRI score to assess virologic response [hepatitis C virus (HCV) RNA <50 IU/mL] by week 4 of treatment (rapid virologic response) and 24 weeks after untreated follow-up ]sustained virologic response (SVR)]. Baseline predictors of SVR were explored by multiple logistic regression, and the strength of the association between each fibrosis measure and SVR was evaluated. Both FIB-4 and APRI scores increased with increasing levels of biopsy-assessed fibrosis. The association between FIB-4 and SVR (p < 0.1 × 10(-30)) was stronger than that between METAVIR (p = 3.86 × 10(-13)) or APRI (p = 5.48 × 10(-6)) and SVR. Baseline factors significantly associated with SVR included male gender, lower HCV RNA, lower FIB-4 score, no steatosis, and higher alanine aminotransferase ratio. The FIB-4 index provides a valuable, noninvasive measure of fibrosis and can be used to predict virologic response in patients treated with peginterferon alfa-2a (40  KD)/ribavirin.

Value of Egy-Score in diagnosis of significant, advanced hepatic fibrosis and cirrhosis compared to aspartate aminotransferase-to-platelet ratio index, FIB-4 and Forns' index in chronic hepatitis C virus.

PubMed

Alboraie, Mohamed; Khairy, Marwa; Elsharkawy, Marwa; Asem, Noha; Elsharkawy, Aisha; Esmat, Gamal

2015-05-01

Serum markers and developed scores are of rising importance in non-invasive diagnosis of hepatic fibrosis. Aspartate aminotransferase-to-platelet ratio index (APRI), FIB-4 and Forns' index are validated scores used for diagnosis of liver fibrosis. The Egy-Score is a newly developed score for detection of hepatic fibrosis with promising results. We aimed to assess the accuracy of the Egy-Score in the diagnosis of significant fibrosis, advanced fibrosis and cirrhosis compared to APRI, FIB-4 and Forns' in chronic hepatitis C virus (HCV) patients. A retrospective study including 100 chronic hepatitis C naïve Egyptian patients was performed. Patients were classified according to stages of fibrosis into three groups: significant fibrosis (≥ F2), advanced fibrosis (≥ F3) and cirrhosis (F4). Egy-Score, APRI, FIB-4 and Forns' index were calculated. Regression analysis and receiver-operator curves were plotted to assess the sensitivity, specificity and predictive values for the significant scores with the best cut-off for diagnosis. An Egy-Score of 3.28 or more was superior to APRI, FIB-4 and Forns' index for detecting advanced fibrosis with a sensitivity of 91% and specificity of 78%. An Egy-Score of 3.67 or more was superior to APRI, FIB-4 and Forns' index for detecting cirrhosis with a sensitivity of 82% and specificity of 87%. Forns' index was superior to Egy-Score, FIB-4 and APRI for detecting significant fibrosis. The Egy-Score is a promising, accurate, easily calculated, cost-effective score in the prediction of hepatic fibrosis in chronic HCV patients with superiority over APRI, FIB-4 and Forns' index in advanced hepatic fibrosis and cirrhosis. © 2014 The Japan Society of Hepatology.

Directed self-assembly of metal oxide quantum dots: Copper oxide on strontium titanium trioxide

NASA Astrophysics Data System (ADS)

Du, Yingge

2007-12-01

This dissertation explores the use of focused ion-beams (FIB) to direct the self-assembly of Cu2O quantum dots (QDs) on SrTiO3 (100) substrates via point implants of Ga+ at 30 keV After Ga+ implant and subsequent chemical and thermal surface preparation, oxygen plasma-assisted molecular beam-epitaxy (OPA-MBE) is used to grow Cu 2O QDs. The research of this dissertation finds that, for high FIB implant dose (5.6x1018 ions/cm2) and large interdot spacing (1000 nm), multiple QDs can be formed preferentially on the edges of FIB modified pits. For lower doses and/or smaller interdot spacings (8.8x1014 ions/cm2 and lower, 130 or 167 nm), individual QDs nucleate first within the pits. Under carefully controlled conditions, the separation and arrangement of the Cu2O QDs follows the FIB patterned template. This study finds that the FIB directed self-assembly technique works for different FIB doses, FIB interdot spacings and OPA-MBE deposition thicknesses, suggesting that this method is robust and flexible. Examination of QD growth on low-dose implant surfaces revealed a multi-step growth process. Initial deposition filled the pits just to the level of the original unmodified crystal growth surface. Following a pause in QD growth and the deposition of additional material, QD growth resumed on top of these perfectly filled pits. As growth continued, the dots reached a self-limiting size such that additional material deposition generated more QDs of similar size rather than continued growth of the large dots. This dissertation also seeks to increase understanding of the relative rolls played in the directed self-assembly process by local substrate chemistry, surface morphology, crystal-linity, and stress/strain. Experimental results revealed that although Ga concentration was noticeably higher on modified regions after FIB implant, no measurable Ga was found on the surface after high temperature annealing performed prior to QD growth. Thus Ga related chemistry/reactivity changes appear unlikely to be primary motivators of directed self-assembly. Low dose implant patterning created local depressions on the surface. This pit shape topography appears to be a strong contributor to the preferred nucleation within the pits, as the sidewalls of those surface pits could contain a high density of surface steps, which are known to decrease the adatom diffusion length and act as sinks to absorb the diffusing species. To further interpret the low dose implant results, calculations of total free-energy changes have been performed to study the differences between nucleation on a flat substrate surface and nucleation within a surface pit. This analysis shows that nucleation within a pit is almost always energetically favorable. In some special cases, assuming the pits have an inverted pyramidal shape, calculations show that island formation within the pits lowers the system total free-energy from the beginning of growth, i.e. there is no critical radius or energy barrier before a stable nucleus can be formed. The major geometric difference between high and low dose implantation area was revealed by AFM studies, which showed that pits generated by high implantation dose were still rounded after annealing and before growth, while pits from lower doses patterning had developed square edges oriented along the <100> directions of the substrate. These geometric differences suggest differences in crystalline or strain/stress states, either/both of which could have caused the subsequent different island growth characteristics. Continued study of directed self-assembly of metal oxide quantum dots should lead to better understanding of the creation of well ordered, precisely controlled, high density QD arrays, ultimately contributing to the development of next generation nanoelectronic, magnetic, and optical devices.

Search for Fluid Inclusions in a Carbonaceous Chondrite Using a New X-Ray Micro-Tomography Technique Combined with FIB Sampling

NASA Technical Reports Server (NTRS)

Tsuchiyama, A.; Miyake, A.; Zolensky, M. E.; Uesugi, K.; Nakano, T.; Takeuchi, A.; Suzuki, Y.; Yoshida, K.

2014-01-01

Early solar system aqueous fluids are preserved in some H chondrites as aqueous fluid inclusions in halite (e.g., [1]). Although potential fluid inclusions are also expected in carbonaceous chondrites [2], they have not been surely confirmed. In order to search for these fluid inclusions, we have developped a new X-ray micro-tomography technique combined with FIB sampling and applied this techniqu to a carbanaceous chondrite. Experimental: A polished thin section of Sutter's Mill meteorite (CM) was observed with an optical microscope and FE-SEM (JEOL 7001F) for chosing mineral grains of carbonates (mainly calcite) and sulfides (FeS and ZnS) 20-50 microns in typical size, which may have aqueous fluid inclusions. Then, a "house" similar to a cube with a roof (20-30 microns in size) is sampled from the mineral grain by using FIB (FEI Quanta 200 3DS). Then, the house was atached to a thin W-needle by FIB and imaged by a SR-based imaging microtomography system with a Fresnel zone plate at beamline BL47XU, SPring-8, Japan. One sample was imaged at two X-ray energies, 7 and 8 keV, to identify mineral phases (dual-enegy microtomography: [3]). The size of voxel (pixel in 3D) was 50-80 nm, which gave the effective spatial resolution of approx. 200 nm. A terrestrial quartz sample with an aqueous fluid inclusion with a bubble was also examined as a test sample by the same method. Results and discussion: A fluid inclusion of 5-8 microns in quartz was clearly identified in a CT image. A bubble of approx. 4 microns was also identified as refraction contrast although the X-ray absorption difference between fluid and bubble is small. Volumes of the fluid and bubble were obtained from the 3D CT images. Fourteen grains of calcite, two grains of iron sulfide and one grain of (Zn,Fe)S were examined. Ten calcite, one iron sulfide and one (Zn,Fe)S grains have inclusions >1 micron in size (the maximum: approx. 5 microns). The shapes are spherical or irregular. Tiny inclusions (<1 micron) are also present in all the grains examined. These results show that mineral grains have more inclusions than expected from 2D observations. The X-ray absorption of the inclusions shows that they are not solid inclusions. No bubbles were observed inside, indicating that we cannot determine whether they are really aqueous fluids or merely voids. One calcite grain has an inclusion approx. 2 microns in size, which seems to have a bubble and a tiny solid daughter crystal inside (three-phase inclusion). As we know the exact 3D position of the inclusion, we will anlyze the inclusion by SIMS after freezing the sample as has been done for a halite sample [3]. The present technique is useful for finding small inclusions not only in carbonaceous chondrites but also for terrestrial materials.

Constraints on Exposure Ages of Lunar and Asteroidal Regolith Particles

NASA Technical Reports Server (NTRS)

Berger, Eve L.; Keller, Lindsay P

2014-01-01

Mineral grains in lunar and asteroidal regolith samples provide a unique record of their interaction with the space environment. Exposure to the solar wind results in implantation effects that are preserved in the rims of grains (typically the outermost 100 nm), while impact processes result in the accumulation of vapor-deposited elements, impact melts and adhering grains on particle surfaces. These processes are collectively referred to as space weathering. A critical element in the study of these processes is to determine the rate at which these effects accumulate in the grains during their space exposure. For small particulate samples, one can use the density of solar flare particle tracks to infer the length of time the particle was at the regolith surface (i.e., its exposure age). We have developed a new technique that enables more accurate determination of solar flare particle track densities in mineral grains <50 micron in size that utilizes focused ion beam (FIB) sample preparation combined with transmission electron microscopy (TEM) imaging. We have applied this technique to lunar soil grains from the Apollo 16 site (soil 64501) and most recently to samples from asteroid 25143 Itokawa returned by the Hayabusa mission. Our preliminary results show that the Hayabusa grains have shorter exposure ages compared to typical lunar soil grains. We will use these techniques to re-examine the track density-exposure age calibration from lunar samples reported by Blanford et al. (1975).

Metabolic and Epigenetic Interactions Regulate Vascular Phenotypic Change and Maintenance in Pulmonary Hypertension

DTIC Science & Technology

2016-10-01

Krebs cycle through the generation of alpha-ketoglutarate. However, increased oxidative stress affected oxygen consumption rates at the Complex I...machinery and respiration in PH-Fibs. The difference in endogenous respiration, (i.e., oxygen consumption ) was not statistically different compared...driven through complex I. We found a roughly17% drop in oxygen consumption in PH-Fibs versus Co-Fibs (Figure 3C), which corresponded to the down

In situ micro-compression testing of He2+ ion irradiated titanium aluminide

NASA Astrophysics Data System (ADS)

Wei, Tao; Xu, Alan; Zhu, Hanliang; Ionescu, Mihail; Bhattacharyya, Dhriti

2017-10-01

A titanium aluminide (TiAl) alloy 45XD has been irradiated by a He ion beam with an energy of 5 MeV on a tandem accelerator at the Australian Nuclear Science and Technology Organization (ANSTO). The total fluence of He ions was 5 × 1017 ion cm-2. A 17 μm uniform damage region from the material surface with a helium concentration of about 5000 appm was achieved by using an energy degrading wheel in front of the TiAl target. The micro-size test specimens from the damage layer were fabricated using a focused ion beam & scanning electron microscope (FIB-SEM) system. The in situ SEM micromechanical compressive testing was carried out inside an SEM and the results indicated irradiation embrittlement in the helium affected region. Electron back scatter diffraction (EBSD) analysis has been applied to reveal the orientation of the lamellae in the TiAl specimens, and used to understand the deformation processes in the sample. The irradiation damage of gallium ion beam from FIB on the surface of TiAl sample was also investigated.

Thermal stability of tungsten sub-nitride thin film prepared by reactive magnetron sputtering

NASA Astrophysics Data System (ADS)

Zhang, X. X.; Wu, Y. Z.; Mu, B.; Qiao, L.; Li, W. X.; Li, J. J.; Wang, P.

2017-03-01

Tungsten sub-nitride thin films deposited on silicon samples by reactive magnetron sputtering were used as a model system to study the phase stability and microstructural evolution during thermal treatments. XRD, SEM&FIB, XPS, RBS and TDS were applied to investigate the stability of tungsten nitride films after heating up to 1473 K in vacuum. At the given experimental parameters a 920 nm thick crystalline film with a tungsten and nitrogen stoichiometry of 2:1 were achieved. The results showed that no phase and microstructure change occurred due to W2N film annealing in vacuum up to 973 K. Heating up to 1073 K led to a partial decomposition of the W2N phase and the formation of a W enrichment layer at the surface. Increasing the annealing time at the same temperature, the further decomposition of the W2N phase was negligible. The complete decomposition of W2N film happened as the temperature reached up to 1473 K.

Interfacial microanalysis of rubber tyre-cord adhesion and the influence of cobalt

NASA Astrophysics Data System (ADS)

Fulton, W. Stephen; Smith, Graham C.; Titchener, Keith J.

2004-01-01

The effect of cobalt-containing adhesion promoters on the structure and morphology of rubber-brass and rubber-tyre-cord interfaces before and after ageing has been investigated by X-ray photoelectron spectroscopy (XPS) depth profiling, glancing incidence X-ray diffraction (XRD) and transmission electron microscopy (TEM). The effect the cobalt adhesion promoters had upon the interface morphology as they suppressed the growth of crystalline dendrites normally associated with the ageing process was imaged in TEM using samples prepared by the focused ion beam (FIB) milling technique. XPS depth profiling through the interfaces revealed that different types of adhesion promoter influenced the amount and distribution of cobalt ions in the bonding layer. XRD demonstrated the influence that cobalt had upon the structure of the interface and subsequent crystallinity, with a lesser degree of crystallinity being associated with better adhesion performance. From the results a model for the effect of the Co chemistry of the adhesion promotor has been developed.

Quantitative HAADF STEM of SiGe in presence of amorphous surface layers from FIB preparation.

PubMed

Grieb, Tim; Tewes, Moritz; Schowalter, Marco; Müller-Caspary, Knut; Krause, Florian F; Mehrtens, Thorsten; Hartmann, Jean-Michel; Rosenauer, Andreas

2018-01-01

The chemical composition of four Si 1-x Ge x layers grown on silicon was determined from quantitative scanning transmission electron microscopy (STEM). The chemical analysis was performed by a comparison of the high-angle annular dark field (HAADF) intensity with multislice simulations. It could be shown that amorphous surface layers originating from the preparation process by focused-ion beam (FIB) at 30 kV have a strong influence on the quantification: the local specimen thickness is overestimated by approximately a factor of two, and the germanium concentration is substantially underestimated. By means of simulations, the effect of amorphous surface layers on the HAADF intensity of crystalline silicon and germanium is investigated. Based on these simulations, a method is developed to analyze the experimental HAADF-STEM images by taking the influence of the amorphous layers into account which is done by a reduction of the intensities by multiplication with a constant factor. This suggested modified HAADF analysis gives germanium concentrations which are in agreement with the nominal values. The same TEM lamella was treated with low-voltage ion milling which removed the amorphous surface layers completely. The results from subsequent quantitative HAADF analyses are in agreement with the nominal concentrations which validates the applicability of the used frozen-lattice based multislice simulations to describe the HAADF scattering of Si 1-x Ge x in STEM. Copyright © 2017 Elsevier B.V. All rights reserved.

Impact of FIB-4 index on hepatocellular carcinoma incidence during nucleos(t)ide analogue therapy in patients with chronic hepatitis B: An analysis using time-dependent receiver operating characteristic.

PubMed

Tada, Toshifumi; Kumada, Takashi; Toyoda, Hidenori; Tsuji, Kunihiko; Hiraoka, Atsushi; Tanaka, Junko

2017-02-01

Nucleos(t)ide analogue (NA) therapy has been reported to reduce the risk of hepatocellular carcinoma (HCC) development in patients with chronic hepatitis B (CHB). However, even during NA therapy, development of HCC has been observed in patients with CHB. Therefore, we clarified the predictive power of clinical factors for HCC incidence using receiver operating characteristic (ROC) analysis that takes time dependence into account. A total of 539 patients with CHB treated with NAs were enrolled. Univariate, multivariate, and time-dependent ROC curves for clinical factors associated with the development of HCC were analyzed. Eighty-one patients developed HCC during the follow-up period (median duration, 5.9 years). α-fetoprotein (AFP) and FIB-4 index at 24 weeks from the initiation of treatment and sex were significantly associated with HCC incidence according to the log-rank test. Cox proportional hazards models including the covariates of sex, hepatitis B genotype, basal core promoter mutations, AFP at 24 weeks, and FIB-4 index at 24 weeks showed that FIB-4 index >2.65 (HR, 5.03; 95% CI, 3.06-8.26; P < 0.001) and male sex were independently associated with HCC incidence. In addition, time-dependent ROC analysis showed that compared with AFP at 24 weeks, FIB-4 index at 24 weeks had higher predictive power for HCC incidence throughout the follow-up period. Elevated FIB-4 index at 24 weeks in patients with CHB receiving NA therapy is a risk factor for developing HCC. The FIB-4 index is an excellent predictor of HCC development. © 2016 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Evaluation of APRI and FIB-4 scoring systems for non-invasive assessment of hepatic fibrosis in chronic hepatitis B patients.

PubMed

Kim, W Ray; Berg, Thomas; Asselah, Tarik; Flisiak, Robert; Fung, Scott; Gordon, Stuart C; Janssen, Harry L A; Lampertico, Pietro; Lau, Daryl; Bornstein, Jeffrey D; Schall, Raul E Aguilar; Dinh, Phillip; Yee, Leland J; Martins, Eduardo B; Lim, Seng Gee; Loomba, Rohit; Petersen, Jörg; Buti, Maria; Marcellin, Patrick

2016-04-01

While the gold standard in the assessment of liver fibrosis remains liver biopsy, non-invasive methods have been increasingly used for chronic hepatitis B (CHB). This study aimed to evaluate the performance of two commonly used non-invasive scoring systems (aspartate aminotransferase-to-platelet ratio index (APRI) and fibrosis index based on four factors (FIB-4)) to predict fibrosis stage in CHB patients. Demographic, histologic and clinical laboratory data from two trials investigating tenofovir disoproxil fumarate in CHB were analyzed. Predicted fibrosis stage, based on established scales and cut-off values for APRI and FIB-4 scores, was compared with Ishak scores obtained from liver biopsy at baseline and at 240 week follow-up. In the 575 patients with a baseline liver biopsy, APRI and FIB-4 scores correlated with Ishak stage (p<0.01); however extensive overlap in the distribution of both scores across Ishak stages prevented accurate determination of fibrosis. The majority (81-89%) of patients with advanced fibrosis or cirrhosis were missed by the scores. Similarly, 71% patients without fibrosis were misclassified as having clinically significant fibrosis. APRI and FIB-4 scores at week 240 tended to be low and underestimate fibrosis stage in the patients with liver biopsies after 240 weeks of therapy. APRI or FIB-4 reduction did not correlate with fibrosis regression after 240 weeks of antiviral therapy. APRI and FIB-4 scores are not suitable for use in clinical practice in CHB patients for assessment of hepatic fibrosis according to Ishak stage, especially in gauging improvements in liver fibrosis following therapy. Copyright © 2015 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Clinical significance of the FIB-4 index for non-B non-C hepatocellular carcinoma treated with surgical resection.

PubMed

Nishikawa, Hiroki; Osaki, Yukio; Komekado, Hideyuki; Sakamoto, Azusa; Saito, Sumio; Nishijima, Norihiro; Nasu, Akihiro; Arimoto, Akira; Kita, Ryuichi; Kimura, Toru

2015-01-01

The aims of the present study were to examine the relationship between the preoperative FIB-4 index and background liver fibrosis in non-tumor parts obtained from surgical specimens and to investigate whether the FIB-4 index can be a useful predictor for non-B non-C hepatocellular carcinoma (NBNC-HCC) patients treated with surgical resection (SR). A total of 118 patients with NBNC-HCC treated with SR with curative intent were analyzed. Receiver operating characteristic (ROC) curve analysis was performed for calculating the area under the ROC (AUROC) for the FIB-4 index, aspartate aminotransferase (AST) to platelet ratio index, AST to alanine aminotransferase ratio, serum albumin, total bilirubin and platelet count for cirrhosis. We also examined predictors linked to overall survival (OS) and recurrence-free survival (RFS) after SR. The mean patient age was 68.9±9.0 years (93 males and 25 females) with a median observation period of 3.2 years. In extracted surgical specimens, background liver cirrhosis (F4) was observed in 39 patients (33.1%). The mean maximum tumor size was 5.7±3.2 cm. The mean body mass index was 24.3±3.9 kg/m2. The FIB-4 index yielded the highest AUROC for cirrhosis with a level of 0.887 at an optimal cut-off value of 2.97 (sensitivity, 92.3; specificity, 69.6%). In the multivariate analysis, serum α-fetoprotein >40 ng/ml (P=0.026) was the only significant independent predictor linked to OS, while tumor number (P=0.002) and FIB-4 index >2.97 (P=0.044) were significant factors linked to RFS. In conclusion, preoperative FIB-4 index can be a useful predictor for NBNC-HCC patients who undergo SR.

Impact of age on the diagnostic performances and cut-offs of APRI and FIB-4 for significant fibrosis and cirrhosis in chronic hepatitis B.

PubMed

Li, Qiang; Lu, Chuan; Li, Weixia; Huang, Yuxian; Chen, Liang

2017-07-11

Assessing the diagnostic performances of APRI and FIB-4 using age as a categorical marker. 822 chronic hepatitis B (CHB) patients were included. Using METAVIR scoring system as a reference, the performances of APRI and FIB-4 were compared between patients aged≥30 and patients aged<30 years. The APRI AUROC in patients aged<30 years was lower than that in patients aged≥30 years for significant fibrosis (0.61 vs 0.70, p<0.001) and cirrhosis (0.64 vs 0.78, p<0.001). The FIB-4 AUROC in patients aged<30 years was lower than that in patients aged≥30 years for significant fibrosis (0.57 vs 0.65, p<0.001) and cirrhosis (0.63 vs 0.72, p<0.001). Using specificity≥90%, the APRI cut-off in patients aged<30 years was lower than patients aged≥30 years for significant fibrosis (1.0 vs 1.2) and cirrhosis (1.2 vs 1.5). Using sensitivity≥90%, the APRI cut-off in patients aged<30 years was also lower than patients aged≥30 years for significant fibrosis (0.2 vs 0.4) and cirrhosis (0.3 vs 0.5). Using specificity≥90%, the FIB-4 cut-off in patients aged<30 years was lower than that in patients aged≥30 years for significant fibrosis (1.2 vs 2.1) and cirrhosis (1.4 vs 2.6). Using sensitivity≥90%, the FIB-4 cut-off in patients aged<30 years was also lower than that in patients aged≥30 years for significant fibrosis (0.5 vs 0.8) and cirrhosis (0.8 vs 1.2). Evaluation of the diagnostic performances of APRI and FIB-4 should take age into consideration.

High FIB-4 index as an independent risk factor of prevalent chronic kidney disease in patients with nonalcoholic fatty liver disease.

PubMed

Xu, Huang-Wei; Hsu, Yung-Chien; Chang, Chia-Hao; Wei, Kuo-Liang; Lin, Chun-Liang

2016-03-01

Growing evidence suggests that non-alcoholic fatty liver disease (NAFLD) is linked to an increased risk for chronic kidney disease (CKD); liver fibrosis with biopsy-proven NAFLD has also been shown to associate with an increased risk of CKD. This study compares the diagnostic performance of simple noninvasive tests in identifying prevalent CKD among individuals with ultrasonography-diagnosed NAFLD. A total of 755 with ultrasonography-diagnosed NAFLD were included. Estimated glomerular filtration rate and noninvasive markers for hepatic fibrosis: aspartate transaminase to alanine transaminase ratio (AAR), aspartate transaminase to platelet ratio index (APRI), FIB-4 score, NAFLD fibrosis score (NFS) and BARD score were assessed. Binary logistic regression to generate a propensity score and receiver operating characteristic curves were developed for each of the noninvasive markers for predicting CKD, and the area under the receiver operating characteristic curve was greatest for FIB-4 score (0.750), followed by NFS (0.710), AAR (0.594), APRI (0.587), and BARD score (0.561). A cut-off value of 1.100 for FIB-4 score gave a sensitivity of 68.85% and a specificity of 71.07% for predicting CKD. The positive predictive value and negative predictive value were 37.50 and 90.05%, respectively. In multiple logistic regression analysis, only FIB-4 score ≧1.100 (OR 2.660, 95% CI 1.201-5.889; p = .016), older age, higher diastolic blood pressure and higher uric acid were independent predictors of CKD. High noninvasive fibrosis score is associated with an increased risk of prevalent CKD; the FIB-4 is the better predictor. With a cut-off value of 1.100 for FIB-4, it is useful in excluding the presence of CKD in patients with NAFLD.

Fibrin-Genipin Adhesive Hydrogel for Annulus Fibrosus Repair: Performance Evaluation with Large Animal Organ Culture, In Situ Biomechanics, and In Vivo Degradation Tests

PubMed Central

Likhitpanichkul, M.; Dreischarf, M.; Illien-Junger, S.; Walter, B. A.; Nukaga, T.; Long, R. G; Sakai, D.; Hecht, A. C.; Iatridis, J. C.

2015-01-01

Annulus fibrosus (AF) defects from annular tears, herniation, and discectomy procedures are associated with painful conditions and accelerated intervertebral disc (IVD) degeneration. Currently, no effective treatments exist to repair AF damage, restore IVD biomechanics and promote tissue regeneration. An injectable fibrin-genipin adhesive hydrogel (Fib-Gen) was evaluated for its performance repairing large AF defects in a bovine caudal IVD model using ex vivo organ culture and biomechanical testing of motion segments, and for its in vivo longevity and biocompatibility in a rat model by subcutaneous implantation. Fib-Gen sealed AF defects, prevented IVD height loss, and remained well-integrated with native AF tissue following approximately 14,000 cycles of compression in 6-day organ culture experiments. Fib-Gen repair also retained high viability of native AF cells near the repair site, reduced nitric oxide released to the media, and showed evidence of AF cell migration into the gel. Biomechanically, Fib-Gen fully restored compressive stiffness to intact levels validating organ culture findings. However, only partial restoration of tensile and torsional stiffness was obtained, suggesting opportunities to enhance this formulation. Subcutaneous implantation results, when compared with the literature, suggested Fib-Gen exhibited similar biocompatibility behaviour to fibrin alone but degraded much more slowly. We conclude that injectable Fib-Gen successfully sealed large AF defects, promoted functional restoration with improved motion segment biomechanics, and served as a biocompatible adhesive biomaterial that had greatly enhanced in vivo longevity compared to fibrin. Fib-Gen offers promise for AF repairs that may prevent painful conditions and accelerated degeneration of the IVD, and warrants further material development and evaluation. PMID:25036053

Fibrin-genipin adhesive hydrogel for annulus fibrosus repair: performance evaluation with large animal organ culture, in situ biomechanics, and in vivo degradation tests.

PubMed

Likhitpanichkul, M; Dreischarf, M; Illien-Junger, S; Walter, B A; Nukaga, T; Long, R G; Sakai, D; Hecht, A C; Iatridis, J C

2014-07-18

Annulus fibrosus (AF) defects from annular tears, herniation, and discectomy procedures are associated with painful conditions and accelerated intervertebral disc (IVD) degeneration. Currently, no effective treatments exist to repair AF damage, restore IVD biomechanics and promote tissue regeneration. An injectable fibrin-genipin adhesive hydrogel (Fib-Gen) was evaluated for its performance repairing large AF defects in a bovine caudal IVD model using ex vivo organ culture and biomechanical testing of motion segments, and for its in vivo longevity and biocompatibility in a rat model by subcutaneous implantation. Fib-Gen sealed AF defects, prevented IVD height loss, and remained well-integrated with native AF tissue following approximately 14,000 cycles of compression in 6-day organ culture experiments. Fib-Gen repair also retained high viability of native AF cells near the repair site, reduced nitric oxide released to the media, and showed evidence of AF cell migration into the gel. Biomechanically, Fib-Gen fully restored compressive stiffness to intact levels validating organ culture findings. However, only partial restoration of tensile and torsional stiffness was obtained, suggesting opportunities to enhance this formulation. Subcutaneous implantation results, when compared with the literature, suggested Fib-Gen exhibited similar biocompatibility behaviour to fibrin alone but degraded much more slowly. We conclude that injectable Fib-Gen successfully sealed large AF defects, promoted functional restoration with improved motion segment biomechanics, and served as a biocompatible adhesive biomaterial that had greatly enhanced in vivo longevity compared to fibrin. Fib-Gen offers promise for AF repairs that may prevent painful conditions and accelerated degeneration of the IVD, and warrants further material development and evaluation.

Super-resolution for asymmetric resolution of FIB-SEM 3D imaging using AI with deep learning.

PubMed

Hagita, Katsumi; Higuchi, Takeshi; Jinnai, Hiroshi

2018-04-12

Scanning electron microscopy equipped with a focused ion beam (FIB-SEM) is a promising three-dimensional (3D) imaging technique for nano- and meso-scale morphologies. In FIB-SEM, the specimen surface is stripped by an ion beam and imaged by an SEM installed orthogonally to the FIB. The lateral resolution is governed by the SEM, while the depth resolution, i.e., the FIB milling direction, is determined by the thickness of the stripped thin layer. In most cases, the lateral resolution is superior to the depth resolution; hence, asymmetric resolution is generated in the 3D image. Here, we propose a new approach based on an image-processing or deep-learning-based method for super-resolution of 3D images with such asymmetric resolution, so as to restore the depth resolution to achieve symmetric resolution. The deep-learning-based method learns from high-resolution sub-images obtained via SEM and recovers low-resolution sub-images parallel to the FIB milling direction. The 3D morphologies of polymeric nano-composites are used as test images, which are subjected to the deep-learning-based method as well as conventional methods. We find that the former yields superior restoration, particularly as the asymmetric resolution is increased. Our super-resolution approach for images having asymmetric resolution enables observation time reduction.

Modeling Fecal Indicator Bacteria Like Salt in Newport Bay

NASA Astrophysics Data System (ADS)

Ciglar, A. M.; Rippy, M.; Grant, S. B.

2015-12-01

Newport Bay is a harbor and estuary located in Orange County, CA that provides many water sports and recreational activities for millions of southern California residents and tourists. The aim of this study is to quickly assess exceedances of FIB in the Newport Bay which pose a health risk to recreational users. The ability to quickly assess water quality is made possible with an advection-diffusion mass transport model that uses easily measurable parameters such as volumetric flow rate from tributaries. Current FIB assessment methods for Newport Bay take a minimum of 24 hours to evaluate health risk by either culturing for FIB or running a more complex fluid dynamics model. By this time the FIB may have already reached the ocean outlet thus no longer posing a risk in the bay or recreationists may have already come in close contact with contaminated waters. The advection-diffusion model can process and disseminate health risk information within a few hours of flow rate measurements, minimizing time between an FIB exceedance and public awareness about the event. Data used to calibrate and validate the model was collected from January 2006 through February 2007. Salinity data was used for calibration and FIB data was used for validation. Both steady-state and transient conditions were assessed to determine if dry weather patterns can be simplified to the steady-state condition.

Fabrication of single Ga-doped ZnS nanowires as high-gain photosensors by focused ion beam deposition

NASA Astrophysics Data System (ADS)

Yen, Shih-Hsiang; Hung, Yu-Chen; Yeh, Ping-Hung; Su, Ya-Wen; Wang, Chiu-Yen

2017-09-01

ZnS nanowires were synthesized via a vapor-liquid-solid mechanism and then fabricated into a single-nanowire field-effect transistor by focused ion beam (FIB) deposition. The field-effect electrical properties of the FIB-fabricated ZnS nanowire device, namely conductivity, mobility and hole concentration, were 9.13 Ω-1 cm-1, 13.14 cm2 V-1 s-1and 4.27 × 1018 cm-3, respectively. The photoresponse properties of the ZnS nanowires were studied and the current responsivity, current gain, response time and recovery time were 4.97 × 106 A W-1, 2.43 × 107, 9 s and 24 s, respectively. Temperature-dependent I-V measurements were used to analyze the interfacial barrier height between ZnS and the FIB-deposited Pt electrode. The results show that the interfacial barrier height is as low as 40 meV. The energy-dispersive spectrometer elemental line scan shows the influence of Ga ions on the ZnS nanowire surface on the FIB-deposited Pt contact electrodes. The results of temperature-dependent I-V measurements and the elemental line scan indicate that Ga ions were doped into the ZnS nanowire, reducing the barrier height between the FIB-deposited Pt electrodes and the single ZnS nanowire. The small barrier height results in the FIB-fabricated ZnS nanowire device acting as a high-gain photosensor.

Ultrasonic Micro-Blades for the Rapid Extraction of Impact Tracks from Aerogel

NASA Technical Reports Server (NTRS)

Ishii, H. A.; Graham, G. A.; Kearsley, A. T.; Grant, P. G.; Snead, C. J.; Bradley, J. P.

2005-01-01

The science return of NASA's Stardust Mission with its valuable cargo of cometary debris hinges on the ability to efficiently extract particles from silica aerogel collectors. The current method for extracting cosmic dust impact tracks is a mature procedure involving sequential perforation of the aerogel with glass needles on computer controlled micromanipulators. This method is highly successful at removing well-defined aerogel fragments of reasonable optical clarity while causing minimal damage to the surrounding aerogel collector tile. Such a system will be adopted by the JSC Astromaterials Curation Facility in anticipation of Stardust s arrival in early 2006. In addition to Stardust, aerogel is a possible collector for future sample return missions and is used for capture of hypervelocity ejecta in high power laser experiments of interest to LLNL. Researchers will be eager to obtain Stardust samples for study as quickly as possible, and rapid extraction tools requiring little construction, training, or investment would be an attractive asset. To this end, we have experimented with micro-blades for the Stardust impact track extraction process. Our ultimate goal is a rapid extraction system in a clean electron beam environment, such as an SEM or dual-beam FIB, for in situ sample preparation, mounting and analysis.

Reconstructing the microstructure of polyimide-silicalite mixed-matrix membranes and their particle connectivity using FIB-SEM tomography.

PubMed

Diblíková, P; Veselý, M; Sysel, P; Čapek, P

2018-03-01

Properties of a composite material made of a continuous matrix and particles often depend on microscopic details, such as contacts between particles. Focusing on processing raw focused-ion beam scanning electron microscope (FIB-SEM) tomography data, we reconstructed three mixed-matrix membrane samples made of 6FDA-ODA polyimide and silicalite-1 particles. In the first step of image processing, backscattered electron (BSE) and secondary electron (SE) signals were mixed in a ratio that was expected to obtain a segmented 3D image with a realistic volume fraction of silicalite-1. Second, after spatial alignment of the stacked FIB-SEM data, the 3D image was smoothed using adaptive median and anisotropic nonlinear diffusion filters. Third, the image was segmented using the power watershed method coupled with a seeding algorithm based on geodesic reconstruction from the markers. If the resulting volume fraction did not match the target value quantified by chemical analysis of the sample, the BSE and SE signals were mixed in another ratio and the procedure was repeated until the target volume fraction was achieved. Otherwise, the segmented 3D image (replica) was accepted and its microstructure was thoroughly characterized with special attention paid to connectivity of the silicalite phase. In terms of the phase connectivity, Monte Carlo simulations based on the pure-phase permeability values enabled us to calculate the effective permeability tensor, the main diagonal elements of which were compared with the experimental permeability. In line with the hypothesis proposed in our recent paper (Čapek, P. et al. (2014) Comput. Mater. Sci. 89, 142-156), the results confirmed that the existence of particle clusters was a key microstructural feature determining effective permeability. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Human cardiac telocytes: 3D imaging by FIB-SEM tomography.

PubMed

Cretoiu, D; Hummel, E; Zimmermann, H; Gherghiceanu, M; Popescu, L M

2014-11-01

Telocyte (TC) is a newly identified type of cell in the cardiac interstitium (www.telocytes.com). TCs are described by classical transmission electron microscopy as cells with very thin and long telopodes (Tps; cellular prolongations) having podoms (dilations) and podomers (very thin segments). TCs' three-dimensional (3D) morphology is still unknown. Cardiac TCs seem to be particularly involved in long and short distance intercellular signalling and, therefore, their 3D architecture is important for understanding their spatial connections. Using focused ion beam scanning electron microscopy (FIB-SEM) we show, for the first time, the whole ultrastructural anatomy of cardiac TCs. 3D reconstruction of cardiac TCs by FIB-SEM tomography confirms that they have long, narrow but flattened (ribbon-like) telopodes, with humps generated by the podoms. FIB-SEM tomography also confirms the network made by TCs in the cardiac interstitium through adherens junctions. This study provides the first FIB-SEM tomography of a human cell type. © 2014 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Bacteriophages as indicators of faecal pollution and enteric ...

EPA Pesticide Factsheets

Bacteriophages are an attractive alternative to fecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport due to their closer morphological and biological properties compared to FIB. Based on a meta-analysis of published data, we summarize concentrations of coliphages (F+ and somatic), Bacteroides spp. and enterococci bacteriophages (phages) in human waste, non-human waste, fresh and marine waters as well as removal through wastewater treatment processes. We also provide comparisons with FIB and enteric viruses whenever possible. Lastly, we examine fate and transport characteristics in the environment and provide an overview of the methods available for detection and enumeration of bacteriophages. In summary, concentrations of FIB bacteriophages in various sources were consistently lower than FIB, but more reflective of infectious enteric virus levels. Our investigation supports use of bacteriophages as viral surrogates especially for wastewater treatment processes, while additional research is needed to clarify their utility as indicators of viral fate and transport in the ambient water. Describes concentrations and removal through environmental and engineered systems of bacteriophages, fecal indicator bacteria and viral pathogens.

APRI and FIB-4 are good predictors of the stage of liver fibrosis in chronic hepatitis B: the Chronic Hepatitis Cohort Study (CHeCS).

PubMed

Teshale, E; Lu, M; Rupp, L B; Holmberg, S D; Moorman, A C; Spradling, P; Vijayadeva, V; Boscarino, J A; Schmidt, M A; Gordon, S C

2014-12-01

We aim to determine the predictive ability of APRI, FIB-4 and AST/ALT ratio for staging of liver fibrosis and to differentiate significant fibrosis (F2-F4) from none to minimal fibrosis (F0-F1) in chronic hepatitis B (CHB). Liver biopsy results were mapped to an F0-4 equivalent fibrosis stage. Mean APRI and FIB-4 scores were significantly higher for each successive fibrosis level from F1 to F4 (P < 0.05). Based on optimized cut-offs, the AUROCs in distinguishing F2-F4 from F0 to F1 were 0.81 (0.76-0.87) for APRI, 0.81 (0.75-0.86) for FIB-4 and 0.56 (0.49-0.64) for AST/ALT ratio. APRI and FIB-4 distinguished F2-F4 from F0 to F1 with good sensitivity and specificity and can be useful for treatment decisions and monitoring progression of fibrosis. © 2014 John Wiley & Sons Ltd.

The impact of hospital and urban wastewaters on the bacteriological contamination of the water resources in Kinshasa, Democratic Republic of Congo.

PubMed

Kilunga, Pitchouna I; Kayembe, John M; Laffite, Amandine; Thevenon, Florian; Devarajan, Naresh; Mulaji, Crispin K; Mubedi, Josué I; Yav, Zéphirin G; Otamonga, Jean-Paul; Mpiana, Pius T; Poté, John

2016-10-14

Although the United Nations General Assembly recognized in 2010 the right to safe and clean drinking water and sanitation as a human right that is essential to the full enjoyment of life and all other human rights, the contamination of water supplies with faecal pathogens is still a major and unsolved problem in many parts of the world. In this study, faecal indicator bacteria (FIB), including Escherichia coli (E. coli) and Enterococcus (ENT), were quantified over the period of June/July 2014 and June/July 2015 to assess the quality of hospital effluents (n = 3: H1, H2 and H3) and of rivers receiving wastewaters from the city of Kinshasa, Democratic Republic of Congo. The water and sediment samples from the river-receiving systems were collected in, upstream and downstream of the hospital outlet pipe (HOP) discharge. The analysis of E. coli and ENT in water and sediment suspension was performed using the cultural membrane filter method. The FIB characterization was performed for general E. coli, Enterococcus faecalis(E. faecalis) and human-specific Bacteroides by PCR using specific primers. The results revealed very high FIB concentration in the hospital effluent waters, with E. coli reaching the values of 4.2 × 10(5), 16.1 × 10(5) and 5.9 × 10(5) CFU 100 mL(-1), for the hospital effluents from H1, H2, and H3, respectively; and Enterococcus reaching the values of 2.3 × 10(4), 10.9 × 10(4) and 4.1 × 10(4) CFU 100 mL(-1), respectively. Interestingly, the FIB levels in the water and sediment samples from river-receiving systems are spatially and temporally highly variable and present in some samples with higher values than the hospital effluents. The PCR assays for human-specific Bacteroides HF183/HF134 further indicate that more than 98% of bacteria were from human origin. The results of this research therefore confirm the hypothesis of our previous studies, indicating that in developing countries (e.g., Democratic Republic of Congo and South India), the hospital effluent waters can be a significant source of the deterioration of the bacteriological quality for urban rivers. The approach used in this investigation can be further used to decipher the pollution of water resources by human faecal contamination. The results of this research will help to better understand the microbiological pollution problems in river-receiving systems and will guide municipality decisions on improving the urban water quality.

Focused ion beam system

DOEpatents

Leung, Ka-Ngo; Gough, Richard A.; Ji, Qing; Lee, Yung-Hee Yvette

1999-01-01

A focused ion beam (FIB) system produces a final beam spot size down to 0.1 .mu.m or less and an ion beam output current on the order of microamps. The FIB system increases ion source brightness by properly configuring the first (plasma) and second (extraction) electrodes. The first electrode is configured to have a high aperture diameter to electrode thickness aspect ratio. Additional accelerator and focusing electrodes are used to produce the final beam. As few as five electrodes can be used, providing a very compact FIB system with a length down to only 20 mm. Multibeamlet arrangements with a single ion source can be produced to increase throughput. The FIB system can be used for nanolithography and doping applications for fabrication of semiconductor devices with minimum feature sizes of 0.1 .mu.m or less.

Focused ion beam system

DOEpatents

Leung, K.; Gough, R.A.; Ji, Q.; Lee, Y.Y.

1999-08-31

A focused ion beam (FIB) system produces a final beam spot size down to 0.1 {mu}m or less and an ion beam output current on the order of microamps. The FIB system increases ion source brightness by properly configuring the first (plasma) and second (extraction) electrodes. The first electrode is configured to have a high aperture diameter to electrode thickness aspect ratio. Additional accelerator and focusing electrodes are used to produce the final beam. As few as five electrodes can be used, providing a very compact FIB system with a length down to only 20 mm. Multibeamlet arrangements with a single ion source can be produced to increase throughput. The FIB system can be used for nanolithography and doping applications for fabrication of semiconductor devices with minimum feature sizes of 0.1 m or less. 13 figs.

Structure-composition-property relationships in 5xxx series aluminum alloys

NASA Astrophysics Data System (ADS)

Unocic, Kinga A.

Al-Mg alloys are well suited for marine applications due to their low density, ease of fabrication, structural durability, and most notably resistance to corrosion. The purpose of this study is to investigate the effects of alloying additions, mechanical processing and heat treatments on the development of grain boundary phases that have an effect on intergranular corrosion (IGC). Cu, Zn, and Si modified compositions of AA5083 were produced that were subjected to a low and high degree of cold work and various heat treatments. ASTM G67 (NAMLT) intergranular corrosion testing and detailed microstructural characterization for various alloys was carried out. An optimal composition and processing condition that yielded the best intergranular corrosion resistant material was identified based on the ASTM G67 test screening. Further, the outstanding modified AA5083 was selected for further microstructural analysis. This particular alloy with has a magnesium level high enough to make it susceptible to intergranular corrosion is very resistant to IGC. It was found that development of the appropriate sub-structure with some Cu, Si and Zn resulted in a material very resistant to IGC. Formation of many sinks, provided by sub-boundaries, within microstructure is very beneficial since it produces a relatively uniform distribution of Mg in the grain interiors, and this can suppress sensitization of this alloy very successfully. This is a very promising rote for the production of high-strength, and corrosion resistant aluminum alloys. Additionally in this study, TEM sample preparation become very crucial step in grain boundary phase investigation. Focus Ion Beam (FIB) milling was used as a primary TEM sample preparation technique because it enables to extract the samples from desired and very specific locations without dissolving grain boundary phases as it was in conventional electropolishing method. However, other issues specifically relevant to FIB milling of aluminum alloys related to Ga accumulation were discovered, that produce significant microstructural artifacts. It is well known that liquid gallium can cause Liquid Metal Embitterment (LME) aluminum alloys, and gallium readily penetrates aluminum grain boundaries. Low energy Ar ion nanomilling is potentially quite effective at removing gallium from the external and internal surfaces of aluminum thin foils, but can still leave persistent artifacts. Al-Mg alloys can be also susceptible to localized corrosion such as pitting corrosion in the presence of chloride ions. In this study the phases responsible for this type of corrosion were identified. ASSET (ASTM G66) test was used to determine the influence of heat-treatment on pitting corrosion on various modified AA5083 alloys. Additionally, potentiodynamic polarization as well as potentiostatic measurements in conjunction with SEM analysis were carried out to obtain pitting potential (Epit) and to determine the location of metastable pit initiation, respectively.

Relationship between virological response and FIB-4 index in chronic hepatitis B patients with entecavir therapy.

PubMed

Li, Ni; Xu, Jing-Hang; Yu, Min; Wang, Sa; Si, Chong-Wen; Yu, Yan-Yan

2015-11-21

To investigate whether long-term low-level hepatitis B virus (HBV) DNA influences dynamic changes of the FIB-4 index in chronic hepatitis B (CHB) patients receiving entecavir (ETV) therapy with partial virological responses. We retrospectively analyzed 231 nucleos(t)ide (NA) naïve CHB patients from our previous study (NCT01926288) who received continuous ETV or ETV maleate therapy for three years. The patients were divided into partial virological response (PVR) and complete virological response (CVR) groups according to serum HBV DNA levels at week 48. Seventy-six patients underwent biopsies at baseline and at 48 wk. The performance of the FIB-4 index and area under the receiver operating characteristic (AUROC) curve for predicting fibrosis were determined for the patients undergoing biopsy. The primary objective of the study was to compare the cumulative probabilities of virological responses between the two groups during the treatment period. The secondary outcome was to observe dynamic changes of the FIB-4 index between CVR patients and PVR patients. For hepatitis B e antigen (HBeAg)-positive patients (n = 178), the cumulative probability of achieving undetectable levels at week 144 was 95% and 69% for CVR and PVR patients, respectively (P < 0.001). In the Cox proportional hazards model, a lower pretreatment serum HBV DNA level was an independent factor predicting maintained viral suppression. The cumulative probability of achieving undetectable levels of HBV DNA for HBeAg-negative patients (n = 53) did not differ between the two groups. The FIB-4 index efficiently identified fibrosis, with an AUROC of 0.80 (95%CI: 0.69-0.89). For HBeAg-positive patients, the FIB-4 index was higher in CVR patients than in PVR patients at baseline (1.89 ± 1.43 vs 1.18 ± 0.69, P < 0.001). There was no significant difference in the reduction of the FIB-4 index between the CVR and PVR groups from weeks 48 to 144 (-0.11 ± 0.47 vs -0.13 ± 0.49, P = 0.71). At week 144, the FIB-4 index levels were similar between the two groups (1.24 ± 0.87 vs 1.02 ± 0.73, P = 0.06). After multivariate logistic regression analysis, a lower baseline serum HBV DNA level was associated with improvement of liver fibrosis. In HBeAg-negative patients, the FIB-4 index did not differ between the two groups. The cumulative probabilities of HBV DNA responses showed significant differences between CVR and PVR HBeAg-positive CHB patients undergoing entecavir treatment for 144 wk. However, long-term low-level HBV DNA did not deteriorate the FIB-4 index, which was used to evaluate liver fibrosis, at the end of three years.

A Molecular MST Approach to Investigate Fecal Indicator Bacteria in Bioaerosols, Bathing Water, Seaweed Wrack, and Sand at Recreational Beaches

NASA Astrophysics Data System (ADS)

Thoren, K. M.; Sinigalliano, C. D.

2016-02-01

Despite numerous cases of beach bacteria affecting millions of people worldwide, the persistence of the bacteria populations in coastal areas is still not well understood. The purpose of this study was to test the levels of persistence of Fecal Indicating Bacteria (FIB) of enterococci, Escherichia coli, and Human-source Bacteroidales, within the intertidal "swash zone" and the deeper waist zone in which people commonly bathe and play. In addition, the study sought to determine if these bacterial contaminants may also be found in aerosols at the beach. Measuring solar insolation in relation to bacterial persistence in seaweed wrack was used to determine if sunlight plays a role in modifying concentrations of FIB at the beach. Light intensity measured by a solar photometer and air quality measured by aerosol plate counts and qPCR Microbial Source Tracking (MST) was compared to varying locations where the beach samples were collected. Results from water samples demonstrate that bacteria measured using plate counts and qPCR were indeed higher within the swash zone than in the waist zone. This is in contrast with the way that the EPA currently measures and determines the public safety of beach waters. They commonly measure the waist zone, but disregard the swash zone. Results from beach bio-aerosol samples showed a wide variety of fungi and bacteria in the beach air, and qPCR MST analysis of these bio-aerosols showed the presence of FIBs such as enterococci on several of the aerosol collection plates. This emphasizes the need to collect samples from the entire beach instead of just measuring at an isolated area, and that exposure to microbial contaminants may include bathing water, beach sand, seaweed wrack, and bio-aerosols. Thus, the data reveals a potential way to identify harmful levels of bacteria and dangerous levels of poor air quality at recreational beaches. These results expound the need for broader assessment of potential beach contamination, not only the swimming water, but also the beach air, shoreline, and also varying depths of water, which can be extremely beneficial to reduce people's risk from microbial contamination exposure.

Transmission Electron Microscopy of Iron Metal in Almahata Sitta Ureilite

NASA Technical Reports Server (NTRS)

Mikouchi, T.; Yubuta, K.; Sugiyama, K.; Aoyagi, Y.; Yasuhara, A.; Mihira, T.; Zolensky, M. E.; Goodrich, C. A.

2013-01-01

Almahata Sitta (AS) is a polymict breccia mainly composed of variable ureilite lithologies with small amounts of chondritic lithologies [1]. Fe metal is a common accessory phase in ureilites, but our earlier study on Fe metals in one of AS fragments (#44) revealed a unique mineralogy never seen in other ureilites [2,3]. In this abstract we report detailed transmission electron microscopy (TEM) on these metal grains to better understand the thermal history of ureilites. We prepared FIB sections of AS#44 by JEOL JIB-4000 from the PTS that was well characterized by SEM-EBSD in our earlier study [2]. The sections were then observed by STEM (JEOL JEM- 2100F). One of the FIB sections shows a submicron-sized symplectic intergrown texture composed of Fe metal (kamacite), Fe carbide (cohenite), Fe phosphide (schreibersite), and Fe sulfide (troilite). Each phase has an identical SAED pattern in spite of its complex texture, suggesting co-crystallization of all phases. This is probably caused by shock re-melting of pre-existing metal + graphite to form a eutectic-looking texture. The other FIB section is mostly composed of homogeneous Fe metal (93 wt% Fe, 5 wt% Ni, and 2 wt% Si), but BF-STEM images exhibited the presence of elongated lathy grains (approx. 2 microns long) embedded in the interstitial matrix. The SAED patterns from these lath grains could be indexed by alpha-Fe (bcc) while interstitial areas are gamma-Fe (fcc). The elongated alpha-Fe grains show tweed-like structures suggesting martensite transformation. Such a texture can be formed by rapid cooling from high temperature where gamma-Fe was stable. Subsequently alpha-Fe crystallized, but gamma-Fe remained in the interstitial matrix due to quenching from high temperature. This scenario is consistent with very rapid cooling history of ureilites suggested by silicate mineralogy.

Age as a Confounding Factor for the Accurate Non-Invasive Diagnosis of Advanced NAFLD Fibrosis.

PubMed

McPherson, Stuart; Hardy, Tim; Dufour, Jean-Francois; Petta, Salvatore; Romero-Gomez, Manuel; Allison, Mike; Oliveira, Claudia P; Francque, Sven; Van Gaal, Luc; Schattenberg, Jörn M; Tiniakos, Dina; Burt, Alastair; Bugianesi, Elisabetta; Ratziu, Vlad; Day, Christopher P; Anstee, Quentin M

2017-05-01

Non-invasive fibrosis scores are widely used to identify/exclude advanced fibrosis in patients with non-alcoholic fatty liver disease (NAFLD). However, these scores were principally developed and validated in patients aged between 35 and 65 years of age. The objective of this study was to assess the effect of age on the performance of non-invasive fibrosis tests in NAFLD. Patients were recruited from European specialist hepatology clinics. The cohort was divided into five age-based groups: ≤35 (n=74), 36-45 (n=96), 46-55 (n=197), 56-64 (n=191), and ≥65 years (n=76), and the performance of the aspartate aminotransferase (AST)/alanine transaminase (ALT) ratio, fibrosis 4 (FIB-4), and NAFLD fibrosis score (NFS) for advanced fibrosis (stage F3-F4) for each group was assessed using liver biopsy as the standard. Six hundred and thirty-four patients were included. The diagnostic accuracy of the AST/ALT ratio was lower than NFS and FIB-4 in all the age groups. The AST/ALT ratio, NFS, and FIB-4 score performed poorly for a diagnosis of advanced fibrosis in those aged ≤35 years (area under the receiver operating characteristic curves (AUROCs 0.52, 0.52, and 0.60, respectively). For all groups >35 years, AUROCs for advanced fibrosis were similar for the NFS and FIB-4 score (range 0.77-0.84). However, the specificity for advanced fibrosis using the FIB-4 and NFS declined with age, becoming unacceptably low in those aged ≥65 years (35% for FIB-4 and 20% for NFS). New cutoffs were derived (and validated) for those aged ≥65 years, which improved specificity to 70% without adversely affecting sensitivity (FIB-4 2.0, sensitivity 77%; NFS 0.12, sensitivity 80%). The NFS and FIB-4 scores have similar accuracy for advanced fibrosis in patients aged >35 years. However, the specificity for advanced fibrosis is unacceptably low in patients aged ≥65 years, resulting in a high false positive rate. New thresholds for use in patients aged ≥65 years are proposed to address this issue.

Age as a Confounding Factor for the Accurate Non-Invasive Diagnosis of Advanced NAFLD Fibrosis

PubMed Central

McPherson, Stuart; Hardy, Tim; Dufour, Jean-Francois; Petta, Salvatore; Romero-Gomez, Manuel; Allison, Mike; Oliveira, Claudia P; Francque, Sven; Van Gaal, Luc; Schattenberg, Jörn M; Tiniakos, Dina; Burt, Alastair; Bugianesi, Elisabetta; Ratziu, Vlad; Day, Christopher P; Anstee, Quentin M

2017-01-01

OBJECTIVES: Non-invasive fibrosis scores are widely used to identify/exclude advanced fibrosis in patients with non-alcoholic fatty liver disease (NAFLD). However, these scores were principally developed and validated in patients aged between 35 and 65 years of age. The objective of this study was to assess the effect of age on the performance of non-invasive fibrosis tests in NAFLD. METHODS: Patients were recruited from European specialist hepatology clinics. The cohort was divided into five age-based groups: ≤35 (n=74), 36–45 (n=96), 46–55 (n=197), 56–64 (n=191), and ≥65 years (n=76), and the performance of the aspartate aminotransferase (AST)/alanine transaminase (ALT) ratio, fibrosis 4 (FIB-4), and NAFLD fibrosis score (NFS) for advanced fibrosis (stage F3–F4) for each group was assessed using liver biopsy as the standard. RESULTS: Six hundred and thirty-four patients were included. The diagnostic accuracy of the AST/ALT ratio was lower than NFS and FIB-4 in all the age groups. The AST/ALT ratio, NFS, and FIB-4 score performed poorly for a diagnosis of advanced fibrosis in those aged ≤35 years (area under the receiver operating characteristic curves (AUROCs 0.52, 0.52, and 0.60, respectively). For all groups >35 years, AUROCs for advanced fibrosis were similar for the NFS and FIB-4 score (range 0.77–0.84). However, the specificity for advanced fibrosis using the FIB-4 and NFS declined with age, becoming unacceptably low in those aged ≥65 years (35% for FIB-4 and 20% for NFS). New cutoffs were derived (and validated) for those aged ≥65 years, which improved specificity to 70% without adversely affecting sensitivity (FIB-4 2.0, sensitivity 77% NFS 0.12, sensitivity 80%). CONCLUSIONS: The NFS and FIB-4 scores have similar accuracy for advanced fibrosis in patients aged >35 years. However, the specificity for advanced fibrosis is unacceptably low in patients aged ≥65 years, resulting in a high false positive rate. New thresholds for use in patients aged ≥65 years are proposed to address this issue. PMID:27725647

Forest statistics for Arkansas' Ozark counties

Treesearch

T. Richard Quick; Mary S. Hedlund

1979-01-01

These tables were derived from data obtained during a 1978 inventory of 24 counties comprising the Ozark Unit of Arkansas (fib. 1). Forest area was estimated from aerial photos with an adjustment of ground truth at selected locations. Sample plots were systematically established at three-mile intervals using a grid orientated roughly N-S and E-W. At each location,...

Comparing Data Input Requirements of Statistical vs. Process-based Watershed Models Applied for Prediction of Fecal Indicator and Pathogen Levels in Recreational Beaches

EPA Science Inventory

Same day prediction of fecal indicator bacteria (FIB) concentrations and bather protection from the risk of exposure to pathogens are two important goals of implementing a modeling program at recreational beaches. Sampling efforts for modelling applications can be expensive and t...

Microbiological quality of water in a city with persistent and recurrent waterborne diseases under tropical sub-rural conditions: The case of Kikwit City, Democratic Republic of the Congo.

PubMed

Nienie, Alexis B; Sivalingam, Periyasamy; Laffite, Amandine; Ngelinkoto, Patience; Otamonga, Jean-Paul; Matand, Alphonse; Mulaji, Crispin K; Biey, Emmanuel M; Mpiana, Pius T; Poté, John

2017-07-01

The availability of safe drinking water in sub-Saharan countries remains a major challenge because poor sanitation has been the cause of various outbreaks of waterborne disease due to the poor microbiological quality of water used for domestic purposes. The faecal indicator bacteria (FIB) used in the present study included Escherichia coli (E. coli) and Enterococcus (ENT). FIB and aerobic mesophilic bacteria (AMB) were quantified during July 2015 (dry season) and November 2015 (rainy season) in order to assess the quality of drinking water from wells (n=3; P1-P3), and two rivers, the River Lukemi (RLK, n=3) and River Luini (RLN, n=2) in the city of Kikwit, which is located in the province of Kwilu in the Democratic Republic of the Congo. Kikwit is well known for its outbreaks of persistent and recurrent waterborne diseases including Entamoeba, Shigella, typhoid fever, cholera, and Ebola Viral Hemorrhagic Fever. Consequently, E. coli, ENT, and AMB were quantified in water samples according to the standard international methods for water quality determination using the membrane filtration method. The FIB characterization was performed for human-specific Bacteroides by PCR using specific primers. The results obtained revealed high FIB concentrations in river samples collected during both seasons. For example, E. coli respectively reached 4.3×10 4 and 9.2×10 4 CFU 100mL -1 in the dry season and the wet season. ENT reached 5.3×10 3 CFU 100mL -1 during the dry season and 9.8×10 3 CFU 100mL -1 in the wet season. The pollution was significantly worse in the wet season compared to the dry season. Surprisingly, no faecal contamination was observed in well water samples collected in the dry season while E. coli and ENT were detected in all wells in the wet season with values of 6, 7, and 11CFUmL -1 for E. coli in wells P1-P3, respectively and 3, 5, 9 CFU mL -1 for ENT in the same wells. Interestingly, the PCR assays for human-specific Bacteroides HF183/HF134 indicated that 97-100% captured in all analyses of isolated FIB were of human origin. The results indicate that contamination of E. coli, ENT, and AMB in the studied water resources increases during the wet season. This study improves understanding of the microbiological pollution of rivers and wells under tropical conditions and will guide future municipal/local government decisions on improving water quality in this region which is characterised by persistent and recurrent waterborne diseases. Although the epidemiology can be geographically localised, the effects of cross border transmission can be global. Therefore, the research results presented in this article form recommendations to municipalities/local authorities and the approach and procedures can be carried out in a similar environment. Copyright © 2017 Elsevier GmbH. All rights reserved.

Effect of defects, magnetocrystalline anisotropy, and shape anisotropy on magnetic structure of iron thin films by magnetic force microscopy

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

Xu, Ke; Schreiber, Daniel K.; Li, Yulan

Microstructures of magnetic materials, including defects and crystallographic orientations, are known to strongly influence magnetic domain structures. Measurement techniques such as magnetic force microscopy (MFM) thus allow study of correlations between microstructural and magnetic properties. The present work probes effects of anisotropy and artificial defects on the evolution of domain structure with applied field. Single crystal iron thin films on MgO substrates were milled by Focused Ion Beam (FIB) to create different magnetically isolated squares and rectangles in [110] crystallographic orientations, having their easy axis 45° from the sample edge. To investigate domain wall response on encountering non-magnetic defects, amore » 150 nm diameter hole was created in the center of some samples. By simultaneously varying crystal orientation and shape, both magnetocrystalline anisotropy and shape anisotropy, as well as their interaction, could be studied. Shape anisotropy was found to be important primarily for the longer edge of rectangular samples, which exaggerated the FIB edge effects and provided nucleation sites for spike domains in non-easy axis oriented samples. Center holes acted as pinning sites for domain walls until large applied magnetic fields. The present studies are aimed at deepening the understanding of the propagation of different types of domain walls in the presence of defects and different crystal orientations.« less

Effect of defects, magnetocrystalline anisotropy, and shape anisotropy on magnetic structure of iron thin films by magnetic force microscopy

DOE PAGES

Xu, Ke; Schreiber, Daniel K.; Li, Yulan; ...

2017-02-10

Microstructures of magnetic materials, including defects and crystallographic orientations, are known to strongly influence magnetic domain structures. Measurement techniques such as magnetic force microscopy (MFM) thus allow study of correlations between microstructural and magnetic properties. The present work probes effects of anisotropy and artificial defects on the evolution of domain structure with applied field. Single crystal iron thin films on MgO substrates were milled by Focused Ion Beam (FIB) to create different magnetically isolated squares and rectangles in [110] crystallographic orientations, having their easy axis 45° from the sample edge. To investigate domain wall response on encountering non-magnetic defects, amore » 150 nm diameter hole was created in the center of some samples. By simultaneously varying crystal orientation and shape, both magnetocrystalline anisotropy and shape anisotropy, as well as their interaction, could be studied. Shape anisotropy was found to be important primarily for the longer edge of rectangular samples, which exaggerated the FIB edge effects and provided nucleation sites for spike domains in non-easy axis oriented samples. Center holes acted as pinning sites for domain walls until large applied magnetic fields. The present studies are aimed at deepening the understanding of the propagation of different types of domain walls in the presence of defects and different crystal orientations.« less

Probing the Depths of Space Weathering: A Cross-sectional View of Lunar Rock 76015

NASA Technical Reports Server (NTRS)

Noble, Sarah K.; Keller, L. P.; Stroud, Rhonda

2007-01-01

The term "space weathering" refers to the cumulative effects of several processes operating at the surface of any solar system body not protected by a thick atmosphere. These processes include cosmic and solar ray irradiation, solar wind implantation and sputtering, as well as melting and vaporization due to micrometeorite bombardment. Space weathering discussions have generally centered around soils but exposed rocks will also incur the effects of weathering. Rocks have much longer surface lifetimes than an individual soil grain and thus record a longer history of exposure. By studying the weathering products which have built up on a rock surface, we can gain a deeper perspective on the weathering process and better assess the relative importance of various weathering components. The weathered coating, or patina, of the lunar rock 76015 has been previously studied using SEM and TEM. It is a noritic breccia with both "glazed" (smooth glassy) and "classic" (microcratered and pancake-bearing) patina coatings. Previous TEM work on 76015 relied on ultramicrotomy to prepare cross sections of the patina coating, but these sections were limited by the "chatter" and loss of material in these brittle samples. Here we have used a focused ion beam (FIB) instrument to prepare cross sections in which the delicate stratigraphy of the patina coating is beautifully preserved.

Minimal resin embedding of multicellular specimens for targeted FIB-SEM imaging.

PubMed

Schieber, Nicole L; Machado, Pedro; Markert, Sebastian M; Stigloher, Christian; Schwab, Yannick; Steyer, Anna M

2017-01-01

Correlative light and electron microscopy (CLEM) is a powerful tool to perform ultrastructural analysis of targeted tissues or cells. The large field of view of the light microscope (LM) enables quick and efficient surveys of the whole specimen. It is also compatible with live imaging, giving access to functional assays. CLEM protocols take advantage of the features to efficiently retrace the position of targeted sites when switching from one modality to the other. They more often rely on anatomical cues that are visible both by light and electron microscopy. We present here a simple workflow where multicellular specimens are embedded in minimal amounts of resin, exposing their surface topology that can be imaged by scanning electron microscopy (SEM). LM and SEM both benefit from a large field of view that can cover whole model organisms. As a result, targeting specific anatomic locations by focused ion beam-SEM (FIB-SEM) tomography becomes straightforward. We illustrate this application on three different model organisms, used in our laboratory: the zebrafish embryo Danio rerio, the marine worm Platynereis dumerilii, and the dauer larva of the nematode Caenorhabditis elegans. Here we focus on the experimental steps to reduce the amount of resin covering the samples and to image the specimens inside an FIB-SEM. We expect this approach to have widespread applications for volume electron microscopy on multiple model organisms. Copyright © 2017 Elsevier Inc. All rights reserved.

Ultra-high aspect ratio replaceable AFM tips using deformation-suppressed focused ion beam milling.

PubMed

Savenko, Alexey; Yildiz, Izzet; Petersen, Dirch Hjorth; Bøggild, Peter; Bartenwerfer, Malte; Krohs, Florian; Oliva, Maria; Harzendorf, Torsten

2013-11-22

Fabrication of ultra-high aspect ratio exchangeable and customizable tips for atomic force microscopy (AFM) using lateral focused ion beam (FIB) milling is presented. While on-axis FIB milling does allow high aspect ratio (HAR) AFM tips to be defined, lateral milling gives far better flexibility in terms of defining the shape and size of the tip. Due to beam-induced deformation, it has so far not been possible to define HAR structures using lateral FIB milling. In this work we obtain aspect ratios of up to 45, with tip diameters down to 9 nm, by a deformation-suppressing writing strategy. Several FIB milling strategies for obtaining sharper tips are discussed. Finally, assembly of the HAR tips on a custom-designed probe as well as the first AFM scanning is shown.

Measuring and modeling the flux of fecal bacteria across the sediment-water interface in a turbulent stream

NASA Astrophysics Data System (ADS)

Grant, Stanley B.; Litton-Mueller, Rachel M.; Ahn, Jong H.

2011-05-01

Sediments are a pervasive source of fecal indicator bacteria (FIB) in rivers, lakes, estuaries, and oceans and may constitute a long-term reservoir of human disease. Previous attempts to quantify the flux of FIB across the sediment-water interface (SWI) are limited to extreme flow events, for which the primary mechanism of bacterial release is disruption and/or erosion of the sediment substrate. Here we report measurements of FIB flux across the SWI in a turbulent stream that is not undergoing significant erosion. The stream is formed by the steady discharge of bacteria-free disinfected and highly treated wastewater effluent to an earthen channel harboring high concentrations of FIB in the sediment from in situ growth. The flux j″ of FIB across the SWI, estimated from mass balance on FIB measurements in the water column, scales linearly with the concentration of bacteria in sediment pore fluids Cpore over a 3 decade change in both variables: ? The magnitude of the observed mass transfer velocity (? m s-1) is significantly larger than values predicted for either the diffusion of bacteria across a concentration boundary layer (? m s-1) or sweep and eject fluid motions at the SWI (? m s-1) but is similar to the flux of water between the stream and its hyporheic zone estimated from dye injection experiments. These results support the hypothesis that hyporheic exchange controls the trafficking of bacteria, and perhaps other types of particulate organic matter, across the SWI in turbulent streams.

Agrochemicals indirectly increase survival of E. coli O157:H7 and indicator bacteria by reducing ecosystem services.

PubMed

Staley, Zachery R; Rohr, Jason R; Senkbeil, Jacob K; Harwood, Valerie J

Storm water and agricultural runoff frequently contain agrochemicals, fecal indicator bacteria (FIB), and zoonotic pathogens. Entry of such contaminants into aquatic ecosystems may affect ecology and human health. This study tested the hypothesis that the herbicide atrazine and the fungicide chlorothalonil indirectly affect the survival of FIB (Escherichia coli and Enterococcus faecalis) and a pathogen (E. coli O157:H7) by altering densities of protozoan predators or by altering competition from autochthonous bacteria. Streptomycin-resistant E. coli, En. faecalis, and E. coli O157:H7 were added to microcosms composed of Florida river water containing natural protozoan and bacterial populations. FIB, pathogen, and protozoan densities were monitored over six days. Known metabolic inhibitors, cycloheximide and streptomycin, were used to inhibit autochthonous protozoa or bacteria, respectively. The inhibitors made it possible to isolate the effects of predation or competition on survival of allochthonous bacteria, and each treatment increased the survival of FIB and pathogens. Chlorothalonil's effect was similar to that of cycloheximide, significantly reducing protozoan densities and elevating densities of FIB and pathogens relative to the control. Atrazine treatment did not affect protozoan densities, but, through an effect on competition, resulted in significantly greater densities of En. faecalis and E. coli O157:H7. Hence, by reducing predaceous protozoa and bacterial competitors that facilitate purifying water bodies of FIBs and human pathogens, chlorothalonil and atrazine indirectly diminished an ecosystem service of fresh water.

Changes in liver stiffness measurement using acoustic radiation force impulse elastography after antiviral therapy in patients with chronic hepatitis C.

PubMed

Chen, Sheng-Hung; Lai, Hsueh-Chou; Chiang, I-Ping; Su, Wen-Pang; Lin, Chia-Hsin; Kao, Jung-Ta; Chuang, Po-Heng; Hsu, Wei-Fan; Wang, Hung-Wei; Chen, Hung-Yao; Huang, Guan-Tarn; Peng, Cheng-Yuan

2018-01-01

To compare on-treatment and off-treatment parameters acquired using acoustic radiation force impulse elastography, the Fibrosis-4 (FIB-4) index, and aspartate aminotransferase-to-platelet ratio index (APRI) in patients with chronic hepatitis C (CHC). Patients received therapies based on pegylated interferon or direct-acting antiviral agents. The changes in paired patient parameters, including liver stiffness (LS) values, the FIB-4 index, and APRI, from baseline to sustained virologic response (SVR) visit (24 weeks after the end of treatment) were compared. Multiple regression models were used to identify significant factors that explained the correlations with LS, FIB-4, and APRI values and SVR. A total of 256 patients were included, of which 219 (85.5%) achieved SVR. The paired LS values declined significantly from baseline to SVR visit in all groups and subgroups except the nonresponder subgroup (n = 10). Body mass index (P = 0.0062) and baseline LS (P < 0.0001) were identified as independent factors that explained the LS declines. Likewise, the baseline FIB-4 (P < 0.0001) and APRI (P < 0.0001) values independently explained the declines in the FIB-4 index and APRI, respectively. Moreover, interleukin-28B polymorphisms, baseline LS, and rapid virologic response were identified as independent correlates with SVR. Paired LS measurements in patients treated for CHC exhibited significant declines comparable to those in FIB-4 and APRI values. These declines may have correlated with the resolution of necroinflammation. Baseline LS values predicted SVR.

Differential Decay of Cattle-associated Fecal Indicator ...

EPA Pesticide Factsheets

Background: Fecal indicator bacteria (FIB) have a long history of use in the assessment of the microbial quality of recreational waters. However, quantification of FIB provides no information about the pollution source(s) and relatively little is known about their fate in the ambient waters. Microbial source tracking (MST) field has evolved in response to a need to identify pollution source(s), but majority of MST markers suffer from the same caveat as FIB, as our understanding of the factors influencing their fate in the environment is limited. Materials: We assessed the effect of water type (freshwater vs marine) and select environmental parameters (indigenous microbiota, ambient sunlight) on decay of FIB and MST markers from cattle manure. Experiments were conducted in situ using a submersible aquatic mesocosm containing dialysis bags filled with mixture of cattle manure and ambient water. Culturable FIB were enumerated by membrane filtration and via qPCR (Entero1a, EC23S) and MST markers were enumerated via qPCR and included general marker of fecal pollution (GenBac3) and cattle-associated subset (Rum2Bac, CowM2, CowM3). Results: Decay of culturable FIB was significantly faster (P > 0.001) than any of the molecular markers irrespective of the water type or experimental conditions. The water type was a significant factor affecting decay (P: 0.008 to < 0.001), although the magnitude of the effect differed among the microbial targets and over time. Presence o

FIB Secondary Etching Method for Fabrication of Fine CNT Forest Metamaterials

NASA Astrophysics Data System (ADS)

Pander, Adam; Hatta, Akimitsu; Furuta, Hiroshi

2017-10-01

Anisotropic materials, like carbon nanotubes (CNTs), are the perfect substitutes to overcome the limitations of conventional metamaterials; however, the successful fabrication of CNT forest metamaterial structures is still very challenging. In this study, a new method utilizing a focused ion beam (FIB) with additional secondary etching is presented, which can obtain uniform and fine patterning of CNT forest nanostructures for metamaterials and ranging in sizes from hundreds of nanometers to several micrometers. The influence of the FIB processing parameters on the morphology of the catalyst surface and the growth of the CNT forest was investigated, including the removal of redeposited material, decreasing the average surface roughness (from 0.45 to 0.15 nm), and a decrease in the thickness of the Fe catalyst. The results showed that the combination of FIB patterning and secondary etching enabled the growth of highly aligned, high-density CNT forest metamaterials. The improvement in the quality of single-walled CNTs (SWNTs), defined by the very high G/D peak ratio intensity of 10.47, demonstrated successful fine patterning of CNT forest for the first time. With a FIB patterning depth of 10 nm and a secondary etching of 0.5 nm, a minimum size of 150 nm of CNT forest metamaterials was achieved. The development of the FIB secondary etching method enabled for the first time, the fabrication of SWNT forest metamaterials for the optical and infrared regime, for future applications, e.g., in superlenses, antennas, or thermal metamaterials.

FibroScan, aspartate aminotransferase and alanine aminotransferase ratio (AAR), aspartate aminotransferase to platelet ratio index (APRI), fibrosis index based on the 4 factor (FIB-4), and their combinations in the assessment of liver fibrosis in patients with hepatitis B.

PubMed

Ding, Deping; Li, Hongbing; Liu, Ping; Chen, Lingli; Kang, Jian; Zhang, Yinhua; Ma, Deqiang; Chen, Yue; Luo, Jie; Meng, Zhongji

2015-01-01

The aim of this study was to assess the effects of FibroScan, aspartate aminotransferase and alanine aminotransferase ratio (AAR), aspartate aminotransferase to platelet ratio index (APRI), fibrosis index based on the 4 factor (FIB-4) and their combinations on liver fibrosis in patients with hepatitis B. 406 hospitalized patients with chronic hepatitis B (CHB) and cirrhosis in our hospital were analyzed retrospectively and collected patients clinical indicators, including liver stiffness (LS), AAR, APRI and FIB-4, and then compared the differences of these indicators between CHB group and hepatitis B with cirrhosis group. Receiver operating curve (ROC) was used to evaluate the differentiating capacity of these indicators on CHB and liver cirrhosis. Four indicators related to liver cirrhosis had a statistical significance between two groups (P < 0.01); the under ROC curve areas of LS, AAR, APRI and FIB-4 for differential diagnosis of CHB and liver cirrhosis were 0.866, 0.772, 0.632 and 0.885, respectively. The under ROC curve areas of LS, AAR, APRI and FIB-4 for differential diagnosis of liver cirrhosis at compensatory stage and de-compensatory stage were 0.627, 0.666, 0.795 and 0.820, respectively. LS, AAR, APRI and FIB-4 were good indicators as clinical diagnosis and differential diagnosis on hepatitis B related cirrhosis.

Hospital Effluents Are One of Several Sources of Metal, Antibiotic Resistance Genes, and Bacterial Markers Disseminated in Sub-Saharan Urban Rivers

PubMed Central

Laffite, Amandine; Kilunga, Pitchouna I.; Kayembe, John M.; Devarajan, Naresh; Mulaji, Crispin K.; Giuliani, Gregory; Slaveykova, Vera I.; Poté, John

2016-01-01

Data concerning the occurrence of emerging biological contaminants such as antibiotic resistance genes (ARGs) and fecal indicator bacteria (FIB) in aquatic environments in Sub-Saharan African countries is limited. On the other hand, antibiotic resistance remains a worldwide problem which may pose serious potential risks to human and animal health. Consequently, there is a growing number of reports concerning the prevalence and dissemination of these contaminants into various environmental compartments. Sediments provide the opportunity to reconstruct the pollution history and evaluate impacts so this study investigates the abundance and distribution of toxic metals, FIB, and ARGs released from hospital effluent wastewaters and their presence in river sediments receiving systems. ARGs (blaTEM, blaCTX-M, blaSHV, and aadA), total bacterial load, and selected bacterial species FIB [Escherichia coli, Enterococcus (ENT)] and species (Psd) were quantified by targeting species specific genes using quantitative PCR (qPCR) in total DNA extracted from the sediments recovered from 4 hospital outlet pipes (HOP) and their river receiving systems in the City of Kinshasa in the Democratic Republic of the Congo. The results highlight the great concentration of toxic metals in HOP, reaching the values (in mg kg−1) of 47.9 (Cr), 213.6 (Cu), 1434.4 (Zn), 2.6 (Cd), 281.5 (Pb), and 13.6 (Hg). The results also highlight the highest (P < 0.05) values of 16S rRNA, FIB, and ARGs copy numbers in all sampling sites including upstream (control site), discharge point, and downstream of receiving rivers, indicating that the hospital effluent water is not an exclusive source of the biological contaminants entering the urban rivers. Significant correlation were observed between (i) all analyzed ARGs and total bacterial load (16S rRNA) 0.51 to 0.72 (p < 0.001, n = 65); (ii) ARGs (except blaTEM) and FIB and Psd 0.57 < r < 0.82 (p < 0.001, n = 65); and (iii) ARGs (except blaTEM) and toxic metals (Cd, Cr, Cu, and Zn) 0.44 to 0.72, (p < 0.001, n = 65). These findings demonstrate that several sources including hospital and urban wastewaters contribute to the spread of toxic metals and biological emerging contaminants in aquatic ecosystems. PMID:27499749

Staging liver fibrosis in chronic hepatitis B with T1 relaxation time index on gadoxetic acid-enhanced MRI: Comparison with aspartate aminotransferase-to-platelet ratio index and FIB-4.

PubMed

Yang, Li; Ding, Ying; Rao, Shengxiang; Chen, Caizhong; Wu, Lifang; Sheng, Ruofan; Fu, Caixia; Zeng, Mengsu

2017-04-01

To assess the accuracy of the T 1 relaxation time index on gadoxetic acid-enhanced magnetic resonance imaging (MRI) for staging liver fibrosis in chronic hepatitis B (CHB), in comparison and combination with the aspartate aminotransferase-to-platelet ratio index (APRI) and fibrosis-4 (FIB-4). A retrospective study of gadoxetic acid-enhanced T 1 mapping and serum biochemical tests was performed on 126 CHB patients who underwent gadoxetic acid-enhanced 1.5T MRI, and the histological score used as the gold standard. The reduction rate of T 1 relaxation time before and 20 minutes after gadoxetic acid injection (ΔT 1 , ΔR1%), the contrast uptake rate (K Hep ), APRI, and FIB-4 were calculated. The diagnostic efficacy of ΔT 1 , ΔR1%, K Hep , APRI, and FIB-4 for predicting stage 2 or greater (≥S2), stage 3 or greater (≥S3), and stage 4 (S4) was compared. ΔT 1 (r = -0.513, P < 0.001), ΔR1% (r = -0.626, P < 0.001), K Hep (r = -0.527, P < 0.001), APRI (r = 0.519, P < 0.001), and FIB-4 (r = 0.476, P < 0.001) correlated significantly with fibrosis stages. Areas under the curves (AUCs) of ΔR1% for detecting ≥S2, ≥S3, and S4 were 0.849, 0.827, and 0.809, which were greater than that of APRI (0.763, 0.745, 0.787) and FIB-4 (0.727, 0.738, 0.772), but significant difference was found only in discriminating ≥S2 between ΔR1% and FIB-4 (P = 0.027). The combination of all five indices performed best, with AUC, sensitivity, and specificity of 0.860, 87.21%, and 72.50% for diagnosing ≥S2, 0.878, 82.81%, and 85.48% for ≥S3, and 0.867, 80.00%, and 83.95% for S4. The gadoxetic acid-enhanced T 1 relaxation time index appears to be superior to APRI and FIB-4 for predicting hepatic fibrosis. The combined use of gadoxetic acid-enhanced T 1 mapping, APRI, and FIB-4 may be more reliable for staging liver fibrosis in CHB. 4 J. Magn. Reson. Imaging 2017;45:1186-1194. © 2016 International Society for Magnetic Resonance in Medicine.

Evaluation of APRI and FIB-4 for noninvasive assessment of significant fibrosis and cirrhosis in HBeAg-negative CHB patients with ALT ≤ 2 ULN

PubMed Central

Li, Qiang; Ren, Xiaojing; Lu, Chuan; Li, Weixia; Huang, Yuxian; Chen, Liang

2017-01-01

Abstract To evaluate the performance of aspartate transaminase-to-platelet ratio index (APRI) and fibrosis index based on four factors (FIB-4) to predict significant fibrosis and cirrhosis in hepatitis B virus e antigen (HBeAg)-negative chronic hepatitis B (CHB) patients with alanine transaminase (ALT) ≤ twice the upper limit of normal (2 ULN). Histologic and laboratory data of 236 HBeAg-negative CHB patients with ALT ≤ 2 ULN were analyzed. Predicted fibrosis stage, based on established scales and cut-offs for APRI and FIB-4, was compared with METAVIR scores obtained from liver biopsy. In this study, the areas under the receiver operating characteristic curves (AUROCs) of APRI were lower than that of FIB-4 (0.62 vs 0.69; P = 0.019) for diagnosing significant fibrosis; however APRI and FIB-4 were comparable for diagnosing cirrhosis (0.77 vs 0.81; P = 0.374). When the cut-off proposed by WHO HBV guideline for APRI (>2.0) was used, no cirrhotic patients were correctly predicted. For FIB-4, the WHO proposed cut-off of 3.25 correctly identified significant fibrosis 83% of the time; but for APRI, the WHO proposed cut-off of 1.5 identified significant fibrosis 56%. In ruling out significant fibrosis, the WHO proposed APRI cut-off of 0.5 had a predictive value of 39%, and the FIB-4 cut-off of 1.45 correctly identified lack of significant fibrosis in 47% of the patients. In this study, based on ROC analysis, the optimal cut-offs were 0.46 and 0.65 for APRI, and 1.05 and 1.29 for FIB-4, for diagnosing significant fibrosis and cirrhosis, respectively. When the new cut-off of APRI (>0.65) was used, 82% of the cirrhotic patients were correctly predicted. In ruling out significant fibrosis, the new APRI cut-off (<0.46) had a predictive value of 80%, and new FIB-4 cut-off (<1.05) correctly identified lack of significant fibrosis in 84% of the patients. The WHO guidelines proposed cut-offs might be higher for HBeAg-negative CHB patients with ALT ≤2 ULN, and might underestimate the proportion of significant fibrosis and cirrhosis. A new set of cut-offs should be used to predict significant fibrosis and cirrhosis in this specific population. PMID:28328813

Evaluation of APRI and FIB-4 for noninvasive assessment of significant fibrosis and cirrhosis in HBeAg-negative CHB patients with ALT ≤ 2 ULN: A retrospective cohort study.

PubMed

Li, Qiang; Ren, Xiaojing; Lu, Chuan; Li, Weixia; Huang, Yuxian; Chen, Liang

2017-03-01

To evaluate the performance of aspartate transaminase-to-platelet ratio index (APRI) and fibrosis index based on four factors (FIB-4) to predict significant fibrosis and cirrhosis in hepatitis B virus e antigen (HBeAg)-negative chronic hepatitis B (CHB) patients with alanine transaminase (ALT) ≤ twice the upper limit of normal (2 ULN).Histologic and laboratory data of 236 HBeAg-negative CHB patients with ALT ≤ 2 ULN were analyzed. Predicted fibrosis stage, based on established scales and cut-offs for APRI and FIB-4, was compared with METAVIR scores obtained from liver biopsy.In this study, the areas under the receiver operating characteristic curves (AUROCs) of APRI were lower than that of FIB-4 (0.62 vs 0.69; P = 0.019) for diagnosing significant fibrosis; however APRI and FIB-4 were comparable for diagnosing cirrhosis (0.77 vs 0.81; P = 0.374). When the cut-off proposed by WHO HBV guideline for APRI (>2.0) was used, no cirrhotic patients were correctly predicted. For FIB-4, the WHO proposed cut-off of 3.25 correctly identified significant fibrosis 83% of the time; but for APRI, the WHO proposed cut-off of 1.5 identified significant fibrosis 56%. In ruling out significant fibrosis, the WHO proposed APRI cut-off of 0.5 had a predictive value of 39%, and the FIB-4 cut-off of 1.45 correctly identified lack of significant fibrosis in 47% of the patients. In this study, based on ROC analysis, the optimal cut-offs were 0.46 and 0.65 for APRI, and 1.05 and 1.29 for FIB-4, for diagnosing significant fibrosis and cirrhosis, respectively. When the new cut-off of APRI (>0.65) was used, 82% of the cirrhotic patients were correctly predicted. In ruling out significant fibrosis, the new APRI cut-off (<0.46) had a predictive value of 80%, and new FIB-4 cut-off (<1.05) correctly identified lack of significant fibrosis in 84% of the patients.The WHO guidelines proposed cut-offs might be higher for HBeAg-negative CHB patients with ALT ≤2 ULN, and might underestimate the proportion of significant fibrosis and cirrhosis. A new set of cut-offs should be used to predict significant fibrosis and cirrhosis in this specific population.

Inactivation of faecal indicator bacteria in a roof-captured rainwater system under ambient meteorological conditions.

PubMed

Ahmed, W; Richardson, K; Sidhu, J P S; Jagals, P; Toze, S

2014-01-01

In this study, faecal indicator bacteria (FIB) namely Escherichia coli and Enterococcus spp. were seeded into slurries of possum faeces and placed on the roof and in the gutter of a roof-captured rainwater (RCR) system. The persistence of FIB in these circumstances was determined under ambient climatic conditions. FIB persistence was also determined under in situ conditions in tank water using diffusion chambers. The numbers of surviving FIB at different time intervals were enumerated using culture-based methods. Both FIB were rapidly inactivated on the roof under sunlight conditions (T(90) = 2 h) compared with shade conditions (T(90) = 9-53 h). Significant differences were observed between sunlight and shade conditions on the roof for both T90 values of E. coli (P < 0·001) and Enterococcus spp. (P < 0·001). E. coli showed biphasic inactivation patterns under both clean and unclean gutter conditions. Enterococcus spp., however, showed rapid inactivation (T(90) = 2 h for the clean gutter and T(90) = 6 h for the unclean gutter) compared with E. coli (T(90) = 22 h for the clean gutter and T(90) = 20 h for the unclean gutter). Significant differences were also observed between the T(90) values of E. coli and Enterococcus spp. for both clean (P < 0·001) and unclean (P < 0·001) gutters. Both E. coli and Enterococcus spp. showed nonlinear biphasic inactivation in tank water. Significant difference was observed between the T(90) value of E. coli inactivation compared with Enterococcus spp. (P < 0·001) in the tank water. In this study, FIB were observed to survive longer (T(90) = 9-53 h) on the roof under shade conditions compared with sunlight conditions (T(90) = 2 h). If there is a rainfall event within two to three days after the deposition of faecal maters on the roof, it is highly likely that FIB would be transported to the tank water. When introduced into the tank, a relatively slow inactivation process may take place (T(90) = 38-72 h). The presence of FIB in water indicates faecal pollution and potential presence of enteric pathogens. Therefore, the information on the resilience of FIB, as obtained in this study, can be used for indirect assessment of health risks associated with using roof-captured rainwater for potable and nonpotable purposes. © 2013 The Society for Applied Microbiology.

The Relationship between Hydroclimatic Variables and Faecal Indicator Bacteria in River Basins in Pakistan and Bangladesh

NASA Astrophysics Data System (ADS)

Hofstra, Nynke; Shahid Iqbal, M.; Majedul Islam, M. M.

2016-04-01

Water contaminated with pathogenic bacteria causing diarrhoea poses a health risk to the population. Worldwide, diarrhoea is the 3rd leading cause of death. A changing climate may increase the concentration of pathogens in surface water. Increased temperature will mostly increase the inactivation of pathogens and therefore decrease the surface water concentration. Increased precipitation may dilute contaminated water, but may also increase the runoff of pathogens into the surface water. Decreased precipitation may have the opposite effect. Moreover, increased chance of extreme precipitation events and increased risk of floods may also increase the runoff of pathogens into the surface water. The net balance of these effects is uncertain. The objective of our study is to quantify the relationship between hydroclimatic variables (surface air and water temperature, precipitation and runoff) and faecal indicator bacteria (FIB, E. coli and Enterococci) in two rivers in Pakistan and Bangladesh. In these countries health problems are large, particularly in annual periods of flood. We studied FIB instead of pathogens, because of the costs associated with pathogen measurements. The relationship between FIB and hydroclimatic variables is expected to be comparable to the relationship between pathogens and hydroclimatic variables. For both regions the FIB concentrations have been monitored for two years between 2013 and 2015 at several points in the rivers. Concentrations of FIB in Kabul (Pakistan) and Betna (Bangladesh) river basins are very high (up to 5.2 log10 cfu/100ml). Due to a broken waste water treatment system of the city of Peshawar, concentrations are higher in Kabul than in the Betna river. All hydroclimatic variables positively correlate with FIB. An unexpected positive relation with temperature can be explained by the fact that temperature and discharge increase at the same time and possibly FIB growth. The positive relation with precipitation and discharge shows that not the dilution, but the increased runoff of FIB is more important. Regression models for each of the measurement locations in Kabul river show that water temperature, discharge and precipitation together explain a large part of the variance (R2 equals 0.72-0.94) for E. coli. The regression model for Betna river comprises water temperature and discharge and for E. coli R2=0.47 and for Enterococci R2=0.49. We can conclude that FIB concentrations increase with increasing temperature and particularly precipitation and discharge. We expect pathogen concentrationss to increase in a similar way and would therefore expect increased health risk due to climate change in Kabul and Betna river basins.

Predictive Power of Clean Bed Filtration Theory for Fecal Indicator Bacteria Removal in Stormwater Biofilters

NASA Astrophysics Data System (ADS)

Parker, E.; Rippy, M.; Mehring, A.; Winfrey, B.; Ambrose, R. F.; Levin, L. A.; Grant, S. B.

2017-12-01

Green infrastructure (also referred to as low impact development, or LID) has the potential to transform urban stormwater runoff from an environmental threat to a valuable water resource. Here we focus on the removal of fecal indicator bacteria (FIB, a pollutant responsible for runoff associated inland and coastal beach closures) in stormwater biofilters (a common type of green infrastructure). Drawing on a combination of previously published and new laboratory studies of FIB removal in biofilters, we find that 66% of the variance in FIB removal rates can be explained by clean bed filtration theory (CBFT, 31%), antecedent dry period (14%), study effect (8%), biofilter age (7%), and the presence or absence of shrubs (6%). Our analysis suggests that, with the exception of shrubs, plants affect FIB removal indirectly by changing the infiltration rate, not directly by changing the FIB removal mechanisms or altering filtration rates in ways not already accounted for by CBFT. The analysis presented here represents a significant step forward in our understanding of how physicochemical theories (such as CBFT) can be melded with hydrology, engineering design, and ecology to improve the water quality benefits of green infrastructure.

Three-dimensional ultrastructure of osteocytes assessed by focused ion beam-scanning electron microscopy (FIB-SEM).

PubMed

Hasegawa, Tomoka; Yamamoto, Tomomaya; Hongo, Hiromi; Qiu, Zixuan; Abe, Miki; Kanesaki, Takuma; Tanaka, Kawori; Endo, Takashi; de Freitas, Paulo Henrique Luiz; Li, Minqi; Amizuka, Norio

2018-04-01

The aim of this study is to demonstrate the application of focused ion beam-scanning electron microscopy, FIB-SEM for revealing the three-dimensional features of osteocytic cytoplasmic processes in metaphyseal (immature) and diaphyseal (mature) trabeculae. Tibiae of eight-week-old male mice were fixed with aldehyde solution, and treated with block staining prior to FIB-SEM observation. While two-dimensional backscattered SEM images showed osteocytes' cytoplasmic processes in a fragmented fashion, three-dimensional reconstructions of FIB-SEM images demonstrated that osteocytes in primary metaphyseal trabeculae extended their cytoplasmic processes randomly, thus maintaining contact with neighboring osteocytes and osteoblasts. In contrast, diaphyseal osteocytes extended thin cytoplasmic processes from their cell bodies, which ran perpendicular to the bone surface. In addition, these osteocytes featured thick processes that branched into thinner, transverse cytoplasmic processes; at some point, however, these transverse processes bend at a right angle to run perpendicular to the bone surface. Osteoblasts also possessed thicker cytoplasmic processes that branched off as thinner processes, which then connected with cytoplasmic processes of neighboring osteocytes. Thus, FIB-SEM is a useful technology for visualizing the three-dimensional structures of osteocytes and their cytoplasmic processes.

Characterizing Virus Decay in Environmental Freshwater Habitats

EPA Science Inventory

Recreational water quality is typically assessed using fecal indicator bacteria (FIB), however, FIB are inadequate surrogates for the viral pathogens. Bacteriophage share similar morphologies to viral pathogens allowing closer representation of viral behavior, making their inclu...

Large Area Microcorrals and Cavity Formation on Cantilevers using a Focused Ion Beam

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

Saraf, Laxmikant V.; Britt, David W.

2011-09-14

We utilize focused ion beam (FIB) to explore various sputtering parameters to form large area microcorrals and cavities on cantilevers. Microcorrals were rapidly created by modifying ion beam blur and overlaps. Modification in FIB sputtering parameters affects the periodicity and shape of corral microstructure. Cantilever deflections show ion beam amorphization effects as a function of sputtered area and cantilever base cavities with or without side walls. The FIB sputtering parameters address a method for rapid creation of a cantilever tensiometer with integrated fluid storage and delivery.

Through-silicon via plating void metrology using focused ion beam mill

NASA Astrophysics Data System (ADS)

Rudack, A. C.; Nadeau, J.; Routh, R.; Young, R. J.

2012-03-01

3D IC integration continues to increase in complexity, employing advanced interconnect technologies such as throughsilicon vias (TSVs), wafer-to-wafer (W2W) bonding, and multi-chip stacking. As always, the challenge with developing new processes is to get fast, effective feedback to the integration engineer. Ideally this data is provided by nondestructive in-line metrology, but this is not always possible. For example, some form of physical cross-sectioning is still the most practical way to detect and characterize TSV copper plating voids. This can be achieved by cleaving, followed by scanning electron microscope (SEM) inspection. A more effective physical cross-sectioning method has been developed using an automated dual-beam focused ion beam (FIB)-SEM system, in which multiple locations can be sectioned and imaged while leaving the wafer intact. This method has been used routinely to assess copper plating voids over the last 24 months at SEMATECH. FIB-SEM feedback has been used to evaluate new plating chemistries, plating recipes, and process tool requalification after downtime. The dualbeam FIB-SEM used for these studies employs a gallium-based liquid metal ion source (LMIS). The overall throughput of relatively large volumes being milled is limited to 3-4 hours per section due to the maximum available beam current of 20 nA. Despite the larger volumetric removal rates of other techniques (e.g., mechanical polishing, broad-ion milling, and laser ablation), the value of localized, site-specific, and artifact-free FIB milling is well appreciated. The challenge, therefore, has been to reap the desired FIB benefits, but at faster volume removal rates. This has led to several system and technology developments for improving the throughput of the FIB technique, the most recent being the introduction of FIBs based on an inductively coupled plasma (ICP) ion source. The ICP source offers much better performance than the LMIS at very high beam currents, enabling more than 1 μA of ion beam current for fast material removal. At a lower current, the LMIS outperforms the ICP source, but imaging resolution below 30 nm has been demonstrated with ICP-based systems. In addition, the ICP source allows a wide range of possible ion species, with Xe currently the milling species of choice, due to its high mass and favorable ion source performance parameters. Using a 1 μA Xe beam will have an overall milling rate for silicon some 20X higher than a Ga beam operating at 65 nA. This paper will compare the benefits already seen using the Ga-based FIB-SEM approach to TSV metrology, with the improvements in throughput and time-to-data obtained by using the faster material removal capabilities of a FIB based on an ICP ion source. Plasma FIB (PFIB) is demonstrated to be a feasible tool for TSV plating void metrology.

Value of gamma-glutamyltranspeptidase-to-platelet ratio in diagnosis of hepatic fibrosis in patients with chronic hepatitis B

PubMed Central

Hu, Yan-Chao; Liu, Hao; Liu, Xiao-Yan; Ma, Li-Na; Guan, Yu-Hua; Luo, Xia; Ding, Xiang-Chun

2017-01-01

AIM To investigate the value of the gamma-glutamyltraspeptidase (GGT)-to-platelet (PLT) ratio (GPR) in the diagnosis of hepatic fibrosis in patients with chronic hepatitis B (CHB). METHODS We included 390 untreated CHB patients in this study. The GPR, aspartate aminotransferase (AST)-to-PLT ratio index (APRI), and fibrosis-4 (FIB-4) of all patients were analysed to determine if these parameter were correlated with age, gender, medical history, liver function [total bilirubin (TBil), alanine aminotransferase (ALT), and AST], GGT, PLT count, or hepatic fibrosis stage. The GPR, APRI, and FIB-4, as well as the combination of the GPR and APRI or the GPR and FIB-4 were assessed in different cirrhosis stages using receiver operating characteristic (ROC) curve analysis to evaluate their value in diagnosing hepatic fibrosis in CHB patients. RESULTS The GPR, APRI, and FIB-4 were not correlated with CHB patients’ age, gender, or disease duration (P > 0.05), but all of these parameters were positively correlated with serum ALT, AST, GGT, and PLT count (P < 0.01). Additionally, the GPR, APRI, and FIB-4 were positively correlated with hepatic fibrosis (P < 0.01); the areas under the ROC curve for the GPR in F1, F2, F3, and F4 stages were 0.723, 0.741, 0.826, and 0.833, respectively, which were significantly higher than the respective values for the FIB-4 and APRI (F1: 0.581, 0.612; F2: 0.706, 0.711; F3: 0.73, 0.751; and F4: 0.799, 0.778). The respective diagnostic cut-off points for each stage were 0.402, 0.448, 0.548, and 0.833, respectively. The diagnostic sensitivity and specificity were, respectively, 88.8% and 87.5% in F1, 72.7% and 89.7% in F2, 81.3% and 98.6% in F3, and 80% and 97.4% in F4 when the GPR and APRI were connected in parallel; 86.6% and 90.2%, 78.4% and 96%, 78.6% and 97.4%, and 73.2% and 97.9%, respectively, when the GPR and APRI were connected in series; 80.2% and 89%, 65% and 89%, 70.3% and 98.5%, and 78.8% and 96.8%, respectively, when the GPR and FIB-4 were connected in parallel; and 83.6% and 87.9%, 76.8% and 96.6%, 72.7% and 98%, and 74.4% and 97.7%, respectively, when the GPR and FIB-4 were connected in series. CONCLUSION The GPR, as a serum diagnostic index of liver fibrosis, is more accurate, sensitive, and easy to use than the FIB-4 and APRI, and the GPR can significantly improve the sensitivity and specificity of hepatic fibrosis diagnosis in CHB when combined with the FIB-4 or APRI. PMID:29151696

Relationship between virological response and FIB-4 index in chronic hepatitis B patients with entecavir therapy

PubMed Central

Li, Ni; Xu, Jing-Hang; Yu, Min; Wang, Sa; Si, Chong-Wen; Yu, Yan-Yan

2015-01-01

AIM: To investigate whether long-term low-level hepatitis B virus (HBV) DNA influences dynamic changes of the FIB-4 index in chronic hepatitis B (CHB) patients receiving entecavir (ETV) therapy with partial virological responses. METHODS: We retrospectively analyzed 231 nucleos(t)ide (NA) naïve CHB patients from our previous study (NCT01926288) who received continuous ETV or ETV maleate therapy for three years. The patients were divided into partial virological response (PVR) and complete virological response (CVR) groups according to serum HBV DNA levels at week 48. Seventy-six patients underwent biopsies at baseline and at 48 wk. The performance of the FIB-4 index and area under the receiver operating characteristic (AUROC) curve for predicting fibrosis were determined for the patients undergoing biopsy. The primary objective of the study was to compare the cumulative probabilities of virological responses between the two groups during the treatment period. The secondary outcome was to observe dynamic changes of the FIB-4 index between CVR patients and PVR patients. RESULTS: For hepatitis B e antigen (HBeAg)-positive patients (n = 178), the cumulative probability of achieving undetectable levels at week 144 was 95% and 69% for CVR and PVR patients, respectively (P < 0.001). In the Cox proportional hazards model, a lower pretreatment serum HBV DNA level was an independent factor predicting maintained viral suppression. The cumulative probability of achieving undetectable levels of HBV DNA for HBeAg-negative patients (n = 53) did not differ between the two groups. The FIB-4 index efficiently identified fibrosis, with an AUROC of 0.80 (95%CI: 0.69-0.89). For HBeAg-positive patients, the FIB-4 index was higher in CVR patients than in PVR patients at baseline (1.89 ± 1.43 vs 1.18 ± 0.69, P < 0.001). There was no significant difference in the reduction of the FIB-4 index between the CVR and PVR groups from weeks 48 to 144 (-0.11 ± 0.47 vs -0.13 ± 0.49, P = 0.71). At week 144, the FIB-4 index levels were similar between the two groups (1.24 ± 0.87 vs 1.02 ± 0.73, P = 0.06). After multivariate logistic regression analysis, a lower baseline serum HBV DNA level was associated with improvement of liver fibrosis. In HBeAg-negative patients, the FIB-4 index did not differ between the two groups. CONCLUSION: The cumulative probabilities of HBV DNA responses showed significant differences between CVR and PVR HBeAg-positive CHB patients undergoing entecavir treatment for 144 wk. However, long-term low-level HBV DNA did not deteriorate the FIB-4 index, which was used to evaluate liver fibrosis, at the end of three years. PMID:26604649

Subgrain boundary analyses in deformed orthopyroxene by TEM/STEM with EBSD-FIB sample preparation technique

NASA Astrophysics Data System (ADS)

Kogure, Toshihiro; Raimbourg, Hugues; Kumamoto, Akihito; Fujii, Eiko; Ikuhara, Yuichi

2014-12-01

High-resolution structure analyses using electron beam techniques have been performed for the investigation of subgrain boundaries (SGBs) in deformed orthopyroxene (Opx) in mylonite from Hidaka Metamorphic Belt, Hokkaido, Japan, to understand ductile deformation mechanism of silicate minerals in shear zones. Scanning electron microscopy (SEM) and electron backscatter diffraction (EBSD) analysis of Opx porphyroclasts in the mylonitic rock indicated that the crystal orientation inside the Opx crystals gradually changes by rotation about the b-axis by SGBs and crystal folding. In order to observe the SGBs along the b-axis by transmission electron microscopy (TEM) or scanning TEM (STEM), the following sample preparation protocol was adopted. First, petrographic thin sections were slightly etched with hydrofluoric acid to identify SGBs in SEM. The Opx crystals whose b-axes were oriented close to the normal of the surface were identified by EBSD, and the areas containing SGBs were picked and thinned for (S) TEM analysis with a focused ion beam instrument with micro-sampling system. High-resolution TEM imaging of the SGBs in Opx revealed various boundary structures from a periodic array of dissociated (100) [001] edge dislocations to partially or completely incoherent crystals, depending on the misorientation angle. Atomic-resolution STEM imaging clearly confirmed the formation of clinopyroxene (Cpx) structure between the dissociated partial dislocations. Moreover, X-ray microanalysis in STEM revealed that the Cpx contains a considerable amount of calcium replacing iron. Such chemical inhomogeneity may limit glide motion of the dislocation and eventually the plastic deformation of the Opx porphyroclasts at a low temperature. Chemical profiles across the high-angle incoherent SGB also showed an enrichment of the latter in calcium at the boundary, suggesting that SGBs are an efficient diffusion pathway of calcium out of host Opx grain during cooling.

Mechanistic Target of Rapamycin Complex 1 (mTORC1) and mTORC2 as Key Signaling Intermediates in Mesenchymal Cell Activation*

PubMed Central

Walker, Natalie M.; Belloli, Elizabeth A.; Stuckey, Linda; Chan, Kevin M.; Lin, Jules; Lynch, William; Chang, Andrew; Mazzoni, Serina M.; Fingar, Diane C.; Lama, Vibha N.

2016-01-01

Fibrotic diseases display mesenchymal cell (MC) activation with pathologic deposition of matrix proteins such as collagen. Here we investigate the role of mTOR complex 1 (mTORC1) and mTORC2 in regulating MC collagen expression, a hallmark of fibrotic disease. Relative to normal MCs (non-Fib MCs), MCs derived from fibrotic human lung allografts (Fib-MCs) demonstrated increased phosphoinositide-3kinase (PI3K) dependent activation of both mTORC1 and mTORC2, as measured by increased phosphorylation of S6K1 and 4E-BP1 (mTORC1 substrates) and AKT (an mTORC2 substrate). Dual ATP-competitive TORC1/2 inhibitor AZD8055, in contrast to allosteric mTORC1-specific inhibitor rapamycin, strongly inhibited 4E-BP1 phosphorylation and collagen I expression in Fib-MCs. In non-Fib MCs, increased mTORC1 signaling was shown to augment collagen I expression. mTORC1/4E-BP1 pathway was identified as an important driver of collagen I expression in Fib-MCs in experiments utilizing raptor gene silencing and overexpression of dominant-inhibitory 4E-BP1. Furthermore, siRNA-mediated knockdown of rictor, an mTORC2 partner protein, reduced mTORC1 substrate phosphorylation and collagen expression in Fib-, but not non-Fib MCs, revealing a dependence of mTORC1 signaling on mTORC2 function in activated MCs. Together these studies suggest a novel paradigm where fibrotic activation in MCs increases PI3K dependent mTORC1 and mTORC2 signaling and leads to increased collagen I expression via the mTORC1-dependent 4E-BP1/eIF4E pathway. These data provide rationale for targeting specific components of mTORC pathways in fibrotic states and underscore the need to further delineate mTORC2 signaling in activated cell states. PMID:26755732

Impact of age on the diagnostic performances and cut-offs of APRI and FIB-4 for significant fibrosis and cirrhosis in chronic hepatitis B

PubMed Central

Li, Qiang; Lu, Chuan; Li, Weixia; Huang, Yuxian; Chen, Liang

2017-01-01

Aims Assessing the diagnostic performances of APRI and FIB-4 using age as a categorical marker. Methods 822 chronic hepatitis B (CHB) patients were included. Using METAVIR scoring system as a reference, the performances of APRI and FIB-4 were compared between patients aged≥30 and patients aged<30 years. Results The APRI AUROC in patients aged<30 years was lower than that in patients aged≥30 years for significant fibrosis (0.61 vs 0.70, p<0.001) and cirrhosis (0.64 vs 0.78, p<0.001). The FIB-4 AUROC in patients aged<30 years was lower than that in patients aged≥30 years for significant fibrosis (0.57 vs 0.65, p<0.001) and cirrhosis (0.63 vs 0.72, p<0.001). Using specificity≥90%, the APRI cut-off in patients aged<30 years was lower than patients aged≥30 years for significant fibrosis (1.0 vs 1.2) and cirrhosis (1.2 vs 1.5). Using sensitivity≥90%, the APRI cut-off in patients aged<30 years was also lower than patients aged≥30 years for significant fibrosis (0.2 vs 0.4) and cirrhosis (0.3 vs 0.5). Using specificity≥90%, the FIB-4 cut-off in patients aged<30 years was lower than that in patients aged≥30 years for significant fibrosis (1.2 vs 2.1) and cirrhosis (1.4 vs 2.6). Using sensitivity≥90%, the FIB-4 cut-off in patients aged<30 years was also lower than that in patients aged≥30 years for significant fibrosis (0.5 vs 0.8) and cirrhosis (0.8 vs 1.2). Conclusions Evaluation of the diagnostic performances of APRI and FIB-4 should take age into consideration. PMID:28514753

End region detailing of pretensioned concrete bridge girders : [summary].

DOT National Transportation Integrated Search

2013-03-01

Introduction of the Florida-I Beam (FIB) in 2009 renewed interest in prestressed concrete beam design, especially end region details. In this study, University of Florida researchers examined construction detailing at the FIB end region.

Predicting recreational water quality advisories: A comparison of statistical methods

USGS Publications Warehouse

Brooks, Wesley R.; Corsi, Steven R.; Fienen, Michael N.; Carvin, Rebecca B.

2016-01-01

Epidemiological studies indicate that fecal indicator bacteria (FIB) in beach water are associated with illnesses among people having contact with the water. In order to mitigate public health impacts, many beaches are posted with an advisory when the concentration of FIB exceeds a beach action value. The most commonly used method of measuring FIB concentration takes 18–24 h before returning a result. In order to avoid the 24 h lag, it has become common to ”nowcast” the FIB concentration using statistical regressions on environmental surrogate variables. Most commonly, nowcast models are estimated using ordinary least squares regression, but other regression methods from the statistical and machine learning literature are sometimes used. This study compares 14 regression methods across 7 Wisconsin beaches to identify which consistently produces the most accurate predictions. A random forest model is identified as the most accurate, followed by multiple regression fit using the adaptive LASSO.

Graphite nanoplatelet enabled embeddable fiber sensor for in situ curing monitoring and structural health monitoring of polymeric composites.

PubMed

Luo, Sida; Liu, Tao

2014-06-25

A graphite nanoplatelet (GNP) thin film enabled 1D fiber sensor (GNP-FibSen) was fabricated by a continuous roll-to-roll spray coating process, characterized by scanning electron microscopy and Raman spectroscopy and evaluated by coupled electrical-mechanical tensile testing. The neat GNP-FibSen sensor shows very high gauge sensitivity with a gauge factor of ∼17. By embedding the sensor in fiberglass prepreg laminate parts, the dual functionalities of the GNP-FibSen sensor were demonstrated. In the manufacturing process, the resistance change of the embedded sensor provides valuable local resin curing information. After the manufacturing process, the same sensor is able to map the strain/stress states and detect the failure of the host composite. The superior durability of the embedded GNP-FibSen sensor has been demonstrated through 10,000 cycles of coupled electromechanical tests.

Enhanced FIB-SEM systems for large-volume 3D imaging.

PubMed

Xu, C Shan; Hayworth, Kenneth J; Lu, Zhiyuan; Grob, Patricia; Hassan, Ahmed M; García-Cerdán, José G; Niyogi, Krishna K; Nogales, Eva; Weinberg, Richard J; Hess, Harald F

2017-05-13

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 10 6 µm 3 . These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.

Observation of thermally etched grain boundaries with the FIB/TEM technique

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

Palizdar, Y., E-mail: y.palizdar@merc.ac.ir; San Martin, D.; Ward, M.

2013-10-15

Thermal etching is a method which is able to reveal and characterize grain boundaries, twins or dislocation structures and determine parameters such as grain boundary energies, surface diffusivities or study phase transformations in steels, intermetallics or ceramic materials. This method relies on the preferential transfer of matter away from grain boundaries on a polished sample during heating at high temperatures in an inert/vacuum atmosphere. The evaporation/diffusion of atoms at high temperatures results in the formation of grooves at the intersections of the planes of grain/twin boundaries with the polished surface. This work describes how the combined use of Focussed Ionmore » Beam and Transmission Electron Microscopy can be used to characterize not only the grooves and their profile with the surface, but also the grain boundary line below the groove, this method being complementary to the commonly used scanning probe techniques. - Highlights: • Thermally etched low-carbon steel samples have been characterized by FIB/TEM • Grain boundary (GB) lines below the groove have been characterized in this way • Absence of ghost traces and large θ angle suggests that GB are not stationary but mobile • Observations correlate well with previous works and Mullins' investigations [22].« less

Counting Synapses Using FIB/SEM Microscopy: A True Revolution for Ultrastructural Volume Reconstruction.

PubMed

Merchán-Pérez, Angel; Rodriguez, José-Rodrigo; Alonso-Nanclares, Lidia; Schertel, Andreas; Defelipe, Javier

2009-01-01

The advent of transmission electron microscopy (TEM) in the 1950s represented a fundamental step in the study of neuronal circuits. The application of this technique soon led to the realization that the number of synapses changes during the course of normal life, as well as under certain pathological or experimental circumstances. Since then, one of the main goals in neurosciences has been to define simple and accurate methods to estimate the magnitude of these changes. Contrary to analysing single sections, TEM reconstructions are extremely time-consuming and difficult. Therefore, most quantitative studies use stereological methods to define the three-dimensional characteristics of synaptic junctions that are studied in two dimensions. Here, to count the exact number of synapses per unit of volume we have applied a new three-dimensional reconstruction method that involves the combination of focused ion beam milling and scanning electron microscopy (FIB/SEM). We show that the images obtained with FIB/SEM are similar to those obtained with TEM, but with the advantage that FIB/SEM permits serial reconstructions of large volumes of tissue to be generated rapidly and automatically. Furthermore, we compared the estimates of the number of synapses obtained with stereological methods with the values obtained by FIB/SEM reconstructions. We concluded that FIB/SEM not only provides the actual number of synapses per volume but it is also much easier and faster to use than other currently available TEM methods. More importantly, it also avoids most of the errors introduced by stereological methods and overcomes the difficulties associated with these techniques.

Correlation of quantitative PCR for a poultry-specific brevibacterium marker gene with bacterial and chemical indicators of water pollution in a watershed impacted by land application of poultry litter.

PubMed

Weidhaas, Jennifer L; Macbeth, Tamzen W; Olsen, Roger L; Harwood, Valerie J

2011-03-01

The impact of fecal contamination from human and agricultural animal waste on water quality is a major public health concern. Identification of the dominant source(s) of fecal pollution in a watershed is necessary for assessing the safety of recreational water and protecting water resources. A field study was conducted using quantitative PCR (qPCR) for the 16S rRNA gene of Brevibacterium sp. LA35 to track feces-contaminated poultry litter in environmental samples. Based on sensitivity and specificity characteristics of the qPCR method, the Bayesian conditional probability that detection of the LA35 marker gene in a water sample represented a true-positive result was 93%. The marker's covariance with fecal indicator bacteria (FIB) and metals associated with poultry litter was also assessed in litter, runoff, surface water, and groundwater samples. LA35 was detected in water and soil samples collected throughout the watershed, and its concentration covaried with concentrations of Escherichia coli, enterococci, As, Cu, P, and Zn. Significantly greater concentrations of FIB, As, Cu, P, and Zn were observed in edge-of-field runoff samples in which LA35 was detected, compared to samples in which it was not detected. Furthermore, As, Cu, P, and Zn concentrations covaried in environmental samples in which LA35 was detected and typically did not in samples in which the marker gene was not detected. The covariance of the poultry-specific LA35 marker gene with these known contaminants from poultry feces provides further evidence that it is a useful tool for assessing the impact of poultry-derived fecal pollution in environmental waters.

Site-specific characterization of beetle horn shell with micromechanical bending test in focused ion beam system.

PubMed

Lee, Hyun-Taek; Kim, Ho-Jin; Kim, Chung-Soo; Gomi, Kenji; Taya, Minoru; Nomura, Shûhei; Ahn, Sung-Hoon

2017-07-15

Biological materials are the result of years of evolution and possess a number of efficient features and structures. Researchers have investigated the possibility of designing biomedical structures that take advantage of these structural features. Insect shells, such as beetle shells, are among the most promising types of biological material for biomimetic development. However, due to their intricate geometries and small sizes, it is challenging to measure the mechanical properties of these microscale structures. In this study, we developed an in-situ testing platform for site-specific experiments in a focused ion beam (FIB) system. Multi-axis nano-manipulators and a micro-force sensor were utilized in the testing platform to allow better results in the sample preparation and data acquisition. The entire test protocol, consisting of locating sample, ion beam milling and micro-mechanical bending tests, can be carried out without sample transfer or reattachment. We used our newly devised test platform to evaluate the micromechanical properties and structural features of each separated layer of the beetle horn shell. The Young's modulus of both the exocuticle and endocuticle layers was measured. We carried out a bending test to characterize the layers mechanically. The exocuticle layer bent in a brick-like manner, while the endocuticle layer exhibited a crack blunting effect. This paper proposed an in-situ manipulation/test method in focused ion beam for characterizing micromechanical properties of beetle horn shell. The challenge in precise and accurate fabrication for the samples with complex geometry was overcome by using nano-manipulators having multi-degree of freedom and a micro-gripper. With the aid of this specially designed test platform, bending tests were carried out on cantilever-shaped samples prepared by focused ion beam milling. Structural differences between exocuticle and endocuticle layers of beetle horn shell were explored and the results provided insight into the structural advantages of each biocomposite structure. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Water quality prediction of marine recreational beaches receiving watershed baseflow and stormwater runoff in southern California, USA.

PubMed

He, Li-Ming Lee; He, Zhen-Li

2008-05-01

Beach advisories are issued to the public in California when the concentration of fecal indicator bacteria (FIB), including total coliform, fecal coliform (or Escherichia coli), and Enterococcus, exceed their recreational water health standards, or when the amount of a rainfall event is above the pre-determined threshold. However, it is not fully understood about how and to what degree stormwater runoff or baseflow exerts impacts on beach water quality. Furthermore, current laboratory methods used to determine the FIB levels take 18-96 h, which is too slow to keep pace with changes in FIB levels in water. Thus, a beach may not be posted when it is contaminated, and may be posted under advisory when bacterial levels have already decreased to within water quality standards. The study was designed to address the above critical issues. There were large temporal and spatial variations in FIB concentrations along two popular State Beaches in San Diego, CA, USA. The rainstorm-induced runoff from the watersheds exerts significant impacts on the marine recreational water quality of the beaches adjacent to lagoons during the first 24-48 h after a rain event. The large volume of stormwater runoff discharging to beaches caused high FIB concentrations in beach water not only at the lagoon outlet channel and the mixing zone, but also at the locations 90 m away from the channel northward or southward along the shoreline. The geomorphology of beach shoreline, distance from the outlet channel, wind strength, wind direction, tide height, wave height, rainfall, time lapse after a rainstorm, or channel flow rate played a role in affecting the distribution of FIB concentrations in beach water. Despite the great temporal and spatial variability of FIB concentrations along a shoreline, the artificial neural network-based models developed in this study are capable of successfully predicting FIB concentrations at different beaches, different locations, and different times under baseflow or rainstorm conditions. The models are based on readily measurable variables including temperature, conductivity, pH, turbidity, channel water flow, rainfall, and/or time lapse after a rainstorm. The established models will help fill the current gap between beach posting and actual water quality and make more meaningful and effective decisions on beach closures and advisories.

Matrices pattern using FIB; 'Out-of-the-box' way of thinking.

PubMed

Fleger, Y; Gotlib-Vainshtein, K; Talyosef, Y

2017-03-01

Focused ion beam (FIB) is an extremely valuable tool in nanopatterning and nanofabrication for potentially high-resolution patterning, especially when refers to He ion beam microscopy. The work presented here demonstrates an 'out-of-the-box' method of writing using FIB, which enables creating very large matrices, up to the beam-shift limitation, in short times and with high accuracy unachievable by any other writing technique. The new method allows combining different shapes in nanometric dimensions and high resolutions for wide ranges. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Mapping Strain Gradients in the FIB-Structured InGaN/GaN Multilayered Films with 3D X-ray Microbeam

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

Barabash, Rozaliya; Gao, Yanfei; Ice, Gene E

2010-01-01

This research presents a combined experimental-modeling study of lattice rotations and deviatoric strain gradients induced by focused-ion beam (FIB) milling in nitride heterostructures. 3D X-ray polychromatic microdiffraction (PXM) is used to map the local lattice orientation distribution in FIB-structured areas. Results are discussed in connection with microphotoluminescence ({mu}-PL), fluorescent analysis, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) data. It is demonstrated that FIB-milling causes both direct and indirect damage to the InGaN/GaN layers. In films subjected to direct ion beam impact, a narrow amorphidized top layer is formed. Near the milling area, FIB-induced stress relaxation and formation ofmore » complicated 3D strain fields are observed. The resulting lattice orientation changes are found to correlate with a decrease and/or loss of PL intensity, and agree well with finite element simulations of the three-dimensional strain fields near the relaxed trenches. Experimentally, it is found that the lattice surface normal has an in-plane rotation, which only appears in simulations when the GaN-substrate lattice mismatch annihilates the InGaN-substrate mismatch. This behavior further supports the notion that the film/substrate interface is incoherent.« less

Mapping strain gradients in the FIB-structured InGaN/GaN multilayered films with 3D x-ray microbeam.

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

Barabash, R. I.; Gao, Y. F.; Ice, G. E.

2010-11-25

This research presents a combined experimental-modeling study of lattice rotations and deviatoric strain gradients induced by focused-ion beam (FIB) milling in nitride heterostructures. 3D X-ray polychromatic microdiffraction (PXM) is used to map the local lattice orientation distribution in FIB-structured areas. Results are discussed in connection with microphotoluminescence ({mu}-PL), fluorescent analysis, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) data. It is demonstrated that FIB-milling causes both direct and indirect damage to the InGaN/GaN layers. In films subjected to direct ion beam impact, a narrow amorphidized top layer is formed. Near the milling area, FIB-induced stress relaxation and formation ofmore » complicated 3D strain fields are observed. The resulting lattice orientation changes are found to correlate with a decrease and/or loss of PL intensity, and agree well with finite element simulations of the three-dimensional strain fields near the relaxed trenches. Experimentally, it is found that the lattice surface normal has an in-plane rotation, which only appears in simulations when the GaN-substrate lattice mismatch annihilates the InGaN-substrate mismatch. This behavior further supports the notion that the film/substrate interface is incoherent.« less

Speculation of the Time-Dependent Change of FIB4 Index in Patients with Nonalcoholic Fatty Liver Disease: A Retrospective Study.

PubMed

Miyata, Hiroshi; Miyata, Satoru

2018-01-01

To speculate on the time-dependent change of FIB4 index in patients with nonalcoholic fatty liver disease (NAFLD) and its increase-decrease rate per year, simply and accurately. In all 23 patients with NAFLD with the value of FIB4 index over 1.30 at the peak, the period from the first to each examination date was calculated and this period (years) was regarded as x . Next, the mean value of FIB4 index during the past year to each examination date was regarded as y . In every y , the minimum and the maximum y value were found out. Between x corresponding to this minimum y and x corresponding to this maximum y , the correlation between x and y was analyzed as the main subject. Then, the slope of each correlation was investigated, because it should indicate increase-decrease rate per year. In all 23 patients, the correlations as the main subject were recognized and the mean absolute value of correlation coefficient ( r ) was 0.91 ± 0.08. As for the slope, the mean absolute value was 0.1371 ± 0.1147 (/year). Simply and accurately, the time-dependent change of FIB4 index and its increase-decrease rate per year could be approximately speculated.

Urban Water Services in Fragile States: An Analysis of Drinking Water Sources and Quality in Port Harcourt, Nigeria, and Monrovia, Liberia.

PubMed

Kumpel, Emily; Albert, Jeff; Peletz, Rachel; de Waal, Dominick; Hirn, Maximilian; Danilenko, Alexander; Uhl, Vincent; Daw, Ashish; Khush, Ranjiv

2016-07-06

Establishing and maintaining public water services in fragile states is a significant development challenge. In anticipation of water infrastructure investments, this study compares drinking water sources and quality between Port Harcourt, Nigeria, and Monrovia, Liberia, two cities recovering from political and economic instability. In both cities, access to piped water is low, and residents rely on a range of other private and public water sources. In Port Harcourt, geographic points for sampling were randomly selected and stratified by population density, whereas in Monrovia, locations for sampling were selected from a current inventory of public water sources. In Port Harcourt, the sampling frame demonstrated extensive reliance on private boreholes and a preference, in both planned and unplanned settlements, for drinking bottled and sachet water. In Monrovia, sample collection focused on public sources (predominantly shallow dug wells). In Port Harcourt, fecal indicator bacteria (FIB) were detected in 25% of sources (N = 566), though concentrations were low. In Monrovia, 57% of sources contained FIB and 22% of sources had nitrate levels that exceeded standards (N = 204). In Monrovia, the convenience of piped water may promote acceptance of the associated water tariffs. However, in Port Harcourt, the high prevalence of self-supply and bottled and sachet drinking water suggests that the consumer's willingness to pay for ongoing municipal water supply improvements may be determined by service reliability and perceptions of water quality. © The American Society of Tropical Medicine and Hygiene.

Urban Water Services in Fragile States: An Analysis of Drinking Water Sources and Quality in Port Harcourt, Nigeria, and Monrovia, Liberia

PubMed Central

Kumpel, Emily; Albert, Jeff; Peletz, Rachel; de Waal, Dominick; Hirn, Maximilian; Danilenko, Alexander; Uhl, Vincent; Daw, Ashish; Khush, Ranjiv

2016-01-01

Establishing and maintaining public water services in fragile states is a significant development challenge. In anticipation of water infrastructure investments, this study compares drinking water sources and quality between Port Harcourt, Nigeria, and Monrovia, Liberia, two cities recovering from political and economic instability. In both cities, access to piped water is low, and residents rely on a range of other private and public water sources. In Port Harcourt, geographic points for sampling were randomly selected and stratified by population density, whereas in Monrovia, locations for sampling were selected from a current inventory of public water sources. In Port Harcourt, the sampling frame demonstrated extensive reliance on private boreholes and a preference, in both planned and unplanned settlements, for drinking bottled and sachet water. In Monrovia, sample collection focused on public sources (predominantly shallow dug wells). In Port Harcourt, fecal indicator bacteria (FIB) were detected in 25% of sources (N = 566), though concentrations were low. In Monrovia, 57% of sources contained FIB and 22% of sources had nitrate levels that exceeded standards (N = 204). In Monrovia, the convenience of piped water may promote acceptance of the associated water tariffs. However, in Port Harcourt, the high prevalence of self-supply and bottled and sachet drinking water suggests that the consumer's willingness to pay for ongoing municipal water supply improvements may be determined by service reliability and perceptions of water quality. PMID:27114291

Quantitative risk analysis for potentially resistant E. coli in surface waters caused by antibiotic use in agricultural systems.

PubMed

Limayem, Alya; Martin, Elizabeth M

2014-01-01

Antibiotics are frequently used in agricultural systems to promote livestock health and to control bacterial contaminants. Given the upsurge of the resistant fecal indicator bacteria (FIB) in the surface waters, a novel statistical method namely, microbial risk assessment (MRA) was performed, to evaluate the probability of infection by resistant FIB on populations exposed to recreational waters. Diarrheagenic Escherichia coli, except E. coli O157:H7, were selected for their prevalence in aquatic ecosystem. A comparative study between a typical E. coli pathway and a case scenario aggravated by antibiotic use has been performed via Crystal Ball® software in an effort to analyze a set of available inputs provided by the US institutions including E. coli concentrations in US Great Lakes through using random sampling and probability distributions. Results from forecasting a possible worst-case scenario dose-response, accounted for an approximate 50% chance for 20% of the exposed human populations to be infected by recreational water in the U.S. However, in a typical scenario, there is a 50% chance of infection for only 1% of the exposed human populations. The uncertain variable, E. coli concentration accounted for approximately 92.1% in a typical scenario as the major contributing factor of the dose-response model. Resistant FIB in recreational waters that are exacerbated by a low dose of antibiotic pollutants would increase the adverse health effects in exposed human populations by 10 fold.

Correlative tomography at the cathode/electrolyte interfaces of solid oxide fuel cells

NASA Astrophysics Data System (ADS)

Wankmüller, Florian; Szász, Julian; Joos, Jochen; Wilde, Virginia; Störmer, Heike; Gerthsen, Dagmar; Ivers-Tiffée, Ellen

2017-08-01

This paper introduces a correlative tomography technique. It visualizes the spatial organization of primary and secondary phases at the interface of La0.58Sr0.4Co0.2Fe0.8O3-δ cathode/10 mol% Gadolinia doped Ceria/8 mol% Yttria stabilized Zirconia electrolyte. It uses focused ion beam/scanning electron microscope tomography (FIB/SEM), and combines data sets from Everhart-Thornley and Inlens detector differentiating four primary and two secondary material phases. In addition, grayscale information is correlated to elemental distribution gained by energy dispersive X-ray spectroscopy in a scanning transmission electron microscope. Interdiffusion of GDC into YSZ and SrZrO3 as secondary phases depend (in both amount and spatial organization) on the varied co-sintering temperature of the GDC/YSZ electrolyte. The ion-blocking SrZrO3 forms a continuous layer on top of the temperature-dependent GDC/YSZ interdiffusion zone (ID) at and below a co-sintering temperature of 1200 °C; above it becomes intermittent. 2D FIB/SEM images of primary and secondary phases at 1100, 1200, 1300 and 1400 °C were combined with a 3D FIB/SEM reconstruction (1300 °C). This reveals that ;preferred; oxygen ion transport pathways from the LSCF cathode through GDC and the ID into the YSZ electrolyte only exist in samples sintered above 1200 °C. The applied correlative technique expands our understanding of this multiphase cathode/electrolyte interface region.

Demonstration of a focused ion-beam cross-sectioning technique for ultrastructural examination of resin-dentin interfaces.

PubMed

Van Meerbeek, B; Conn, L J; Duke, E S; Schraub, D; Ghafghaichi, F

1995-03-01

focused ion-beam (FIB) etching, commonly used as a cross-sectioning technique for failure analysis of semiconductor devices, has recently been applied to biological tissues to expose their ultrastructure for examination. It was the aim of this investigation to determine the practical utility of FIB to cross-section resin-dentin interfaces in order to morphologically evaluate the completeness of resin penetration into the exposed collagen scaffold at the resin-dentin bond interface. Two representative commercially available dentin adhesive systems were bonded to mid-coronal dentin. After appropriate fixation and dehydration of the resin-bonded dentin samples, a scanned focused ion-beam of a few tens of nano-meters in diameter was used to cross=section the resin-dentin interface. Examination of the interfacial ultrastructure was accomplished using a field-emission SEM. Results indicate possible artifact production at the cross-sectioned interface, hiding its actual ultrastructure, probably due to a heat-effect with possible recrystallization. Further studies of FIB are needed to optimize its usefulness for resin-dentin interface examinations and other biological tissue applications. Complete resin saturation of the demineralized dentin surface-layer has been claimed to be the key factor for a long-lasting resin-dentin bond. A "clean" artifact-free micro-cross-sectioning technique may provide indisputable ultra-structural information about the depth of resin penetration into the demineralized zone. Such a test would be useful in the development of dentin adhesive systems.

Beach monitoring criteria: reading the fine print

USGS Publications Warehouse

Nevers, Meredith B.; Whitman, Richard L.

2011-01-01

Beach monitoring programs aim to decrease swimming-related illnesses resulting from exposure to harmful microbes in recreational waters, while providing maximum beach access. Managers are advised by the U.S. EPA to estimate microbiological water quality based on a 5-day geometric mean of fecal indicator bacteria (FIB) concentrations or on a jurisdiction-specific single-sample maximum; however, most opt instead to apply a default single-sample maximum to ease application. We examined whether re-evaluation of the U.S. EPA ambient water quality criteria (AWQC) and the epidemiological studies on which they are based could increase public beach access without affecting presumed health risk. Single-sample maxima were calculated using historic monitoring data for 50 beaches along coastal Lake Michigan on various temporal and spatial groupings to assess flexibility in the application of the AWQC. No calculation on either scale was as low as the default maximum (235 CFU/100 mL) that managers typically use, indicating that current applications may be more conservative than the outlined AWQC. It was notable that beaches subject to point source FIB contamination had lower variation, highlighting the bias in the standards for these beaches. Until new water quality standards are promulgated, more site-specific application of the AWQC may benefit beach managers by allowing swimmers greater access to beaches. This issue will be an important consideration in addressing the forthcoming beach monitoring standards.

Distribution factors for construction loads and girder capacity equations [project summary].

DOT National Transportation Integrated Search

2017-03-01

This project focused on the use of Florida I-beams (FIBs) in bridge construction. University of Florida researchers used analytical models and finite element analysis to update equations used in the design of bridges using FIBs. They were particularl...

Bacteriophages as indicators of faecal pollution and enteric virus removal

EPA Science Inventory

Bacteriophages are an attractive alternative to fecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport due to their closer morphological and biological properties compared to FIB. Based on a meta-analysis of published data, we summarize con...

Quantification of silver nanoparticle uptake and distribution within individual human macrophages by FIB/SEM slice and view.

PubMed

Guehrs, Erik; Schneider, Michael; Günther, Christian M; Hessing, Piet; Heitz, Karen; Wittke, Doreen; López-Serrano Oliver, Ana; Jakubowski, Norbert; Plendl, Johanna; Eisebitt, Stefan; Haase, Andrea

2017-03-21

Quantification of nanoparticle (NP) uptake in cells or tissues is very important for safety assessment. Often, electron microscopy based approaches are used for this purpose, which allow imaging at very high resolution. However, precise quantification of NP numbers in cells and tissues remains challenging. The aim of this study was to present a novel approach, that combines precise quantification of NPs in individual cells together with high resolution imaging of their intracellular distribution based on focused ion beam/ scanning electron microscopy (FIB/SEM) slice and view approaches. We quantified cellular uptake of 75 nm diameter citrate stabilized silver NPs (Ag 75 Cit) into an individual human macrophage derived from monocytic THP-1 cells using a FIB/SEM slice and view approach. Cells were treated with 10 μg/ml for 24 h. We investigated a single cell and found in total 3138 ± 722 silver NPs inside this cell. Most of the silver NPs were located in large agglomerates, only a few were found in clusters of fewer than five NPs. Furthermore, we cross-checked our results by using inductively coupled plasma mass spectrometry and could confirm the FIB/SEM results. Our approach based on FIB/SEM slice and view is currently the only one that allows the quantification of the absolute dose of silver NPs in individual cells and at the same time to assess their intracellular distribution at high resolution. We therefore propose to use FIB/SEM slice and view to systematically analyse the cellular uptake of various NPs as a function of size, concentration and incubation time.

[Non-invasive fibrosis indexes in predicting acute liver function deterioration after transcatheter arterial chemoembolization].

PubMed

Song, Y P; Zhao, Q Y; Li, S; Wang, H; Wu, P H

2016-03-08

To investigate the ability of two non-invasive fibrosis indexes-APRI, i. e. aspartate transaminase (AST) to platelet (PLT) ratio index, and fibrosis index based on the 4 factors (FIB-4)score in predicting ALFD in patients with unresectable primary HCC and underwent TACE. Clinical data of those patients treated with TACE in Department of Interventional Radiology of the Center from Jan 2010 to Aug 2014 were investigated retrospectively. A total of 366 cases were enrolled after randomized selection, 62 (18.5%) of which developed ALFD after TACE. Child-Pugh score, APRI and FIB-4 score in every case were calculated, receiver operating characteristic (ROC) curve of each model were performed and the predictive abilities of them were assessed by area under the curve (AUC), positive predictive value (PPV), negative predictive value (NPV), sensitivity and specificity. The AUC of Child-Pugh score, APRI and FIB-4 score were 0.783, 0.752 and 0.758 respectively, while the difference had no significance in statistics, indicating that predictive accuracies of them were similar. APRI≤1.15 and FIB-4≤3.08 had better NPV (90.6% and 93.6%) and sensitivity (65.6% and 80.0%) than Child-Pugh score>6 (NPV=85.8%, sensitivity=27.4%), PPV and specificity of them are 35.7%, 32.9%, 89.5% and 73.7%, 64.2%, 99.3% respectively. Comparing to Child-Pugh score, APRI and FIB-4 score have similar accuracy but better NPV and sensitivity in predicting post-TACE ALFD. Thereafter they are good for selection of low-risk patients for TACE treatment. Candidates with an APRI≤1.15 or a FIB-4≤3.08 or in Child-Pugh a stage are unlikely to develop ALFD thus could receive TACE safely.

Can transient elastography, Fib-4, Forns Index, and Lok Score predict esophageal varices in HCV-related cirrhotic patients?

PubMed

Hassan, Eman M; Omran, Dalia A; El Beshlawey, Mohamad L; Abdo, Mahmoud; El Askary, Ahmad

2014-02-01

Gastroesophageal varices are present in approximately 50% of patients with liver cirrhosis. The aim of this study was to evaluate liver stiffness measurement (LSM), Fib-4, Forns Index and Lok Score as noninvasive predictors of esophageal varices (EV). This prospective study included 65 patients with HCV-related liver cirrhosis. All patients underwent routine laboratory tests, transient elastograhy (TE) and esophagogastroduodenoscopy. FIB-4, Forns Index and Lok Score were calculated. The diagnostic performances of these methods were assessed using sensitivity, specificity, positive predictive value, negative predictive value, accuracy and receiver operating characteristic curves. All predictors (LSM, FIB-4, Forns Index and Lok Score) demonstrated statistically significant correlation with the presence and the grade of EV. TE could diagnose EV at a cutoff value of 18.2kPa. Fib-4, Forns Index, and Lok Score could diagnose EV at cutoff values of 2.8, 6.61 and 0.63, respectively. For prediction of large varices (grade 2, 3), LSM showed the highest accuracy (80%) with a cutoff of 22.4kPa and AUROC of 0.801. Its sensitivity was 84%, specificity 72%, PPV 84% and NPV 72%. The diagnostic accuracies of FIB-4, Forns Index and Lok Score were 70%, 70% and76%, respectively, at cutoffs of 3.3, 6.9 and 0.7, respectively. For diagnosis of large esophageal varices, adding TE to each of the other diagnostic indices (serum fibrosis scores) increased their sensitivities with little decrease in their specificities. Moreover, this combination decreased the LR- in all tests. Noninvasive predictors can restrict endoscopic screening. This is very important as non invasiveness is now a major goal in hepatology. Copyright © 2013 Elsevier España, S.L. and AEEH y AEG. All rights reserved.

The relationship between liver histology and noninvasive markers in primary biliary cirrhosis.

PubMed

Olmez, Sehmus; Sayar, Suleyman; Avcioglu, Ufuk; Tenlik, İlyas; Ozaslan, Ersan; Koseoglu, Hasan T; Altiparmak, Emin

2016-07-01

Primary biliary cirrhosis (PBC) is a disease that affects liver with various severity and progression rates. It is important to diagnose advanced stage of the disease to lower liver-related morbidity and mortality. Since liver biopsy is an invasive method, liver biopsy tends to be replaced by noninvasive methods. In this study, we aim to show the role of aminotransferase to platelet ratio index (APRI) and fibrosis index on the basis of the four factors (FIB-4) scores, laboratory values, and their effectiveness in predicting advanced disease. PBC patients diagnosed pathologically at Numune Education and Research Hospital were included in the study between the years 1995 and 2013. Patients were grouped according to their fibrosis level: group 1 (early stage) included 18 patients with F1 and F2 fibrosis and group 2 (advanced stage) included 22 patients with F3 and F4 fibrosis. APRI and FIB-4 scores, routine laboratory values, and their proportions were compared. The effectiveness of parameters showing advanced stage was further compared. There were statistically significant differences in APRI, FIB-4 scores, and aspartate aminotransferase (AST) levels between the groups with early and advanced stages of disease. Receiver operating curve analysis was used to determine APRI, FIB-4 and AST levels. The most effective parameters for diagnosing an advanced stage were APRI, AST levels, and FIB-4 scores, respectively. In conclusion, APRI and FIB-4 scores can be calculated simply and easily by routine laboratory tests at low cost and also these scores may be a predictor of advanced stage of the disease in PBC. These tests may be reproducible and may be used to monitor disease progression.

Comparison of FIB-4 index and aspartate aminotransferase to platelet ratio index on carcinogenesis in chronic hepatitis B treated with entecavir

PubMed Central

Nishikawa, Hiroki; Nishijima, Norihiro; Enomoto, Hirayuki; Sakamoto, Azusa; Nasu, Akihiro; Komekado, Hideyuki; Nishimura, Takashi; Kita, Ryuichi; Kimura, Toru; Iijima, Hiroko; Nishiguchi, Shuhei; Osaki, Yukio

2017-01-01

Aims: We sought to compare the effects of FIB-4 index and aspartate aminotransferase to platelet ratio index (APRI) on hepatocellular carcinoma (HCC) incidence in chronic hepatitis B (CHB) patients undergoing entecavir (ETV) therapy. Patient and methods: A total of 338 nucleosides analogue therapy naïve CHB patients initially treated with ETV were analyzed. The optimal cutoff points in each continuous variable were determined by receiver operating curve (ROC) analysis. The effects of FIB-4 index and APRI on HCC incidence were compared using time-dependent ROC analysis and factors linked to HCC incidence were also examined using univariate and multivariate analyses. Results: There were 215 males and 123 females with the median age of 52 years and the median baseline HBV-DNA level of 6.6 log copies/ml. The median follow-up interval after the initiation of ETV therapy was 4.99 years. During the follow-up period, 33 patients (9.8%) developed HCC. The 3-, 5- 7-year cumulative HCC incidence rates in all cases were 4.4%, 9.2% and 13.5%, respectively. In the multivariate analysis, FIB-4 index revealed to be an independent predictor associated with HCC incidence, while APRI was not. In the time-dependent ROC analyses for all cases and for all subgroups analyses stratified by viral status or cirrhosis status, all area under the ROCs in each time point (2-, 3-, 4-, 5-, 6-, and 7-year) of FIB-4 index were higher than those of APRI. Conclusion: FIB-4 index rather than APRI can be a useful predictor associated with HCC development for CHB patients undergoing ETV therapy. PMID:28243319

Infection with hepatitis viruses, FIB-4 index and risk of hepatocellular carcinoma in southern Italy: a population-based cohort study.

PubMed

Fusco, Mario; Piselli, Pierluca; Virdone, Saverio; Di Cicco, Pietro; Scognamiglio, Paola; De Paoli, Paolo; Ciullo, Valerio; Verdirosi, Diana; D'Orazio, Michele; Dal Maso, Luigino; Girardi, Enrico; Franceschi, Silvia; Serraino, Diego

2016-01-01

The incidence of hepatocellular carcinoma (HCC) and its association with hepatitis C (HCV) and hepatitis B virus (HBV) infections, FIB-4 index and liver enzymes was assessed in an area of the province of Naples covered by a population-based cancer registry. We conducted a cohort investigation on 4492 individuals previously enrolled in a population-based seroprevalent survey on HCV and HBV infections. The diagnosis of HCC was assessed through a record linkage with the cancer registry. Hepatic metabolic activity was measured through serum alanine transaminase, aspartate aminotransferase, gamma-glutamyl-transferase, and platelet. The FIB-4 index was used as a marker of fibrosis. We computed HCC incidence rates (IR) for 100,000 (10 5 ) person-years of observation, and multivariable hazard ratios (HR) with 95 % confidence intervals (CI) to assess risk factors for HCC. Twenty two cases of HCC were diagnosed during follow-up (IR = 63.3 cases/10 5 ). Significantly increased HCC risks were documented in individuals with higher than normal liver enzymes and low platelet count; in the 239 HCV RNA-positives (HR = 61.8, 95 % CI:13.3-286); and in the 95 HBsAg-positives (HR = 75.0) -as compared to uninfected individuals. The highest FIB-4 score was associated with a 17.6-fold increased HCC risk. An elevated FIB-4 index turned out to be an important predictor of HCC occurrence. Although the standard method to assess hepatic fibrosis in chronic hepatitis remains the histologic staging of liver biopsy specimen, the assessment of FIB-4 in HCV RNA-positive individuals may help in identifying the highest HCC-risk individuals who need anti-HCV treatment most urgently.

Comparison of FIB-4 index and aspartate aminotransferase to platelet ratio index on carcinogenesis in chronic hepatitis B treated with entecavir.

PubMed

Nishikawa, Hiroki; Nishijima, Norihiro; Enomoto, Hirayuki; Sakamoto, Azusa; Nasu, Akihiro; Komekado, Hideyuki; Nishimura, Takashi; Kita, Ryuichi; Kimura, Toru; Iijima, Hiroko; Nishiguchi, Shuhei; Osaki, Yukio

2017-01-01

We sought to compare the effects of FIB-4 index and aspartate aminotransferase to platelet ratio index (APRI) on hepatocellular carcinoma (HCC) incidence in chronic hepatitis B (CHB) patients undergoing entecavir (ETV) therapy. A total of 338 nucleosides analogue therapy naïve CHB patients initially treated with ETV were analyzed. The optimal cutoff points in each continuous variable were determined by receiver operating curve (ROC) analysis. The effects of FIB-4 index and APRI on HCC incidence were compared using time-dependent ROC analysis and factors linked to HCC incidence were also examined using univariate and multivariate analyses. There were 215 males and 123 females with the median age of 52 years and the median baseline HBV-DNA level of 6.6 log copies/ml. The median follow-up interval after the initiation of ETV therapy was 4.99 years. During the follow-up period, 33 patients (9.8%) developed HCC. The 3-, 5- 7-year cumulative HCC incidence rates in all cases were 4.4%, 9.2% and 13.5%, respectively. In the multivariate analysis, FIB-4 index revealed to be an independent predictor associated with HCC incidence, while APRI was not. In the time-dependent ROC analyses for all cases and for all subgroups analyses stratified by viral status or cirrhosis status, all area under the ROCs in each time point (2-, 3-, 4-, 5-, 6-, and 7-year) of FIB-4 index were higher than those of APRI. FIB-4 index rather than APRI can be a useful predictor associated with HCC development for CHB patients undergoing ETV therapy.

Liver stiffness measurement, better than APRI, Fibroindex, Fib-4, and NBI gastroscopy, predicts portal hypertension in patients with cirrhosis.

PubMed

Zhang, Wei; Wang, Liqiong; Wang, Lei; Li, Gang; Huang, Aoshuang; Yin, Ping; Yang, Zhenhua; Ling, Changquan; Wang, Lingtai

2015-03-01

Liver stiffness measurement (LSM) is frequently used as non-invasive alternative for liver fibrosis including cirrhosis, which can lead to portal hypertension. This study was conducted to evaluate the predictive value of LSM in cirrhosis-induced portal hypertension patients. Between July 2011 and December 2013, 153 participants were enrolled into a single-center, prospective, cross-sectional study. Each subject received both gastroscopy and LSM. Baseline biochemical, APRI, Fibroindex, and Fib-4 were also performed. LSM of cirrhosis patients with portal hypertension was significantly higher compared to those without portal hypertension (P < 0.05). A LSM ≥ 13.6 kPa had a sensitivity of 83.87 % and a specificity of 72.53 % with an accuracy of 77.1 for the prediction of portal hypertension, which are higher than those of APRI, Fib-4, and Fibroscan separately. A combination of Fibroscan combined with Fib-4 achieved a maximum AUC of 0.833 and accuracy of 77.8. Discriminant and internal validation analysis showed that Fibroscan plus APRI obtained a lower false negative rate compared to Fibroscan plus Fib-4 and Fibroscan plus Fibroindex (9.68, 17.74, and 11.29 %, respectively). A good relationship was found between LSM and NBI mean optical density both by linear and polynomial correlation analysis (r = 0.5533 and r = 0.7349, both P < 0.001). There was a trend toward a better performance of LSM for assessing portal hypertension compared with NBI gastroscopy mean optical density (P = 0.028 and P = 0.05, respectively). Better than APRI, Fibroindex, Fib-4, and NBI gastroscopy, LSM can predict portal hypertension in cirrhosis patients. A LSM of 13.6 kPa can be considered to be the predictive value for portal hypertension.

Effect of beach management policies on recreational water quality.

PubMed

Kelly, Elizabeth A; Feng, Zhixuan; Gidley, Maribeth L; Sinigalliano, Christopher D; Kumar, Naresh; Donahue, Allison G; Reniers, Adrianus J H M; Solo-Gabriele, Helena M

2018-04-15

When beach water monitoring programs identify poor water quality, the causes are frequently unknown. We hypothesize that management policies play an important role in the frequency of fecal indicator bacteria (FIB) exceedances (enterococci and fecal coliform) at recreational beaches. To test this hypothesis we implemented an innovative approach utilizing large amounts of monitoring data (n > 150,000 measurements per FIB) to determine associations between the frequency of contaminant exceedances and beach management practices. The large FIB database was augmented with results from a survey designed to assess management policies for 316 beaches throughout the state of Florida. The FIB and survey data were analyzed using t-tests, ANOVA, factor analysis, and linear regression. Results show that beach geomorphology (beach type) was highly associated with exceedance of regulatory standards. Low enterococci exceedances were associated with open coast beaches (n = 211) that have sparse human densities, no homeless populations, low densities of dogs and birds, bird management policies, low densities of seaweed, beach renourishment, charge access fees, employ lifeguards, without nearby marinas, and those that manage storm water. Factor analysis and a linear regression confirmed beach type as the predominant factor with secondary influences from grooming activities (including seaweed densities and beach renourishment) and beach access (including charging fees, employing lifeguards, and without nearby marinas). Our results were observable primarily because of the very large public FIB database available for analyses; similar approaches can be adopted at other beaches. The findings of this research have important policy implications because the selected beach management practices that were associated with low levels of FIB can be implemented in other parts of the US and around the world to improve recreational beach water quality. Copyright © 2018 Elsevier Ltd. All rights reserved.

FIB preparation of a NiO Wedge-Lamella and STEM X-ray microanalysis for the determination of the experimental k(O-Ni) Cliff-Lorimer coefficient.

PubMed

Armigliato, Aldo; Frabboni, Stefano; Gazzadi, Gian Carlo; Rosa, Rodolfo

2013-02-01

A method for the fabrication of a wedge-shaped thin NiO lamella by focused ion beam is reported. The starting sample is an oxidized bulk single crystalline, <100> oriented, Ni commercial standard. The lamella is employed for the determination, by analytical electron microscopy at 200 kV of the experimental k(O-Ni) Cliff-Lorimer (G. Cliff & G.W. Lorimer, J Microsc 103, 203-207, 1975) coefficient, according to the extrapolation method by Van Cappellen (E. Van Cappellen, Microsc Microstruct Microanal 1, 1-22, 1990). The result thus obtained is compared to the theoretical k(O-Ni) values either implemented into the commercial software for X-ray microanalysis quantification of the scanning transmission electron microscopy/energy dispersive spectrometry equipment or calculated by the Monte Carlo method. Significant differences among the three values are found. This confirms that for a reliable quantification of binary alloys containing light elements, the choice of the Cliff-Lorimer coefficients is crucial and experimental values are recommended.

Enhanced FIB-SEM systems for large-volume 3D imaging

PubMed Central

Xu, C Shan; Hayworth, Kenneth J; Lu, Zhiyuan; Grob, Patricia; Hassan, Ahmed M; García-Cerdán, José G; Niyogi, Krishna K; Nogales, Eva; Weinberg, Richard J; Hess, Harald F

2017-01-01

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 106 µm3. These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology. DOI: http://dx.doi.org/10.7554/eLife.25916.001 PMID:28500755

Scanning electron microscopical and cross-sectional analysis of extraterrestrial carbonaceous nanoglobules

NASA Astrophysics Data System (ADS)

Garvie, Laurence A. J.; Baumgardner, Grant; Buseck, Peter R.

2008-05-01

Carbonaceous nanoglobules are ubiquitous in carbonaceous chondrite (CC) meteorites. The Tagish Lake (C2) meteorite is particularly intriguing in containing an abundance of nanoglobules, with a wider range of forms and sizes than encountered in other CC meteorites. Previous studies by transmission electron microscopy (TEM) have provided a wealth of information on chemistry and structure. In this study low voltage scanning electron microscopy (SEM) was used to characterize the globule forms and external structures. The internal structure of the globules was investigated after sectioning by focused ion beam (FIB) milling. The FIB-SEM analysis shows that the globules range from solid to hollow. Some hollow globules show a central open core, with adjoining smaller cores. The FIB with an SEM is a valuable tool for the analysis of extraterrestrial materials, even of sub-micron-sized "soft" carbonaceous particles. The rapid site-specific cross-sectioning capabilities of the FIB allow the preservation of the internal morphology of the nanoglobules, with minimal damage or alteration of the unsectioned areas.

Enhanced FIB-SEM systems for large-volume 3D imaging

DOE PAGES

Xu, C. Shan; Hayworth, Kenneth J.; Lu, Zhiyuan; ...

2017-05-13

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 10 6 ?m 3 . These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processesmore » and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.« less

Diagnostic Accuracy of APRI, AAR, FIB-4, FI, King, Lok, Forns, and FibroIndex Scores in Predicting the Presence of Esophageal Varices in Liver Cirrhosis

PubMed Central

Deng, Han; Qi, Xingshun; Guo, Xiaozhong

2015-01-01

Abstract Aspartate aminotransferase-to-platelet ratio (APRI), aspartate aminotransferase-to-alanine aminotransferase ratio (AAR), FIB-4, FI, King, Lok, Forns, and FibroIndex scores may be simple and convenient noninvasive diagnostic tests, because they are based on the regular laboratory tests and demographic data. This study aimed to systematically evaluate their diagnostic accuracy for the prediction of varices in liver cirrhosis. All relevant papers were searched via PubMed, EMBASE, CNKI, and Wanfang databases. The area under the summary receiver operating characteristic curve (AUSROC), sensitivity, specificity, positive and negative likelihood ratio (PLR and NLR), and diagnostic odds ratio (DOR) were calculated. Overall, 12, 4, 5, 0, 0, 4, 3, and 1 paper was identified to explore the diagnostic accuracy of APRI, AAR, FIB-4, FI, King, Lok, Forns, and FibroIndex scores, respectively. The AUSROCs of APRI, AAR, FIB-4, Lok, and Forns scores for the prediction of varices were 0.6774, 0.7275, 0.7755, 0.7885, and 0.7517, respectively; and those for the prediction of large varices were 0.7278, 0.7448, 0.7095, 0.7264, and 0.6530, respectively. The diagnostic threshold effects of FIB-4 and Forns scores for the prediction of varices were statistically significant. The sensitivities/specificities/PLRs/NLRs/DORs of APRI, AAR, and Lok scores for the prediction of varices were 0.60/0.67/1.77/0.58/3.13, 0.64/0.63/1.97/0.54/4.18, and 0.74/0.68/2.34/0.40/5.76, respectively. The sensitivities/specificities/PLRs/NLRs/DORs of APRI, AAR, FIB-4, Lok, and Forns scores for the prediction of large varices were 0.65/0.66/2.15/0.47/4.97, 0.68/0.58/2.07/0.54/3.93, 0.62/0.64/2.02/0.56/3.57, 0.78/0.63/2.09/0.37/5.55, and 0.65/0.61/1.62/0.59/2.75, respectively. APRI, AAR, FIB-4, Lok, and Forns scores had low to moderate diagnostic accuracy in predicting the presence of varices in liver cirrhosis. PMID:26496312

Comparing Child-Pugh, MELD, and FIB-4 to Predict Clinical Outcomes in Hepatitis C Virus-Infected Persons: Results From ERCHIVES.

PubMed

Butt, Adeel A; Ren, Yanjie; Lo Re, Vincent; Taddei, Tamar H; Kaplan, David E

2017-07-01

Identifying hepatitis C virus (HCV)-positive persons at high risk of early complications can help prioritize treatment decisions. We conducted this study to compare Child-Turcotte-Pugh (CP), MELD, and FIB-4 scores for predicting clinical outcomes and to identify those at low risk of complications. Within electronically retrieved cohort of HCV-infected veterans, we identified HCV-positive persons and excluded those with human immunodeficiency virus (HIV), hepatitis B surface antigen (HBsAg), prevalent hepatic decompensation (HD), hepatocellular carcinoma (HCC), and those treated for HCV. We calculated incidence rates for HD, HCC, and all-cause mortality at 1, 3, and 5 years after HCV diagnosis. Using receiver operating characteristic (ROC) curves, we determined the optimal cut-off values for each score for these outcomes. Among 21 116 persons evaluated, 89.7% were CP Class-A, 79.9% had MELD<9, and 43.4% had FIB-4<1.45. AUROC for HD at 1, 3, and 5 years was higher for FIB-4 (0.84-0.86) compared with MELD (0.70-0.76) (P < .001). AUROC for HCC at 1, 3, and 5 years was 0.81-0.82 for FIB-4 but 0.61-0.68 for CP and MELD scores. (P < .001) AUROC for all-cause mortality at 3 and 5 years was 0.65-0.68. The optimal cut-off scores to identify persons at low risk of complications were as follows: CP <5; MELD <8; FIB-4 <3 for HD and HCC, and <2 for all-cause mortality, below which <1.5% developed HD and HCC and ≤2.5% died at 3 years. FIB-4 score is a better predictor of HD and HCC in HCV-positive persons. A score of <3 is associated with a low risk of HD and HCC 1 and 3 years after HCV diagnosis. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com

Allochthonous Addition of Meteoritic Organics to the Lunar Regolith

NASA Technical Reports Server (NTRS)

Thomas-Keprta, K. L.; Clemett, S.; Ross, D. K.; Le, L.; Rahman, Z.; McKay, D. S.; Gibson, E. K.; Gonzalez, C.

2013-01-01

Preparation of lunar samples 74220,861 was discussed in detail in [3, 4]. Our analysis sequence was as follows: optical microscopy, UV fluorescence imaging, -Raman, FESEM-EDX imaging and mapping, FETEMEDX imaging and mapping of a Focused Ion Beam (FIB) extracted section, and NanoSIMs analysis. We observed fluffytextured C-rich regions of interest (ROI) on three different volcanic glass beads. Each ROI was several m2 in size and fluoresced when exposed to UV. Using FESEM/EDX, the largest ROI measured 36 m and was located on an edge of a plateau located on the uppermost surface of the bead. The ROI was covered on one edge by a siliceous filament emanating from the plateau surface indicating it was attached to the bead while on the Moon. EDX mapping of the ROI shows it is composed primarily of heterogeneously distributed C. Embedded with the carbonaceous phase are localized concentrations of Si, Fe, Al and Ti indicating the presence of glass and/or minerals grains. -Raman showed strong D- and G-bands and their associated second order bands; intensity and location of these bands indicates the carbonaceous matter is structurally disorganized. A TEM thin section was extracted from the surface of a glass bead using FIB microscopy. High resolution TEM imaging and selected area electron diffraction demonstrate the carbonaceous layer to be amorphous; it lacked any long or short range order characteristic of micro- or nanocrystalline graphite. Additionally TEM imaging also revealed the presence of submicron mineral grains, typically < 50 nm in size, dispersed within the carbonaceous layer. NanoSIMs data will be presented and discussed at the meeting. Given the noted similarities between the carbonaceous matter present on 74220 glass beads and meteoritic kerogen, we suggest the allochthonous addition of meteoritic organics as the most probable source for the C-rich ROIs.

Multidimensional characterisation of biomechanical structures by combining Atomic Force Microscopy and Focused Ion Beam: A study of the rat whisker.

PubMed

Adineh, Vahid Reza; Liu, Boyin; Rajan, Ramesh; Yan, Wenyi; Fu, Jing

2015-07-01

Understanding the heterogeneity of biological structures, particularly at the micro/nano scale can offer insights valuable for multidisciplinary research in tissue engineering and biomimicry designs. Here we propose to combine nanocharacterisation tools, particularly Focused Ion Beam (FIB) and Atomic Force Microscopy (AFM) for three dimensional mapping of mechanical modulus and chemical signatures. The prototype platform is applied to image and investigate the fundamental mechanics of the rat face whiskers, a high-acuity sensor used to gain detailed information about the world. Grazing angle FIB milling was first applied to expose the interior cross section of the rat whisker sample, followed by a "lift-out" method to retrieve and position the target sample for further analyses. AFM force spectroscopy measurements revealed a non-uniform pattern of elastic modulus across the cross section, with a range from 0.8GPa to 13.5GPa. The highest elastic modulus was found at the outer cuticle region of the whisker, and values gradually decreased towards the interior cortex and medulla regions. Elemental mapping with EDS confirmed that the interior of the rat whisker is dominated by C, O, N, S, Cl and K, with a significant change of elemental distribution close to the exterior cuticle region. Based on these data, a novel comprehensive three dimensional (3D) elastic modulus model was constructed, and stress distributions under realistic conditions were investigated with Finite Element Analysis (FEA). The simulations could well account for the passive whisker deflections, with calculated resonant frequency as well as force-deflection for the whiskers being in good agreement with reported experimental data. Limitations and further applications are discussed for the proposed FIB/AFM approach, which holds good promise as a unique platform to gain insights on various heterogeneous biomaterials and biomechanical systems. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Distributions of Fecal Markers in Wastewater from Different Climatic Zones for Human Fecal Pollution Tracking in Australian Surface Waters

PubMed Central

Sidhu, J. P. S.; Smith, K.; Beale, D. J.; Gyawali, P.; Toze, S.

2015-01-01

Recreational and potable water supplies polluted with human wastewater can pose a direct health risk to humans. Therefore, sensitive detection of human fecal pollution in environmental waters is very important to water quality authorities around the globe. Microbial source tracking (MST) utilizes human fecal markers (HFMs) to detect human wastewater pollution in environmental waters. The concentrations of these markers in raw wastewater are considered important because it is likely that a marker whose concentration is high in wastewater will be more frequently detected in polluted waters. In this study, quantitative PCR (qPCR) assays were used to determine the concentrations of fecal indicator bacteria (FIB) Escherichia coli and Enterococcus spp., HFMs Bacteroides HF183, human adenoviruses (HAdVs), and polyomaviruses (HPyVs) in raw municipal wastewater influent from various climatic zones in Australia. E. coli mean concentrations in pooled human wastewater data sets (from various climatic zones) were the highest (3.2 × 106 gene copies per ml), followed by those of HF183 (8.0 × 105 gene copies per ml) and Enterococcus spp. (3.6 × 105 gene copies per ml). HAdV and HPyV concentrations were 2 to 3 orders of magnitude lower than those of FIB and HF183. Strong positive and negative correlations were observed between the FIB and HFM concentrations within and across wastewater treatment plants (WWTPs). To identify the most sensitive marker of human fecal pollution, environmental water samples were seeded with raw human wastewater. The results from the seeding experiments indicated that Bacteroides HF183 was more sensitive for detecting human fecal pollution than HAdVs and HPyVs. Since the HF183 marker can occasionally be present in nontarget animal fecal samples, it is recommended that HF183 along with a viral marker (HAdVs or HPyVs) be used for tracking human fecal pollution in Australian environmental waters. PMID:26682850

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

Faraby, H.; DiBattista, M.; Bandaru, P. R., E-mail: pbandaru@ucsd.edu

The electrical impedance (both the resistive and capacitive aspects) of focused ion beam (FIB) deposited SiO{sub 2} has been correlated to the specific composition of the ion beam, in Ga- and Xe-based FIB systems. The presence of electrically percolating Ga in concert with carbon (inevitably found as the product of the hydrocarbon precursor decomposition) has been isolated as a major cause for the observed decrease in the resistivity of the deposited SiO{sub 2}. Concomitant with the decreased resistivity, an increased capacitance and effective dielectric constant was observed. Our study would be useful to understand the constraints to the deposition ofmore » high quality insulator films through FIB based methodologies.« less

Characterization of BOR-60 Irradiated 14YWT-NFA1 Tubes

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

Saleh, Tarik A.; Maloy, Stuart Andrew; Aydogan, Eda

2017-02-15

Tubes of FCRD 14YWT-NFA1 Alloy were placed in the BOR-60 reactor and irradiated under a fast flux neutron environment to two conditions: 7 dpa at 360-370 °C and 6 dpa at 385-430 °C. Small sections of the tube were cut and sent to UC Berkeley for nanohardness testing and focused ion beam (FIB) milling of TEM specimens. FIB specimens were sent back to LANL for final FIB milling and TEM imaging. Hardness data and TEM images are presented in this report. This is the first fast reactor neutron irradiated information on the 14YWT-NFA1 alloy.

Improving Recreational Water Quality Assessments Through Novel Approaches to Quantifying Measurement Uncertainty

EPA Science Inventory

Bacteriological water quality in the Great Lakes is typically measured by the concentration of fecal indicator bacteria (FIB), and is reported via most probable number (MPN) or colony forming unit (CFU) values derived from algorithms relating \\raw data" in a FIB analysis procedu...

Three dimensional (3D) microstructure-based finite element modeling of Al-SiC nanolaminates using focused ion beam (FIB) tomography

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

Mayer, Carl R.

Al-SiC nanolaminate composites show promise as high performance coating materials due to their combination of strength and toughness. Although a significant amount of modeling effort has been focused on materials with an idealized flat nanostructure, experimentally these materials exhibit complex undulating layer geometries. This work utilizes FIB tomography to characterize this nanostructure in 3D and finite element modeling to determine the effect that this complex structure has on the mechanical behavior of these materials. A sufficiently large volume was characterized such that a 1 × 2 μm micropillar could be generated from the dataset and compared directly to experimental results.more » The mechanical response from this nanostructure was then compared to pillar models using simplified structures with perfectly flat layers, layers with sinusoidal waviness, and layers with arc segment waviness. The arc segment based layer geometry showed the best agreement with the experimentally determined structure, indicating it would be the most appropriate geometry for future modeling efforts. - Highlights: •FIB tomography was used to determine the structure of an Al-SiC nanolaminate in 3D. •FEM was used to compare the deformation of the nanostructure to experimental results. •Idealized structures from literature were compared to the FIB determined structure. •Arc segment based structures approximated the FIB determined structure most closely.« less

Current and future trends in fecal source tracking and deployment in the Lake Taihu Region of China

NASA Astrophysics Data System (ADS)

Hagedorn, Charles; Liang, Xinqiang

The emerging discipline of microbial and/or chemical source tracking (collectively termed fecal source tracking (FST)) is being used to identify origins of fecal contamination in polluted waters in many countries around the world. FST has developed rapidly because standard methods of measuring contamination in water by enumerating fecal indicator bacteria (FIB) such as fecal coliforms and enterococci do not identify the sources of the contamination. FST is an active area of research and development in both the academic and private sectors and includes: Developing and testing new microbial and chemical FST methods. Determining the geographic application and animal host ranges of existing and emerging FST techniques. Conducting experimental comparisons of FST techniques. Combining direct monitoring of human pathogens associated with waterborne outbreaks and zoonotic pathogens responsible for infections among people, wildlife, or domesticated animals with the use of FST techniques. Applying FST to watershed analysis and coastal environments. Designing appropriate statistical and probability analysis of FST data and developing models for mass loadings of host-specific fecal contamination. This paper includes a critical review of FST with emphasis on the extent to which methods have been tested (especially in comparison with other methods and/or with blind samples), which methods are applicable to different situations, their shortcomings, and their usefulness in predicting public health risk or pathogen occurrence. In addition, the paper addresses the broader question of whether FST and fecal indicator monitoring is the best approach to regulate water quality and protect human health. Many FST methods have only been tested against sewage or fecal samples or isolates in laboratory studies (proof of concept testing) and/or applied in field studies where the “real” answer is not known, so their comparative performance and accuracy cannot be assessed. For FST to be quantitative, stability of ratios between host-specific markers in the environment must be established. In addition, research is needed on the correlation between host-specific markers and pathogens, and survival of markers after waste treatments. As a result of the exclusive emphasis on FIB by regulatory agencies, monitoring and FST development has concentrated on FIB rather than the actual pathogens. A more rational approach to regulating water quality might be to use available epidemiological data to identify pathogens of concern in a particular water body, and then use targeted pathogen monitoring coupled with very specific FST approaches to control the pathogens. Baseline monitoring of FIB would be just one tool among many in this example.

Newly recognized hosts for uranium in the Hanford Site vadose zone

USGS Publications Warehouse

Stubbs, J.E.; Veblen, L.A.; Elbert, D.C.; Zachara, J.M.; Davis, J.A.; Veblen, D.R.

2009-01-01

Uranium contaminated sediments from the U.S. Department of Energy's Hanford Site have been investigated using electron microscopy. Six classes of solid hosts for uranium were identified. Preliminary sediment characterization was carried out using optical petrography, and electron microprobe analysis (EMPA) was used to locate materials that host uranium. All of the hosts are fine-grained and intergrown with other materials at spatial scales smaller than the analytical volume of the electron microprobe. A focused ion beam (FIB) was used to prepare electron-transparent specimens of each host for the transmission electron microscope (TEM). The hosts were identified as: (1) metatorbernite [Cu(UO2)2(PO4)2??8H2O]; (2) coatings on sediment clasts comprised mainly of phyllosilicates; (3) an amorphous zirconium (oxyhydr)oxide found in clast coatings; (4) amorphous and poorly crystalline materials that line voids within basalt lithic fragments; (5) amorphous palagonite surrounding fragments of basaltic glass; and (6) Fe- and Mn-oxides. These findings demonstrate the effectiveness of combining EMPA, FIB, and TEM to identify solid-phase contaminant hosts. Furthermore, they highlight the complexity of U geochemistry in the Hanford vadose zone, and illustrate the importance of microscopic transport in controlling the fate of contaminant metals in the environment. ?? 2008 Elsevier Ltd.

Chemical Imaging Analysis of Environmental Particles Using the Focused Ion Beam/Scanning Electron Microscopy Technique. Microanalysis Insights into Atmospheric Chemistry of Fly Ash

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

Chen, Haihan; Grassian, Vicki H.; Saraf, Laxmikant V.

2012-11-08

Airborne fly ash from coal combustion may represent a source of bioavailable iron (Fe) in the open ocean. However, few studies have been made focusing on Fe speciation and distribution in coal fly ash. In this study, chemical imaging of fly ash has been performed using a dual-beam FIB/SEM (focused ion beam/scanning electron microscope) system for a better understanding of how simulated atmospheric processing modify the morphology, chemical compositions and element distributions of individual particles. A novel approach has been applied for cross-sectioning of fly ash specimen with a FIB in order to explore element distribution within the interior ofmore » individual particles. Our results indicate that simulated atmospheric processing causes disintegration of aluminosilicate glass, a dominant material in fly ash particles. Aluminosilicate-phase Fe in the inner core of fly ash particles is more easily mobilized compared with oxide-phase Fe present as surface aggregates on fly ash spheres. Fe release behavior depends strongly on Fe speciation in aerosol particles. The approach for preparation of cross-sectioned specimen described here opens new opportunities for particle microanalysis, particular with respect to inorganic refractive materials like fly ash and mineral dust.« less

Structural analysis of reactionary dentin formed in response to polymicrobial invasion

PubMed Central

Charadram, Nattida; Austin, Christine; Trimby, Patrick; Simonian, Mary; Swain, Michael V.; Hunter, Neil

2013-01-01

In response to microbial invasion of dentin odontoblasts secrete an altered calcified matrix termed reactionary dentin (Rd). 3D reconstruction of focused-ion-beam scanning electron microscopy (FIB-SEM) image slices revealed helical tubular structures in Rd that contrasted with regular cylindrical tubules characteristic of dentin from healthy teeth and affected so-called physiological dentin (Pd) lying exterior to Rd. This helical structure in Rd provided effective constriction of tubule lumen diameter that formed a barrier to bacterial advance towards the dental pulp. SEM of resin cast preparations revealed altered extension of odontoblast processes through Rd. The distribution of key mineral elements was studied by combination of 3D reconstruction of focused-ion-beam based X-ray microanalysis (FIB-EDS), laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). There was a marked redistribution of calcium and phosphorous in Rd together with an increase of diffusely deposited magnesium compatible with the mineral deposition phase of synthesis of this altered matrix. Changes in tubule structure and mineral content characteristic of Rd are consistent with reduced hardness and lower elastic modulus reported for this matrix. Findings provide insight into the unique structure of Rd synthesised as a primary response to infection. PMID:23261402

RAPIDLY-MEASURED INDICATORS OF RECREATIONAL WATER QUALITY ARE PREDICTIVE OF SWIMMING-ASSOCIATED GASTROINTESTINAL ILLNESS

EPA Science Inventory

Fecal indicator bacteria (FIB) are used to monitor recreational water quality worldwide. Current methods of measuring FIB require at least 24-hours for growth of bacterial colonies. We conducted studies at four Great Lake beaches to examine the relationship between novel and fas...

A FASTER METHOD OF MEASURING RECREATIONAL WATER QUALITY FOR BETTER PROTECTION OF SWIMMER'S HEALTH

EPA Science Inventory

Introduction

Fecal indicator bacteria (FIB) are used to monitor recreational water quality worldwide. Current methods of measuring FIB require at least 24-hours for visible bacterial colonies to grow. We previously reported that a faster method (< 2 hours) of measuring FI...

QPCR Determined Fecal Indicator Bacterial Densities in Marine Waters from Two Recreational Beaches

EPA Science Inventory

The use of real-time qPCR to determine fecal indicator bacteria (FIB) densities is currently being investigated by the U.S. EPA. The present recreational water quality guidelines, based on culturable FIB, prevent same day determinations of water quality whereas results from the ...

Focussed Ion Beam Milling and Scanning Electron Microscopy of Brain Tissue

PubMed Central

Knott, Graham; Rosset, Stéphanie; Cantoni, Marco

2011-01-01

This protocol describes how biological samples, like brain tissue, can be imaged in three dimensions using the focussed ion beam/scanning electron microscope (FIB/SEM). The samples are fixed with aldehydes, heavy metal stained using osmium tetroxide and uranyl acetate. They are then dehydrated with alcohol and infiltrated with resin, which is then hardened. Using a light microscope and ultramicrotome with glass knives, a small block containing the region interest close to the surface is made. The block is then placed inside the FIB/SEM, and the ion beam used to roughly mill a vertical face along one side of the block, close to this region. Using backscattered electrons to image the underlying structures, a smaller face is then milled with a finer ion beam and the surface scrutinised more closely to determine the exact area of the face to be imaged and milled. The parameters of the microscope are then set so that the face is repeatedly milled and imaged so that serial images are collected through a volume of the block. The image stack will typically contain isotropic voxels with dimenions as small a 4 nm in each direction. This image quality in any imaging plane enables the user to analyse cell ultrastructure at any viewing angle within the image stack. PMID:21775953

Solute removal capacity of high cut-off membrane plasma separators.

PubMed

Ohkubo, Atsushi; Kurashima, Naoki; Nakamura, Ayako; Miyamoto, Satoko; Iimori, Soichiro; Rai, Tatemitsu

2013-10-01

In vitro blood filtration was performed by a closed circuit using high cut-off membrane plasma separators, EVACURE EC-2A10 (EC-2A) and EVACURE EC-4A10 (EC-4A). Samples were obtained from sampling sites before the plasma separator, after each plasma separator, and from the ultrafiltrate of each separator. The sieving coefficient (S.C.) of total protein (TP), albumin (Alb), IgG, interleukin-6 (IL-6), interleukin-8 (IL-8), tumor necrosis factor-α (TNF-α), fibrinogen (Fib), antithrombin III (AT-III), and coagulation factor XIII (FXIII) were calculated. The S.C. of each solute using EC-2A and EC-A4 were as follows; TP: 0.25 and 0.56, Alb: 0.32 and 0.73, IgG: 0.16 and 0.50, IL-6:0.73 and 0.95, IL-8:0.85 and 0.82, TNF-α: 1.07 and 0.99, Fib: 0 and 0, FXIII: 0.07 and 0.17, respectively. When compared with the conventional type of membrane plasma separators, EVACURE could efficiently remove cytokines while retaining coagulation factors such as fibrinogen. Moreover, EC-2A prevented protein loss, whereas EC-4A could remove approximately 50% of IgG. © 2013 The Authors. Therapeutic Apheresis and Dialysis © 2013 International Society for Apheresis.

Non-Equilibrium Effects on the Hidden Order of Microstructured URu2Si2

NASA Astrophysics Data System (ADS)

Winter, Laurel E.; Moll, Philip J. W.; Ramshaw, B. J.; Shekhter, Arkady; Harrison, N.; Bauer, Eric D.; McDonald, Ross D.

Despite extensive studies on the heavy-fermion URu2Si2, the order parameter associated with the hidden order state has yet to be established. It is known, however that the hidden order can be suppressed with pressure and high magnetic fields, which results in the development of antiferromagnetism, and the realization of a polarized state respectively. Focused Ion Beam lithography (FIB) of URu2Si2 has enabled high magnetic field observation of quantum oscillations in the resistance, indicating the preservation of sample quality to micron scale structures. These recent advances in FIB lithography have enabled the application of unprecedented electric fields while minimizing the effects of Joule heating in highly conductive metals at cryogenic temperatures. To this end, we have been able to create the necessary sample geometry to study the effect of an electric field upon hidden order in magnetic fields up to 15 T. Preliminary results suggest that above a characteristic threshold electric field, hidden order is suppressed revealing a state with similar magnetoresistive properties to the Kondo lattice in the absence of hidden order. Work supported by US Dept. of Energy through LANL/LDRD Program and G.T. Seaborg Institute, as well as NSF DMR-1157490 and the State of Florida.

Quantification of pathogens and markers of fecal contamination during storm events along popular surfing beaches in San Diego, California.

PubMed

Steele, Joshua A; Blackwood, A Denene; Griffith, John F; Noble, Rachel T; Schiff, Kenneth C

2018-06-01

Along southern California beaches, the concentrations of fecal indicator bacteria (FIB) used to quantify the potential presence of fecal contamination in coastal recreational waters have been previously documented to be higher during wet weather conditions (typically winter or spring) than those observed during summer dry weather conditions. FIB are used for management of recreational waters because measurement of the bacterial and viral pathogens that are the potential causes of illness in beachgoers exposed to stormwater can be expensive, time-consuming, and technically difficult. Here, we use droplet digital Polymerase Chain Reaction (digital PCR) and digital reverse transcriptase PCR (digital RT-PCR) assays for direct quantification of pathogenic viruses, pathogenic bacteria, and source-specific markers of fecal contamination in the stormwater discharges. We applied these assays across multiple storm events from two different watersheds that discharge to popular surfing beaches in San Diego, CA. Stormwater discharges had higher FIB concentrations as compared to proximal beaches, often by ten-fold or more during wet weather. Multiple lines of evidence indicated that the stormwater discharges contained human fecal contamination, despite the presence of separate storm sewer and sanitary sewer systems in both watersheds. Human fecal source markers (up to 100% of samples, 20-12440 HF183 copies per 100 ml) and human norovirus (up to 96% of samples, 25-495 NoV copies per 100 ml) were routinely detected in stormwater discharge samples. Potential bacterial pathogens were also detected and quantified: Campylobacter spp. (up to 100% of samples, 16-504 gene copies per 100 ml) and Salmonella (up to 25% of samples, 6-86 gene copies per 100 ml). Other viral human pathogens were also measured, but occurred at generally lower concentrations: adenovirus (detected in up to 22% of samples, 14-41 AdV copies per 100 ml); no enterovirus was detected in any stormwater discharge sample. Higher concentrations of avian source markers were noted in the stormwater discharge located immediately downstream of a large bird sanctuary along with increased Campylobacter concentrations and notably different Campylobacter species composition than the watershed that had no bird sanctuary. This study is one of the few to directly measure an array of important bacterial and viral pathogens in stormwater discharges to recreational beaches, and provides context for stormwater-based management of beaches during high risk wet-weather periods. Furthermore, the combination of culture-based and digital PCR-derived data is demonstrated to be valuable for assessing hydrographic relationships, considering delivery mechanisms, and providing foundational exposure information for risk assessment. Copyright © 2018 Elsevier Ltd. All rights reserved.

The relationship between land management, fecal indicator bacteria, and the occurrence of Campylobacter and Listeria spp. in water and sediments during synoptic sampling in the S. Fork Broad River Watershed, N.E. Georgia, U.S.A

NASA Astrophysics Data System (ADS)

Bradshaw, J. K.; Molina, M.; Sidle, R. C.; Sullivan, K.; Oakley, B.; Berrang, M.; Meinersmann, R.

2013-12-01

Fecal indicator bacteria (FIB) and pathogens stored in the bed sediments of streams and rivers may be mobilized into the water column affecting overall water quality. Furthermore, land management may play an important role in the concentrations of FIB and the occurrence of pathogens in stream water and sediments. The purpose of this study was to determine the relationship between FIB and pathogens in stream water and sediment based on three land management-affected categories: agricultural, forest, and waters receiving treated municipal wastewater. Two synoptic sampling events were conducted under baseflow conditions (<0.64 cm of rain within 24h) between October-November, 2012 and May-June, 2013. Counts of the E. coli and E. faecalis and occurrences of the enteric pathogens Campylobacter and Listeria spp. were measured in stream water and sediment samples collected at 15 locations (six agricultural (AG); six forested (FORS); and three receiving discharge from water pollution control plants (WPCP)) in the S. Fork Broad River watershed located in northeast Georgia, USA. Mean E. coli and E. faecalis concentrations were highest in the AG stream water samples (3.08 log MPN 100 mL -1 for E. coli and 3.07 log CFU 100 mL -1 for E. faecalis ) and lowest in the FORS water samples for E. coli (2.37 log MPN 100 mL -1 ) and WPCP water samples for E. faecalis (2.53 log CFU 100 mL -1 ). E. coli concentrations (2.74 log MPN 100 mL -1 ) in the WPCP streams were intermediate. Similar to water samples, E. coli concentrations were highest in the AG sediments (4.31 log MPN g -1 ), intermediate in the WPCP sediments (4.06 log MPN g -1 ), and lowest in the FORS sediments (3.46 log MPN g -1 ). In contrast to E. coli, E. faecalis concentrations were lower (1.10 to 1.31 log CFU g -1 ) and relatively more constant than E. coli in sediments over the three land management categories. Campylobacter was detected in 27% of the water samples and 8% of the sediment samples. The highest occurrence of Campylobacter detection was in the AG streams (15% of the water samples; 5% of the sediment samples). Listeria was detected in 76% of the water samples and 65% of the sediment samples. The FORS and AG streams had the highest occurrence of Listeria in water and sediment (32% and 29% of the water samples, respectively; 24% and 29% of sediment samples, respectively) suggesting Listeria is fairly ubiquitous in these streams. Based on the high concentrations of E. faecalis in water and E. coli in water and sediment, and higher frequency of Campylobacter detection in the AG streams, this study indicates that E. coli and Campylobacter may occur in high concentrations in stream sediments in land management areas where fecal material is deposited directly by livestock into the stream or adjacent land in large doses.

Exploring the interior of cuticles and compressions of fossil plants by FIB-SEM milling and image microscopy.

PubMed

Sender, L M; Escapa, I; Benedetti, A; Cúneo, R; Diez, J B

2018-01-01

We present the first study of cuticles and compressions of fossil leaves by Focused Ion Beam Scanning Electron Microscopy (FIB-SEM). Cavities preserved inside fossil leaf compressions corresponding to substomatal chambers have been observed for the first time and several new features were identified in the cross-section cuts. These results open a new way in the investigation of the three-dimensional structures of both micro- and nanostructural features of fossil plants. Moreover, the application of the FIB-SEM technique to both fossils and extant plant remains represent a new source of taxonomical, palaeoenvironmental and palaeoclimatic information. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Stabilization of the Propagation Delay in Fiber Optics in a Frequency Distribution Link Using Electronic Delay Lines: First Measurement Results

DTIC Science & Technology

2010-11-01

fluctuations may be approximated using eq. 1: LAS g FIB g FIB g FIB n c L T TL L c Ln T T n c L              , (1) where FIBT is...the temperature change of the fiber, LAS  is the shift of the laser wavelength, gn is the group refractive index, L is the length of the fiber...transfer,” Metrologia , 46, 305-314. [6] K. T. V. Grattan and B. T. Meggitt, 1999, Optical Fiber Sensor Technology, Vol. 3 (Kluwer Academic Publishers

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

Yashchuk, Valeriy V; Conley, Raymond; Anderson, Erik H.

We discuss the results of SEM and TEM measurements with the BPRML test samples fabricated from a BPRML (WSi2/Si with fundamental layer thickness of 3 nm) with a Dual Beam FIB (focused ion beam)/SEM technique. In particular, we demonstrate that significant information about the metrological reliability of the TEM measurements can be extracted even when the fundamental frequency of the BPRML sample is smaller than the Nyquist frequency of the measurements. The measurements demonstrate a number of problems related to the interpretation of the SEM and TEM data. Note that similar BPRML test samples can be used to characterize x-raymore » microscopes. Corresponding work with x-ray microscopes is in progress.« less

Advanced Characterization of Rare Earth Elements in Coal Utilization Byproducts

NASA Astrophysics Data System (ADS)

Verba, C.; Scott, M.; Dieterich, M.; Poston, J.; Collins, K.

2016-12-01

Rare earth elements (REE) in various forms (e.g., crystalline mineral phases; adsorbed/absorbed state on and into organic macerals, neoformed glass from flyash or bottom ash) from domestic feedstocks such as coal deposits to coal utilization byproducts (CUB) have the potential to reduce foreign REE dependence and increase domestic resource security. Characterization is critical for understanding environmental risks related to their fate and transport as well as determining the most practical and economical techniques for concentrating the REE and converting them into chemical stocks for manufacturing. Several complementary electron microscopy (SEM-EDS, EPMA-WDS, FIB-SEM, cathodoluminescence, and XRD) and post image processing techniques were used to understand REE transition from coal to CUB. Sites of interest were identified and imaged and respective elemental x-ray maps acquired and montaged. Pixel classification of SEM imagers was completed using image analysis techniques to quantify the distribution of REE associated features. Quantitative elemental analysis of phases were completed using EMPA-WDS followed by FIB-SEM. The FIB-SEM results were reconstructed into 3D volumes and features of interest (e.g. monazite) were analyzed to determine the structure and volumetric estimation of REEs and thus predict detrital REE phases to ICP-MS results. Trace minerals were identified as pyrite, zircon, REE-phosphates' (monazite, xenotime), and barite within the coal tailings. In CUB, amorphous aluminosilicates, iron oxide cenospheres, and calcium oxides were present; monazite appear to be unaltered and unaffected by the combustion process in these samples. Thermal decomposition may have occurred due to presence of detrital zircon and xenotime and subsequent thin Ca-oxide coating enriched in trace REEs.

E. coli release from streambed to water column during base flow periods: a modeling study

USDA-ARS?s Scientific Manuscript database

Microbial quality of stream water is important for recreation, irrigation, and other uses. It is usually evaluated by concentrations of fecal indicator bacteria (FIB) such as E. coli. Streambed sediments have been shown to harbor large FIB populations that could be released into the water column dur...

Differential Decay of Cattle-associated Fecal Indicator Bacteria and Microbial Source Tracking Markers in Fresh and Marine Water

EPA Science Inventory

Background: Fecal indicator bacteria (FIB) have a long history of use in the assessment of the microbial quality of recreational waters. However, quantification of FIB provides no information about the pollution source(s) and relatively little is known about their fate in the amb...

Lack of direct effects of agrochemicals on zoonotic pathogens and fecal indicator bacteria.

PubMed

Staley, Zachery R; Senkbeil, Jacob K; Rohr, Jason R; Harwood, Valerie J

2012-11-01

Agrochemicals, fecal indicator bacteria (FIB), and pathogens frequently contaminate water simultaneously. No significant direct effects of fertilizer, atrazine, malathion, and chlorothalonil on the survival of Escherichia coli, Enterococcus faecalis, Salmonella enterica, human polyomaviruses, and adenovirus were detected, supporting the assertion that previously observed effects of agrochemicals on FIB were indirect.

Labyrinths, columns and cavities: new internal features of pollen grain walls in the Acanthaceae detected by FIB-SEM.

PubMed

House, Alisoun; Balkwill, Kevin

2016-03-01

External pollen grain morphology has been widely used in the taxonomy and systematics of flowering plants, especially the Acanthaceae which are noted for pollen diversity. However internal pollen wall features have received far less attention due to the difficulty of examining the wall structure. Advancing technology in the field of microscopy has made it possible, with the use of a focused ion beam-scanning electron microscope (FIB-SEM), to view the structure of pollen grain walls in far greater detail and in three dimensions. In this study the wall structures of 13 species from the Acanthaceae were investigated for features of potential systematic relevance. FIB-SEM was applied to obtain precise cross sections of pollen grains at selected positions for examining the wall ultrastructure. Exploratory studies of the exine have thus far identified five basic structural types. The investigations also show that similar external pollen wall features may have a distinctly different internal structure. FIB-SEM studies have revealed diverse internal pollen wall features which may now be investigated for their systematic and functional significance.

A Genetic Cascade of let-7-ncl-1-fib-1 Modulates Nucleolar Size and rRNA Pool in Caenorhabditis elegans

PubMed Central

Chiou, Pey-Tsyr; Chen, Po-Hsiang; Lee, Ching-Ming; Chu, Yu-De; Yu, Hsiang; Hsiung, Kuei-Ching; Tsai, Yi-Tzang; Lee, Chi-Chang; Chang, Yu-Sun; Chan, Shih-Peng; Tan, Bertrand Chin-Ming; Lo, Szecheng J.

2015-01-01

Ribosome biogenesis takes place in the nucleolus, the size of which is often coordinated with cell growth and development. However, how metazoans control nucleolar size remains largely unknown. Caenorhabditis elegans provides a good model to address this question owing to distinct tissue distribution of nucleolar sizes and a mutant, ncl-1, which exhibits larger nucleoli than wild-type worms. Here, through a series of loss-of-function analyses, we report that the nucleolar size is regulated by a circuitry composed of microRNA let-7, translation repressor NCL-1, and a major nucleolar pre-rRNA processing protein FIB-1/fibrillarin. In cooperation with RNA binding proteins PUF and NOS, NCL-1 suppressed the translation of FIB-1/fibrillarin, while let-7 targeted the 3’UTR of ncl-1 and inhibited its expression. Consequently, the abundance of FIB-1 is tightly controlled and correlated with the nucleolar size. Together, our findings highlight a novel genetic cascade by which post-transcriptional regulators interplay in developmental control of nucleolar size and function. PMID:26492166

Improving water quality through California's Clean Beach Initiative: an assessment of 17 projects.

PubMed

Dorsey, John H

2010-07-01

California's Clean Beach Initiative (CBI) funds projects to reduce loads of fecal indicator bacteria (FIB) impacting beaches, thus providing an opportunity to judge the effectiveness of various CBI water pollution control strategies. Seventeen initial projects were selected for assessment to determine their effectiveness on reducing FIB in the receiving waters along beaches nearest to the projects. Control strategies included low-flow diversions, sterilization facilities, sewer improvements, pier best management practices (BMPs), vegetative swales, and enclosed beach BMPs. Assessments were based on statistical changes in pre- and postproject mean densities of FIB at shoreline monitoring stations targeted by the projects. Most low-flow diversions and the wetland swale project were effective in removing all contaminated runoff from beaches. UV sterilization was effective when coupled with pretreatment filtration and where effluent was released within a few hundred meters of the beach to avoid FIB regrowth. Other BMPs were less effective because they treated only a portion of contaminant sources impacting their target beach. These findings should be useful to other coastal states and agencies faced with similar pollution control problems.

Bacteriophages as indicators of faecal pollution and enteric virus removal.

PubMed

McMinn, B R; Ashbolt, N J; Korajkic, A

2017-07-01

Bacteriophages are an attractive alternative to faecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport, due to their closer morphological and biological properties. Based on a review of published data, we summarize densities of coliphages (F+ and somatic), Bacteroides spp. and enterococci bacteriophages (phages) in individual human waste, raw wastewater, ambient fresh and marine waters and removal through wastewater treatment processes utilizing traditional treatments. We also provide comparisons with FIB and enteric viruses whenever possible. Lastly, we examine fate and transport characteristics in the aquatic environment and provide an overview of the environmental factors affecting their survival. In summary, concentrations of bacteriophages in various sources were consistently lower than FIB, but more reflective of infectious enteric virus levels. Overall, our investigation indicates that bacteriophages may be adequate viral surrogates, especially in built systems, such as wastewater treatment plants. Bacteriophage are alternative fecal indicators that may be better surrogates for viral pathogens than fecal indicator bacteria (FIB). This report offers a summary of the existing literature concerning the utility of bacteriophage as indicators of viral presence (fecal sources and surface waters) and persistence (in built infrastructure and aquatic environments). Our findings indicate that bacteriophage levels in all matrices examined are consistently lower than FIB, but similar to viral pathogens. Furthermore, in built infrastructure (e.g. wastewater treatment systems) bacteriophage closely mimic viral pathogen persistence suggesting they may be adequate sentinels of enteric virus removal. © 2017 The Society for Applied Microbiology.

Analysis of the Gull Fecal Microbial Community Reveals the Dominance of Catellicoccus marimammalium in Relation to Culturable Enterococci

PubMed Central

Koskey, Amber M.; Fisher, Jenny C.; Traudt, Mary F.; Newton, Ryan J.

2014-01-01

Gulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such as Escherichia coli and enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB. Enterococcaceae and Enterobacteriaceae were the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealed Catellicoccus marimammalium as the most numerous taxon among all samples. The identification of bacteria from gull fecal pellets cultured on membrane-Enterococcus indoxyl-β-d-glucoside (mEI) plates showed that the dominant sequences recovered in our sequence libraries did not represent organisms culturable on mEI. Based on 16S rRNA gene sequencing of gull fecal isolates cultured on mEI plates, 98.8% were identified as Enterococcus spp., 1.2% were identified as Streptococcus spp., and none were identified as C. marimammalium. Illumina deep sequencing indicated that gull fecal samples harbor significantly higher proportions of C. marimammalium 16S rRNA gene sequences (>50-fold) relative to typical mEI culturable Enterococcus spp. C. marimammalium therefore can be confidently utilized as a genetic marker to identify gull fecal pollution in the beach environment. PMID:24242244

Micro-fabric damages in Boom Clay inferred from cryo-BIB-SEM experiment: recent results

NASA Astrophysics Data System (ADS)

Desbois, Guillaume; Schmatz, Joyce; Klaver, Jop; Urai, Janos L.

2017-04-01

The Boom Clay is considered as a potential host rock in Belgium for nuclear waste disposal in a deep geological formation. One of the keys to understand the long-term performance of such a host rock is the fundamental understanding of coupling between microstructural evolution, poromechanical behaviour and the state of hydration of the system. At in situ conditions, Boom Clay is a nearly water-saturated (>94%) clay-rich geomaterial. Subsequently, for measurement of mechanical and transport properties in laboratory, cores of Boom Clay are vacuum-packed in Al-coated-poly-ethylene barrier foil to be best preserved at original hydric state. Because clay microstructures are very sensitive to dehydration, the validity of investigations done on such preserved or/and dried samples is often questionable. Desbois et al. (2009, 2013, 2014) showed the possibility to image fluid-filled porosity in Boom Clay, by using the FIB-cryo-SEM (FIB: Focussed Ion Beam) and FIB-cryo-SEM (BIB: Broad Ion Beam) techniques. However, surprisingly in Desbois et al. (2014), BIB-cryo-SEM experiments on Boom Clay, shown that the majority of the pores were fluid-free, contrasting with result in Desbois et al. (2009). In Desbois et al. (2014), several reasons were discussed to explain such discrepancies. The likely ones are the sealing efficiency of the Al-barrier foil at long term and the volume expansion due to the release of in-situ stress after core extraction, contributing both to dehydration and microfabric damage. This contribution presents the newest results based on cryo-BIB-SEM. Small pieces (30 mm3) of Boom Clay were preserved in liquid nitrogen after the core extraction at the MOL/Dessel Underground Research Laboratory in Belgium. A maximum of ten minutes time span was achieved between opening the core, the sub-sample extraction and the quenching of sub-samples in liquid nitrogen. First results show that all pores visible at cryo-SEM resolution are water saturated. However, water-filled micro-cracks are also present and they are interpreted to result from the releasing of in-situ stress after the core extraction. Moreover, the comparison of the clay micro-fabrics in the same preserved and dried sample suggests collapsing of the clay aggregates' pores in dried sample. These newest results are still preliminary and they need to be analysed in more details. However, if they are confirmed they may be important input to discuss about the validity of measurement of mechanical and transport properties done in laboratory. Desbois G., Urai J.L. and Kukla P.A. (2009). Morphology of the pore space in claystones - evidence from BIB/FIB ion beam sectioning and cryo-SEM observations. E-Earth, 4 :15-22. Desbois G., J.L. Urai, F. Pérez-Willard, Z. Radi, S. van Offern, I. Burkart, P.A. Kukla, U. Wollenberg (2013). Argon broad ion beam tomography in a cryogenic scanning electron microscope: a novel tool for the investigation of representative microstructures in sedimentary rocks containing pore fluid. Journal of Microscopy, 249(3): 215-235. Desbois G., Urai J.L., Hemes S., Brassinnes S., De Craen M., Sillen X. (2014). Nanometer-scale pore fluid distribution and drying damage in preserved clay cores from Belgian clay formations inferred by BIB-cryo-SEM. Engineering Geology, 170:117-131.

Serial combination of non-invasive tools improves the diagnostic accuracy of severe liver fibrosis in patients with NAFLD.

PubMed

Petta, S; Wong, V W-S; Cammà, C; Hiriart, J-B; Wong, G L-H; Vergniol, J; Chan, A W-H; Di Marco, V; Merrouche, W; Chan, H L-Y; Marra, F; Le-Bail, B; Arena, U; Craxì, A; de Ledinghen, V

2017-09-01

The accuracy of available non-invasive tools for staging severe fibrosis in patients with nonalcoholic fatty liver disease (NAFLD) is still limited. To assess the diagnostic performance of paired or serial combination of non-invasive tools in NAFLD patients. We analysed data from 741 patients with a histological diagnosis of NAFLD. The GGT/PLT, APRI, AST/ALT, BARD, FIB-4, and NAFLD Fibrosis Score (NFS) scores were calculated according to published algorithms. Liver stiffness measurement (LSM) was performed by FibroScan. LSM, NFS and FIB-4 were the best non-invasive tools for staging F3-F4 fibrosis (AUC 0.863, 0.774, and 0.792, respectively), with LSM having the highest sensitivity (90%), and the highest NPV (94%), and NFS and FIB-4 the highest specificity (97% and 93%, respectively), and the highest PPV (73% and 79%, respectively). The paired combination of LSM or NFS with FIB-4 strongly reduced the likelihood of wrongly classified patients (ranging from 2.7% to 2.6%), at the price of a high uncertainty area (ranging from 54.1% to 58.2%), and of a low overall accuracy (ranging from 43% to 39.1%). The serial combination with the second test used in patients in the grey area of the first test and in those with high LSM values (>9.6 KPa) or low NFS or FIB-4 values (<-1.455 and <1.30, respectively) overall increased the diagnostic performance generating an accuracy ranging from 69.8% to 70.1%, an uncertainty area ranging from 18.9% to 20.4% and a rate of wrong classification ranging from 9.2% to 11.3%. The serial combination of LSM with FIB-4/NFS has a good diagnostic accuracy for the non-invasive diagnosis of severe fibrosis in NAFLD. © 2017 John Wiley & Sons Ltd.

APRI, the FIB-4 score, and Forn's index have noninvasive diagnostic value for liver fibrosis in patients with chronic hepatitis B.

PubMed

Ucar, Fatma; Sezer, Sevilay; Ginis, Zeynep; Ozturk, Gulfer; Albayrak, Aynur; Basar, Omer; Ekiz, Fuat; Coban, Sahin; Yuksel, Osman; Armutcu, Ferah; Akbal, Erdem

2013-09-01

The aim of this study was to evaluate the potential use of serum transforming growth factor-β1 (TGF-β1), tissue inhibitor of metalloproteinase-1 (TIMP-1), fetuin-A, and fibroblast growth factor 21 (FGF21) in the detection of liver fibrosis in patients with chronic hepatitis B (CHB). The value of the noninvasive fibrosis models - that is, the aspartate aminotransferase to platelet ratio index (APRI), the fibrosis index based on the four factors (FIB-4) score, and Forn's index - was also examined. CHB patients who underwent liver biopsy for the evaluation of fibrosis were included in the study. A total of 73 patients were divided into two groups according to their METAVIR scores (F0-1, no/minimal fibrosis; F2-4, significant fibrosis). Serum levels of TGF-β1, TIMP-1, fetuin-A, and FGF21 were measured besides APRI, FIB-4, and Forn's scores. The area under the receiver operating characteristic curve was measured for each parameter, followed by calculation of sensitivity, specificity, and positive and negative predictive values. APRI, FIB-4, and Forn's index scores were significantly higher in patients with significant fibrosis (P<0.05). There was no difference between no/minimal fibrosis and significant fibrosis groups in terms of serum levels of TGFβ-1, TIMP-1, fetuin-A, and FGF21 (P>0.05). The areas under the receiver operating characteristic curve for TGF-β1, TIMP-1, fetuin-A, FGF21, APRI, FIB-4, and Forn's index were 0.445, 0.483, 0.436, 0.585, 0.662, 0.687, and 0.680, respectively. Our results suggest that serum TGF-β1, TIMP-1, fetuin-A, and FGF21 are not useful for the assessment of the extent of liver fibrosis in CHB in this patient group. However, APRI, FIB-4, and Forn's index have a better diagnostic value in patients with significant fibrosis than in those with no/minimal fibrosis.

Progression of Liver Fibrosis in HIV/HCV Co-Infection: A Comparison between Non-Invasive Assessment Methods and Liver Biopsy

PubMed Central

Schmid, Patrick; Bregenzer, Andrea; Huber, Milo; Rauch, Andri; Jochum, Wolfram; Müllhaupt, Beat; Vernazza, Pietro; Opravil, Milos; Weber, Rainer

2015-01-01

Objectives To evaluate the diagnostic performance of seven non-invasive tests (NITs) of liver fibrosis and to assess fibrosis progression over time in HIV/HCV co-infected patients. Methods Transient elastography (TE) and six blood tests were compared to histopathological fibrosis stage (METAVIR). Participants were followed over three years with NITs at yearly intervals. Results Area under the receiver operating characteristic curve (AUROC) for significant fibrosis (> = F2) in 105 participants was highest for TE (0.85), followed by FIB-4 (0.77), ELF-Test (0.77), APRI (0.76), Fibrotest (0.75), hyaluronic acid (0.70), and Hepascore (0.68). AUROC for cirrhosis (F4) was 0.97 for TE followed by FIB-4 (0.91), APRI (0.89), Fibrotest (0.84), Hepascore (0.82), ELF-Test (0.82), and hyaluronic acid (0.79). A three year follow-up was completed by 87 participants, all on antiretroviral therapy and in 20 patients who completed HCV treatment (9 with sustained virologic response). TE, APRI and Fibrotest did not significantly change during follow-up. There was weak evidence for an increase of FIB-4 (mean increase: 0.22, p = 0.07). 42 participants had a second liver biopsy: Among 38 participants with F0-F3 at baseline, 10 were progessors (1-stage increase in fibrosis, 8 participants; 2-stage, 1; 3-stage, 1). Among progressors, mean increase in TE was 3.35 kPa, in APRI 0.36, and in FIB-4 0.75. Fibrotest results did not change over 3 years. Conclusion TE was the best NIT for liver fibrosis staging in HIV/HCV co-infected patients. APRI-Score, FIB-4 Index, Fibrotest, and ELF-Test were less reliable. Routinely available APRI and FIB-4 performed as good as more expensive tests. NITs did not change significantly during a follow-up of three years, suggesting slow liver disease progression in a majority of HIV/HCV co-infected persons on antiretroviral therapy. PMID:26418061

Progression of Liver Fibrosis in HIV/HCV Co-Infection: A Comparison between Non-Invasive Assessment Methods and Liver Biopsy.

PubMed

Schmid, Patrick; Bregenzer, Andrea; Huber, Milo; Rauch, Andri; Jochum, Wolfram; Müllhaupt, Beat; Vernazza, Pietro; Opravil, Milos; Weber, Rainer

2015-01-01

To evaluate the diagnostic performance of seven non-invasive tests (NITs) of liver fibrosis and to assess fibrosis progression over time in HIV/HCV co-infected patients. Transient elastography (TE) and six blood tests were compared to histopathological fibrosis stage (METAVIR). Participants were followed over three years with NITs at yearly intervals. Area under the receiver operating characteristic curve (AUROC) for significant fibrosis (> = F2) in 105 participants was highest for TE (0.85), followed by FIB-4 (0.77), ELF-Test (0.77), APRI (0.76), Fibrotest (0.75), hyaluronic acid (0.70), and Hepascore (0.68). AUROC for cirrhosis (F4) was 0.97 for TE followed by FIB-4 (0.91), APRI (0.89), Fibrotest (0.84), Hepascore (0.82), ELF-Test (0.82), and hyaluronic acid (0.79). A three year follow-up was completed by 87 participants, all on antiretroviral therapy and in 20 patients who completed HCV treatment (9 with sustained virologic response). TE, APRI and Fibrotest did not significantly change during follow-up. There was weak evidence for an increase of FIB-4 (mean increase: 0.22, p = 0.07). 42 participants had a second liver biopsy: Among 38 participants with F0-F3 at baseline, 10 were progessors (1-stage increase in fibrosis, 8 participants; 2-stage, 1; 3-stage, 1). Among progressors, mean increase in TE was 3.35 kPa, in APRI 0.36, and in FIB-4 0.75. Fibrotest results did not change over 3 years. TE was the best NIT for liver fibrosis staging in HIV/HCV co-infected patients. APRI-Score, FIB-4 Index, Fibrotest, and ELF-Test were less reliable. Routinely available APRI and FIB-4 performed as good as more expensive tests. NITs did not change significantly during a follow-up of three years, suggesting slow liver disease progression in a majority of HIV/HCV co-infected persons on antiretroviral therapy.

Acoustic Radiation Force Impulse (ARFI) Elastography and Serological Markers in Assessment of Liver Fibrosis and Free Portal Pressure in Patients with Hepatitis B.

PubMed

Li, Jun; Yu, Jie; Peng, Xin-Yu; Du, Ting-Ting; Wang, Jia-Jia; Tong, Jin; Lu, Gui-Lin; Wu, Xiang-Wei

2017-07-23

BACKGROUND The aim of this study was to investigate the feasibility of using acoustic radiation force impulse (ARFI) elastography, AST-to-platelet ratio index (APRI), and FIB-4 in assessing liver fibrosis and free portal pressure in patients with hepatitis B. MATERIAL AND METHODS We enrolled 126 patients with hepatitis B who underwent liver surgery at the General Surgery Department of the First Affiliated Hospital of Shihezi University Medical School from February 2013 to August 2015. Preoperatively, shear wave velocity (SWV) of the liver was measured with the Siemens S2000 ultrasound system to reflect liver stiffness. Serological markers were collected and fibrosis indices APRI and FIB-4 were calculated. Intraoperatively, liver tissues were harvested and free portal pressure (FPP) was measured. Postoperatively, fibrosis of liver tissues was pathologically staged. RESULTS The results of SWV, APRI, FIB-4, and FPP were all correlated with the degree of liver fibrosis (Spearman correlation coefficients: r=0.777, P<0.001; r=0.526, P<0.001; r=0.471, P<0.001; p<0.000; r=0.675, p<0.000). Receiver operating characteristic curve (ROC) analysis showed that the areas under the curve (AUC) of ARFI, APRI, and FIB-4 in diagnosing liver fibrosis were 0.830, 0.768, and 0.717, respectively, for stage F≥1; 0.861, 0.773, and 0.754, respectively, for stage F≥2; 0.941, 0.793, and 0.779, respectively, for stage F≥3; and 0.945, 0.783, and 0.754, respectively, for stage F=4. SWV, APRI, and FIB-4 were all correlated with FPP (Pearson correlation coefficients: 0.387, P<0.001; 0.446, P<0.001; 0.419, P<0.001). CONCLUSIONS ARFI, APRI, and FIB-4 can assess liver fibrosis in patients with hepatitis B when assessing the portal venous pressure. The difference in diagnostic efficacy between the 3 was not significant.

Ability of Cytokeratin-18 Fragments and FIB-4 Index to Diagnose Overall and Mild Fibrosis Nonalcoholic Steatohepatitis in Japanese Nonalcoholic Fatty Liver Disease Patients.

PubMed

Kobayashi, Natsuko; Kumada, Takashi; Toyoda, Hidenori; Tada, Toshifumi; Ito, Takanori; Kage, Masayoshi; Okanoue, Takeshi; Kudo, Masatoshi

2017-01-01

Several laboratory markers used in lieu of liver biopsy are reportedly useful in the diagnosis of nonalcoholic steatohepatitis (NASH). In the present study, we investigated the diagnostic impact of various non-invasive markers for predicting NASH. A total of 229 nonalcoholic fatty liver disease (NAFLD) patients who underwent liver biopsy were enrolled for the study. The diagnostic ability of various markers to diagnose NASH from NAFLD was investigated. A total of 140 patients were histologically diagnosed with NASH. Of these, 104 had degree 0-2 fibrosis (F0-2), and 36 had degree 3-4 fibrosis (F3-4). Multiple logistic regression analysis identified hyaluronic acid (HA) (OR 1.014; 95% CI 1.002-1.026; p = 0.024), FIB-4 index (OR 2.097; 95% CI 1.177-3.735; p = 0.012), and cytokeratin-18 fragments (CK-18F) (OR 1.002; 95% CI 1.001-1.002; p < 0.001) as factors independently associated with the diagnosis of NASH. The areas under the receiver operating characteristic curves (AUROCs) of HA, FIB-4 index, and CK-18F for the diagnosis of NASH were 0.77, 0.76, and 0.72, respectively. In addition, FIB-4 index (OR 1.907; 95% CI 1.063-3.419; p = 0.03) and CK-18F (OR 1.002; 95% CI 1.001-1.002; p < 0.001) could differentiate between NASH and NAFL, even when NASH patients with advanced fibrosis (F3-4) were excluded. AUROCs of FIB-4 index and CK-18F for the diagnosis of NASH with mild fibrosis (F0-2) from NAFLD were 0.70 and 0.70, respectively. FIB-4 index and CK-18F have good diagnostic abilities not only for NASH overall, but also for NASH with mild fibrosis. © 2017 S. Karger AG, Basel.

Diagnostic value of FIB-4, aspartate aminotransferase-to-platelet ratio index and liver stiffness measurement in hepatitis B virus-infected patients with persistently normal alanine aminotransferase.

PubMed

Tan, You-Wen; Zhou, Xing-Bei; Ye, Yun; He, Cong; Ge, Guo-Hong

2017-08-21

To assess the diagnostic value of FIB-4, aspartate aminotransferase-to-platelet ratio index (APRI), and liver stiffness measurement (LSM) in patients with hepatitis B virus infection who have persistently normal alanine transaminase (PNALT). We enrolled 245 patients with chronic hepatitis B: 95 in PNALT group, 86 in intermittently elevated alanine transaminase (PIALT1) group [alanine transaminase (ALT) within 1-2 × upper limit of normal value (ULN)], and 64 in PIALT2 group (ALT > 2 × ULN). All the patients received a percutaneous liver biopsy guided by ultrasonography. LSM, biochemical tests, and complete blood cell counts were performed. The pathological examination revealed moderate inflammatory necrosis ratios of 16.81% (16/95), 32.56% (28/86), and 45.31% (28/64), and moderate liver fibrosis of 24.2% (23/95), 33.72% (29/86), and 43.75% (28/64) in the PNALT, PIALT1, and PIALT2 groups, respectively. The degrees of inflammation and liver fibrosis were significantly higher in the PIALT groups than in the PNALT group ( P < 0.05). No significant difference was found in the areas under the curve (AUCs) between APRI and FIB-4 in the PNALT group; however, significant differences were found between APRI and LSM, and between FIB-4 and LSM in the PNALT group ( P < 0.05 for both). In the PIALT1 and PIALT2 groups, no significant difference ( P > 0.05) was found in AUCs for all comparisons ( P > 0.05 for all). In the overall patients, a significant difference in the AUCs was found only between LSM and APRI ( P < 0.05). APRI and FIB-4 are not the ideal noninvasive hepatic fibrosis markers for PNALT patients. LSM is superior to APRI and FIB-4 in PNALT patients because of the influence of liver inflammation and necrosis.

Prevalence of and Progression to Abnormal Non-Invasive Markers of Liver Disease (APRI and FIB-4) among US HIV-infected Youth

PubMed Central

Kapogiannis, Bill G.; Leister, Erin; Siberry, George K.; Van Dyke, Russell B.; Rudy, Bret; Flynn, Patricia; Williams, Paige L.

2015-01-01

Objective To longitudinally characterize non-invasive markers of liver disease in HIV-infected youth. Design HIV infection, without viral hepatitis co-infection, may contribute to liver disease. Non-invasive markers of liver disease [FIB-4 (Fibrosis-4) and APRI (aspartate aminotransferase-to-platelet ratio index)] have been evaluated in adults with concomitant HIV and hepatitis C, but are less studied in children. Methods In prospective cohorts of HIV-infected and HIV-uninfected youth, we used linear regression models to compare log-transformed FIB-4 and APRI measures by HIV status based on a single visit at ages 15–20 years. We also longitudinally modeled trends in these measures in HIV-infected youth with ≥2 visits to compare those with behavioral vs perinatal HIV infection (PHIV) using mixed effect linear regression, adjusting for age, gender, body mass index, and race/ethnicity. Results Of 1785 participants, 41% were male, 57% black non-Hispanic and 27% Hispanic. More HIV-infected than uninfected youth had an APRI score >0.5 (13% vs 3%, p<0.001). Among 1307 HIV-infected participants with longitudinal measures, FIB-4 scores increased 6% per year (p<0.001) among all HIV-infected youth, whereas APRI scores increased 2% per year (p=0.007) only among PHIV youth. The incidence rates (95% CI) of progression of APRI to >0.5 and >1.5 were 7.5 (6.5–8.7) and 1.4 (1.0–1.9) cases per 100 person-years of follow up, respectively. The incidence of progression of FIB-4 to >1.5 and >3.25 were 1.6 (1.2–2.2) and 0.3 (0.2–0.6) cases per 100 person-years, respectively. Conclusions APRI and FIB-4 scores were higher among HIV-infected youth. Progression to scores suggesting subclinical fibrosis or worse was common. PMID:26959353

Diagnostic value of FIB-4, aspartate aminotransferase-to-platelet ratio index and liver stiffness measurement in hepatitis B virus-infected patients with persistently normal alanine aminotransferase

PubMed Central

Tan, You-Wen; Zhou, Xing-Bei; Ye, Yun; He, Cong; Ge, Guo-Hong

2017-01-01

AIM To assess the diagnostic value of FIB-4, aspartate aminotransferase-to-platelet ratio index (APRI), and liver stiffness measurement (LSM) in patients with hepatitis B virus infection who have persistently normal alanine transaminase (PNALT). METHODS We enrolled 245 patients with chronic hepatitis B: 95 in PNALT group, 86 in intermittently elevated alanine transaminase (PIALT1) group [alanine transaminase (ALT) within 1-2 × upper limit of normal value (ULN)], and 64 in PIALT2 group (ALT > 2 × ULN). All the patients received a percutaneous liver biopsy guided by ultrasonography. LSM, biochemical tests, and complete blood cell counts were performed. RESULTS The pathological examination revealed moderate inflammatory necrosis ratios of 16.81% (16/95), 32.56% (28/86), and 45.31% (28/64), and moderate liver fibrosis of 24.2% (23/95), 33.72% (29/86), and 43.75% (28/64) in the PNALT, PIALT1, and PIALT2 groups, respectively. The degrees of inflammation and liver fibrosis were significantly higher in the PIALT groups than in the PNALT group (P < 0.05). No significant difference was found in the areas under the curve (AUCs) between APRI and FIB-4 in the PNALT group; however, significant differences were found between APRI and LSM, and between FIB-4 and LSM in the PNALT group (P < 0.05 for both). In the PIALT1 and PIALT2 groups, no significant difference (P > 0.05) was found in AUCs for all comparisons (P > 0.05 for all). In the overall patients, a significant difference in the AUCs was found only between LSM and APRI (P < 0.05). CONCLUSION APRI and FIB-4 are not the ideal noninvasive hepatic fibrosis markers for PNALT patients. LSM is superior to APRI and FIB-4 in PNALT patients because of the influence of liver inflammation and necrosis. PMID:28883700

Cooling History of Almahata Sitta Ureilite as Inferred from Transmission Electron Microscopy of Iron Metal

NASA Technical Reports Server (NTRS)

Mikouchi, T.; Aoyagi, Y.; Goodrich, C. A.; Yubuta, K.; Sugiyama, K.; Zolensky, M. E.; Goldstein, J. I.

2013-01-01

Almahata Sitta (AS) is a polymict breccia mainly composed of various ureilite lithologies with lesser chondritic lithologies [1]. In the ureilite lithologies, Fe metal is a common accessory phase present either as large grain boundary grains or small particles formed by reduction of olivine and pyroxene. In our earlier studies on grain boundary metals in one of AS fragments (#44) we found unique features never seen in other ureilites [2,3]. In order to further characterize these metal grains, we performed a detailed TEM study on a FIB section prepared from one of AS #44 grain boundary metals and here discuss its thermal history.

Diagnostic Accuracy of APRI, AAR, FIB-4, FI, King, Lok, Forns, and FibroIndex Scores in Predicting the Presence of Esophageal Varices in Liver Cirrhosis: A Systematic Review and Meta-Analysis.

PubMed

Deng, Han; Qi, Xingshun; Guo, Xiaozhong

2015-10-01

Aspartate aminotransferase-to-platelet ratio (APRI), aspartate aminotransferase-to-alanine aminotransferase ratio (AAR), FIB-4, FI, King, Lok, Forns, and FibroIndex scores may be simple and convenient noninvasive diagnostic tests, because they are based on the regular laboratory tests and demographic data. This study aimed to systematically evaluate their diagnostic accuracy for the prediction of varices in liver cirrhosis.All relevant papers were searched via PubMed, EMBASE, CNKI, and Wanfang databases. The area under the summary receiver operating characteristic curve (AUSROC), sensitivity, specificity, positive and negative likelihood ratio (PLR and NLR), and diagnostic odds ratio (DOR) were calculated.Overall, 12, 4, 5, 0, 0, 4, 3, and 1 paper was identified to explore the diagnostic accuracy of APRI, AAR, FIB-4, FI, King, Lok, Forns, and FibroIndex scores, respectively. The AUSROCs of APRI, AAR, FIB-4, Lok, and Forns scores for the prediction of varices were 0.6774, 0.7275, 0.7755, 0.7885, and 0.7517, respectively; and those for the prediction of large varices were 0.7278, 0.7448, 0.7095, 0.7264, and 0.6530, respectively. The diagnostic threshold effects of FIB-4 and Forns scores for the prediction of varices were statistically significant. The sensitivities/specificities/PLRs/NLRs/DORs of APRI, AAR, and Lok scores for the prediction of varices were 0.60/0.67/1.77/0.58/3.13, 0.64/0.63/1.97/0.54/4.18, and 0.74/0.68/2.34/0.40/5.76, respectively. The sensitivities/specificities/PLRs/NLRs/DORs of APRI, AAR, FIB-4, Lok, and Forns scores for the prediction of large varices were 0.65/0.66/2.15/0.47/4.97, 0.68/0.58/2.07/0.54/3.93, 0.62/0.64/2.02/0.56/3.57, 0.78/0.63/2.09/0.37/5.55, and 0.65/0.61/1.62/0.59/2.75, respectively.APRI, AAR, FIB-4, Lok, and Forns scores had low to moderate diagnostic accuracy in predicting the presence of varices in liver cirrhosis.

Evaluation of Bovine Feces-Associated Microbial Source Tracking Markers and Their Correlations with Fecal Indicators and Zoonotic Pathogens in a Brisbane, Australia, Reservoir

PubMed Central

Sritharan, T.; Palmer, A.; Sidhu, J. P. S.; Toze, S.

2013-01-01

This study was aimed at evaluating the host specificity and host sensitivity of two bovine feces-associated bacterial (BacCow-UCD and cowM3) and one viral [bovine adenovirus (B-AVs)] microbial source tracking (MST) markers by screening 130 fecal and wastewater samples from 10 target and nontarget host groups in southeast Queensland, Australia. In addition, 36 water samples were collected from a reservoir and tested for the occurrence of all three bovine feces-associated markers along with fecal indicator bacteria (FIB), Campylobacter spp., Escherichia coli O157, and Salmonella spp. The overall host specificity values of the BacCow-UCD, cowM3, and B-AVs markers to differentiate between bovine and other nontarget host groups were 0.66, 0.88, and 1.00, respectively (maximum value of 1.00). The overall host sensitivity values of these markers, however, in composite bovine wastewater and individual bovine fecal DNA samples were 0.93, 0.90, and 0.60, respectively (maximum value of 1.00). Among the 36 water samples tested, 56%, 22%, and 6% samples were PCR positive for the BacCow-UCD, cowM3, and B-AVs markers, respectively. Among the 36 samples tested, 50% and 14% samples were PCR positive for the Campylobacter 16S rRNA and E. coli O157 rfbE genes, respectively. Based on the results, we recommend that multiple bovine feces-associated markers be used if possible for bovine fecal pollution tracking. Nonetheless, the presence of the multiple bovine feces-associated markers along with the presence of potential zoonotic pathogens indicates bovine fecal pollution in the reservoir water samples. Further research is required to understand the decay rates of these markers in relation to FIB and zoonotic pathogens. PMID:23417003

Subsurface examination of a foliar biofilm using scanning electron- and focused-ion-beam microscopy

USDA-ARS?s Scientific Manuscript database

The dual beam scanning electron microscope, equipped with both a focused ion- and scanning electron- beam (FIB SEM) is a novel tool for the exploration of the subsurface structure of biological tissues. The FIB is capable of removing small cross sections to view the subsurface features and may be s...

Differential Decay of Cattle-associated Fecal Indicator Bacteria and Microbial Source Tracking Markers in Fresh and Marine Water (ASM 2017 Presentation)

EPA Science Inventory

Background: Fecal indicator bacteria (FIB) have a long history of use in the assessment of the microbial quality of recreational waters. However, quantification of FIB provides no information about the pollution source(s) and relatively little is known about their fate in the amb...

Lack of Direct Effects of Agrochemicals on Zoonotic Pathogens and Fecal Indicator Bacteria

PubMed Central

Staley, Zachery R.; Senkbeil, Jacob K.; Rohr, Jason R.

2012-01-01

Agrochemicals, fecal indicator bacteria (FIB), and pathogens frequently contaminate water simultaneously. No significant direct effects of fertilizer, atrazine, malathion, and chlorothalonil on the survival of Escherichia coli, Enterococcus faecalis, Salmonella enterica, human polyomaviruses, and adenovirus were detected, supporting the assertion that previously observed effects of agrochemicals on FIB were indirect. PMID:22961900

Precise and economic FIB/SEM for CLEM: with 2 nm voxels through mitosis.

PubMed

Luckner, Manja; Wanner, Gerhard

2018-05-23

A portfolio is presented documenting economic, high-resolution correlative focused ion beam scanning electron microscopy (FIB/SEM) in routine, comprising: (i) the use of custom-labeled slides and coverslips, (ii) embedding of cells in thin, or ultra-thin resin layers for correlative light and electron microscopy (CLEM) and (iii) the claim to reach the highest resolution possible with FIB/SEM in xyz. Regions of interest (ROIs) defined in light microscope (LM), can be relocated quickly and precisely in SEM. As proof of principle, HeLa cells were investigated in 3D context at all stages of the cell cycle, documenting ultrastructural changes during mitosis: nuclear envelope breakdown and reassembly, Golgi degradation and reconstitution and the formation of the midzone and midbody.

Measuring topographies from conventional SEM acquisitions.

PubMed

Shi, Qiwei; Roux, Stéphane; Latourte, Félix; Hild, François; Loisnard, Dominique; Brynaert, Nicolas

2018-04-27

The present study extends the stereoscopic imaging principle for estimating the surface topography to two orientations, namely, normal to the electron beam axis and inclined at 70° as suited for EBSD analyses. In spite of the large angle difference, it is shown that the topography can be accurately determined using regularized global Digital Image Correlation. The surface topography is compared to another estimate issued from a 3D FIB-SEM procedure where the sample surface is first covered by a Pt layer, and its initial topography is progressively revealed from successive FIB-milling. These two methods are successfully compared on a 6% strained steel specimen in an in situ mechanical test. This analysis is supplemented by a third approach estimating the change of topography from crystal rotations as measured from successive EBSD images. This last technique ignores plastic deformation, and thus only holds in an elastic regime. For the studied example, despite the large plastic flow, it is shown that crystal rotation already accounts for a significant part of the deformation-induced topography. Copyright © 2018 Elsevier B.V. All rights reserved.

Negative to positive crossover of the magnetoresistance in layered WS{sub 2}

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

Zhang, Yangwei; Ning, Honglie; Li, Yanan

2016-04-11

The discovery of graphene ignited intensive investigation of two-dimensional materials. A typical two-dimensional material, transition metal dichalcogenide (TMDC), attracts much attention because of its excellent performance in field effect transistor measurements and applications. Particularly, when TMDC reaches the dimension of a few layers, a wide range of electronic and optical properties can be detected that are in striking contrast to bulk samples. In this letter, we synthesized WS{sub 2} single-crystal nanoflakes using physical vapor deposition and carried out a series of measurements of the contact resistance and magnetoresistance. Focused ion beam (FIB) technology was applied to deposit Pt electrodes onmore » the WS{sub 2} flakes, and the FIB-deposited contacts exhibited linear electrical characteristics. Resistance versus temperature measurements showed similar Mott variable range hopping behavior in different magnetic fields. Additionally, a temperature-modulated negative-to-positive magnetoresistance transition was observed. Our work reveals the magnetotransport characteristics of WS{sub 2} flakes, which may stimulate further studies of the properties of TMDC and its corresponding electronic and optoelectronic applications.« less

Mineralized iron oxidizing bacteria from hydrothermal vents: targeting biosignatures on Mars

NASA Astrophysics Data System (ADS)

Leveille, R. J.

2010-12-01

Putative hydrothermal systems have been identified on Mars based on orbital imagery and rover-based analyses. Based on Earth analogs, hydrothermal systems on Mars would be highly attractive for their potential for preserving organic and inorganic biosignatures. For example, iron oxidizing bacteria are ubiquitous in marine and terrestrial hydrothermal systems, where they often display distinctive cell morphologies and are commonly encrusted by minerals, especially bacteriogenic iron oxides and silica. Microfossils of iron oxidizing bacteria have been found in ancient Si-Fe deposits and iron oxidation may be an ancient and widespread metabolic pathway. In order to investigate mineralized iron oxidizing bacteria as a biosignature, we have examined samples collected from extinct hydrothermal vents along Explorer Ridge, NE Pacific Ocean. In addition, microaerophilic iron oxidizing bacteria, isolated from active Pacific hydrothermal vents, were grown in a Fe-enriched seawater medium at constant pH (6.5) and O2 concentration (5%) in a controlled bioreactor system. Samples and experimental products were examined with a combination of variable-pressure and field-emission scanning electron microscopy (SEM), in some cases by preparing samples with a focused ion beam (FIB) milling system. Light-toned seafloor samples display abundant filamentous forms resembling, in both size and shape (1-5 microns in diameter and up to several microns in length), the twisted stalks of Gallionella and the elongated filaments of Leptothrix. Some samples consist entirely of low-density masses of silica (>90% Si) encrusted filamentous forms. The presence of unmineralized filamentous matter rich in C and Fe suggests that these are the remains of iron oxidizing bacteria. Mineralized filaments sectioned by FIB show variable internal material within semi-hollow, tubular-like features. Silica encrustations also show pseudo-concentric growth bands. In the bioreactor runs, abundant microbial growth and formation of an iron oxyhydroxide precipitate, either in direct association with the cells or within the growth medium, were observed. Preliminary analyses suggest that these precipitates are different from abiotic precipitates. Continuing work includes high-resolution TEM observations of cultured organisms and biogenic iron minerals, Raman and reflectance spectroscopy of precipitates, examination of seafloor incubation experiments, and bioreactor silicification experiments in order to better understand the Fe-Si fossilization process. Microaerophilic iron oxidation could have existed on the early Earth in environments containing small amounts of oxygen produced either by locally-concentrated photosynthetic microorganisms (e.g., cyanobacteria) or by chemical reactions. By analogy, similar subsurface or near-surface microaerophilic environments could have existed on Mars in the past, including in low-temperature hydrothermal systems. The distinctive morphologies and Fe-Si mineralization patterns of iron oxidizing bacteria could be a useful biosignature to search for on Mars. Deposits and features similar to those described here could be identified on Mars with existing technologies, and thus hydrothermal systems represent an attractive target for future surface and sample return missions.

Abundance of Naegleria fowleri in roof-harvested rainwater tank samples from two continents.

PubMed

Waso, Monique; Dobrowsky, Penelope Heather; Hamilton, Kerry Ann; Puzon, Geoffrey; Miller, Haylea; Khan, Wesaal; Ahmed, Warish

2018-02-01

Roof-harvested rainwater (RHRW) has been used as an alternative source of water in water scarce regions of many countries. The microbiological and chemical quality of RHRW has been questioned due to the presence of bacterial and protozoan pathogens. However, information on the occurrence of pathogenic amoeba in RHRW tank samples is needed due to their health risk potential and known associations with opportunistic pathogens. Therefore, this study aims to determine the quantitative occurrence of Naegleria fowleri in RHRW tank samples from Southeast Queensland (SEQ), Australia (AU), and the Kleinmond Housing Scheme located in Kleinmond, South Africa (SA). In all, 134 and 80 RHRW tank samples were collected from SEQ, and the Kleinmond Housing Scheme, Western Cape, SA, respectively. Quantitative PCR (qPCR) assays were used to measure the concentrations of N. fowleri, and culture-based methods were used to measure fecal indicator bacteria (FIB) Escherichia coli (E. coli) and Enterococcus spp. Of the 134 tank water samples tested from AU, 69 and 62.7% were positive for E. coli, and Enterococcus spp., respectively. For the SA tank water samples, FIB analysis was conducted for samples SA-T41 to SA-T80 (n = 40). Of the 40 samples analyzed from SA, 95 and 35% were positive for E. coli and Enterococcus spp., respectively. Of the 134 water samples tested in AU, 15 (11.2%) water samples were positive for N. fowleri, and the concentrations ranged from 1.7 × 10 2 to 3.6 × 10 4 gene copies per 100 mL of water. Of the 80 SA tank water samples screened for N. fowleri, 15 (18.8%) tank water samples were positive for N. fowleri and the concentrations ranged from 2.1 × 10 1 to 7.8 × 10 4 gene copies per 100 mL of tank water. The prevalence of N. fowleri in RHRW tank samples from AU and SA thus warrants further development of dose-response models for N. fowleri and a quantitative microbial risk assessment (QMRA) to inform and prioritize strategies for reducing associated public health risks.

Evolution of procalcitonin, C-reactive protein and fibrinogen levels in neutropenic leukaemia patients with invasive pulmonary aspergillosis or mucormycosis.

PubMed

Roques, Marjorie; Chretien, Marie Lorraine; Favennec, Camille; Lafon, Ingrid; Ferrant, Emmanuelle; Legouge, Caroline; Plocque, Alexia; Golfier, Camille; Duvillard, Laurence; Amoureux, Lucie; Bastie, Jean Noel; Maurin-Bernier, Lory; Dalle, Frederic; Caillot, Denis

2016-06-01

Unlike bacterial infections, the value of procalcitonin (PCT) in detecting fungal infections in leukaemia patients is not clear. To determine whether the monitoring of PCT coupled with C-reactive protein (CRP) and fibrinogen (Fib) could be helpful in the management of pulmonary aspergillosis (IPA) or mucormycosis (PM), we retrospectively analysed the evolution of PCT, CRP and Fib levels in 94 leukaemia patients with proven/probable IPA (n = 77) or PM (n = 17) from D-12 to D12 relative to IFI onset defined as D0. Overall, 2140 assays were performed. From D-12 to D0, 12%, 5% and 1.4% of patients had PCT >0.5, 1 and 1.5 μg l(-1) , respectively, while CRP was >50, 75 and 100 mg l(-1) in 84%, 70% and 57% and Fib was >4, 5 and 6 g l(-1) in 96%, 80% and 61% of cases respectively (P < 10(-7) ). The same trends were observed from D1 to D12. Overall, between D-12 and D12, only 6.4% of patients had PCT >1.5 μg l(-1) , while CRP >100 mg l(-1) and Fib >6 g l(-1) were observed in 80% and 75% of cases respectively (P < 10(-7) ). In leukaemia patients, IPA or PM was accompanied by a significant increase in CRP and Fib while PCT remained low. © 2016 Blackwell Verlag GmbH.

Nanoscale insights on one- and two-dimensional material structures

NASA Astrophysics Data System (ADS)

Floresca, Herman Carlo

The race for smaller, faster and more efficient devices has led researchers to explore the possibilities of utilizing nanostructures for scaling. These one-dimensional and two-dimensional materials have properties that are attractive for this purpose but are still not well controlled. Control comes with a complete understanding of the materials' electrical, thermal, optical and structural characteristics but is difficult to obtain due to their small scale. This work is intended to help researchers overcome the difficulty in studying nanostructures by providing techniques for analysis and insights of nanostructures that have not been previously available. Two nanostructures were studied: silicon nanowires and graphene. The nanowires were prepared for cross-section transmission electron microscopy (TEM) to discover the effects that controlled oxidation has on the dimensions and shape of the nanowires. Since cross-section TEM is not able to provide information about surface structure, a method for manipulating the wires with orientation control was developed. With this ability, all three orthogonal views of the nanowire were compiled for a comprehensive study on its structure in terms of shape and surface roughness. Graphene was used for a two-dimensional analytical technique that took advantage of customized computer programs for data acquisition, measurement and display. With the information provided, distinctions between grain boundary types in polycrystalline graphene were made and supported by statistical information from the software's output. It was also applied to a growth series of graphene samples in conjunction with scanning electron microscopy (SEM) images and electron backscatter diffraction (EBSD) maps. The results help point to origins of graphene's polycrystalline nature. This dissertation concludes with a thought towards the future by highlighting a method that can help analyze nanostructures, which may become incorporated into the structures of large devices. The fold-out method is a TEM sample preparation technique utilizing a focused ion beam (FIB) for site specific thinning across a large sample area. Its process is demonstrated along with advantages over conventional methods.

Focused Ion Beam Recovery of Hypervelocity Impact Residue in Experimental Craters on Metallic Foils

NASA Technical Reports Server (NTRS)

Graham, G. A.; Teslich, N.; Dai, Z. R.; Bradley, J. P.; Kearsley, A. T.; Horz, F.

2006-01-01

The Stardust sample return capsule will return to Earth in January 2006 with primitive debris collected from Comet 81P/Wild-2 during the fly-by encounter in 2004. In addition to the cometary particles embedded in low-density silica aerogel, there will be microcraters preserved in the Al foils (1100 series; 100 micrometers thick) that are wrapped around the sample tray assembly. Soda lime spheres (approximately 49 m in diameter) have been accelerated with a light-gas-gun into flight-grade Al foils at 6.35 km s(sup -1) to simulate the potential capture of cometary debris. The preserved crater penetrations have been analyzed using scanning electron microscopy (SEM) and x-ray energy dispersive spectroscopy (EDX) to locate and characterize remnants of the projectile material remaining within the craters. In addition, ion beam induced secondary electron imaging has proven particularly useful in identifying areas within the craters that contain residue material. Finally, high-precision focused ion beam (FIB) milling has been used to isolate and then extract an individual melt residue droplet from the interior wall of an impact penetration. This enabled further detailed elemental characterization, free from the background contamination of the Al foil substrate. The ability to recover pure melt residues using FIB will significantly extend the interpretations of the residue chemistry preserved in the Al foils returned by Stardust.

Line-width roughness of advanced semiconductor features by using FIB and planar-TEM as reference metrology

NASA Astrophysics Data System (ADS)

Takamasu, Kiyoshi; Takahashi, Satoru; Kawada, Hiroki; Ikota, Masami

2018-03-01

LER (Line Edge Roughness) and LWR (Line Width Roughness) of the semiconductor device are an important evaluation scale of the performance of the device. Conventionally, LER and LWR is evaluated from CD-SEM (Critical Dimension Scanning Electron Microscope) images. However, CD-SEM measurement has a problem that high frequency random noise is large, and resolution is not sufficiently high. For random noise of CD-SEM measurement, some techniques are proposed. In these methods, it is necessary to set parameters for model and processing, and it is necessary to verify the correctness of these parameters using reference metrology. We have already proposed a novel reference metrology using FIB (Focused Ion Beam) process and planar-TEM (Transmission Electron Microscope) method. In this study, we applied the proposed method to three new samples such as SAQP (Self-Aligned Quadruple Patterning) FinFET device, EUV (Extreme Ultraviolet Lithography) conventional resist, and EUV new material resist. LWR and PSD (Power Spectral Density) of LWR are calculated from the edge positions on planar-TEM images. We confirmed that LWR and PSD of LWR can be measured with high accuracy and evaluated the difference by the proposed method. Furthermore, from comparisons with PSD of the same sample by CD-SEM, the validity of measurement of PSD and LWR by CD-SEM can be verified.

Precise measurement of electric potential, field, and charge density profiles across a biased GaAs p-n tunnel junction by in situ phase-shifting electron holography

NASA Astrophysics Data System (ADS)

Anada, Satoshi; Yamamoto, Kazuo; Sasaki, Hirokazu; Shibata, Naoya; Hori, Yujin; Kinugawa, Kouhei; Imamura, Akihiro; Hirayama, Tsukasa

2017-12-01

We combined an in situ biasing technique with phase-shifting electron holography, which can simultaneously achieve a high precision and high spatial resolution, to measure the electric potential, field, and charge density profiles across a GaAs p-n tunnel junction. A thin-film specimen was prepared by thinning one part of a bulk specimen using a cryo focused ion beam (FIB) system. We obtained precise electric potential profiles and successfully converted them into smooth electric field and charge density profiles without any fitting simulations. From the relationship between the applied voltage and measured height of the potential step across the p-n junction, the built-in potential of the p-n junction was determined to be 1.55 ± 0.02 V. The electric field profiles showed that the unbiased p-n junction had a depletion layer with a width of 24 ± 1 nm; the width increased to 26 ± 1 nm under a reverse bias of -0.3 V and decreased to 22 ± 1 nm under a forward bias of 0.5 V. Moreover, the charge density profiles indicated the presence of passivated dopants and/or trapped carriers even in the internal active layer of the specimen, with little damage introduced by FIB milling.

DBR laser with nondynamic plasma grating formed by focused ion beam implanted dopants

NASA Technical Reports Server (NTRS)

Boenke, Myra M.; Wu, M. C.; Wang, Shyh; Clark, William M., Jr.; Stevens, Eugene H.

1989-01-01

A static plasma grating has been demonstrated experimentally (Wu et al., 1988) in a large-optical-cavity focused-ion-beam-distributed-Bragg-reflector (FIB-DBR) GaAlAs/GaAs laser diode. The grating is formed by implanting stripes of dopants with a focused ion beam. The dopants ionize to form periodic fluctuations in the carrier concentration which, through the Kramers-Kronig relations, form an index grating. A model of the grating strength for optimizaton of the laser design is developed and presented. The computed results show that the coupling coefficient k can be increased by more than an order of magnitude over the 15/cm experimentally. Therefore, FIB-DBR or FIB-distributed-feedback (DFB) lasers with performance comparable to that of conventional DBR (or DFB) lasers can be expected.

Genes indicative of zoonotic and swine pathogens are persistent in stream water and sediment following a swine manure spill

USGS Publications Warehouse

Haack, Sheridan K.; Duris, Joseph W.; Kolpin, Dana W.; Fogarty, Lisa R.; Johnson, Heather E.; Gibson, Kristen E.; Focazio, Michael J.; Schwab, Kellogg J.; Hubbard, Laura E.; Foreman, William T.

2015-01-01

Manure spills to streams are relatively frequent, but no studies have characterized stream contamination with zoonotic and veterinary pathogens, or fecal chemicals, following a spill. We tested stream water and sediment over 25 days and downstream for 7.6 km for: fecal indicator bacteria (FIB); the fecal indicator chemicals cholesterol and coprostanol; 20 genes for zoonotic and swine-specific bacterial pathogens by presence/absence polymerase chain reaction (PCR) for viable cells; one swine-specific Escherichia coli toxin gene (STII) by quantitative PCR (qPCR); and nine human and animal viruses by qPCR, or reverse-transcriptase qPCR. Twelve days post-spill, and 4.2 km downstream, water concentrations of FIB, cholesterol, and coprostanol were 1-2 orders of magnitude greater than those detected before, or above, the spill, and genes indicating viable zoonotic or swine-infectious Escherichia coli, were detected in water or sediment. STII increased from undetectable before, or above the spill, to 105 copies/100 mL water 12 days post-spill. Thirteen of 14 water (8/9 sediment) samples had viable STII-carrying cells post-spill. Eighteen days post-spill porcine adenovirus and teschovirus were detected 5.6 km downstream. Sediment FIB concentrations (per gram wet weight) were greater than in water, and sediment was a continuous reservoir of genes and chemicals post-spill. Constituent concentrations were much lower, and detections less frequent, in a runoff event (200 days post-spill) following manure application, although the swine-associated STII and stx2e genes were detected. Manure spills are an underappreciated pathway for livestock-derived contaminants to enter streams, with persistent environmental outcomes, and the potential for human and veterinary health consequences.

Microscopic observations of osteoblast growth on micro-arc oxidized β titanium

NASA Astrophysics Data System (ADS)

Chen, Hsien-Te; Chung, Chi-Jen; Yang, Tsai-Ching; Tang, Chin-Hsin; He, Ju-Liang

2013-02-01

Titanium alloys are widely used in orthopedic and dental implants, owing to their excellent physical properties and biocompatibility. By using the micro-arc oxidation (MAO), we generated anatase-rich (A-TiO2) and rutile-rich (R-TiO2) titanium dioxide coatings, individually on β-Ti alloy, in which the latter achieved an enhanced in vitro and in vivo performance. Thoroughly elucidating how the osteoblasts interact with TiO2 coatings is of worthwhile interest. This study adopts the focused ion beam (FIB) to section off the TiO2 coated samples for further scanning electron microscope (SEM) and transmission electron microscope (TEM) observation. The detailed crystal structures of the TiO2 coated specimens are also characterized. Experimental results indicate osteoblasts adhered more tenaciously and grew conformably with more lamellipodia extent on the R-TiO2 specimen than on the A-TiO2 and raw β-Ti specimens. FIB/SEM cross-sectional images of the cell/TiO2 interface revealed micro gaps between the cell membrane and contact surface of A-TiO2 specimen, while it was not found on the R-TiO2 specimen. Additionally, the number of adhered and proliferated cells on the R-TiO2 specimen was visually greater than the others. Closely examining EDS line scans and elemental mappings of the FIB/TEM cross-sectional images of the cell/TiO2 interface reveals both the cell body and interior space of the TiO2 coating contain nitrogen and sulfur (the biological elements in cell). This finding supports the assumption that osteoblast can grow into the porous structure of TiO2 coatings and demonstrating that the R-TiO2 coating formed by MAO serves the best for β-Ti alloys as orthopedic and dental implants.

A scanning probe mounted on a field-effect transistor: Characterization of ion damage in Si.

PubMed

Shin, Kumjae; Lee, Hoontaek; Sung, Min; Lee, Sang Hoon; Shin, Hyunjung; Moon, Wonkyu

2017-10-01

We have examined the capabilities of a Tip-On-Gate of Field-Effect Transistor (ToGoFET) probe for characterization of FIB-induced damage in Si surface. A ToGoFET probe is the SPM probe which the Field Effect Transistor(FET) is embedded at the end of a cantilever and a Pt tip was mounted at the gate of FET. The ToGoFET probe can detect the surface electrical properties by measuring source-drain current directly modulated by the charge on the tip. In this study, a Si specimen whose surface was processed with Ga+ ion beam was prepared. Irradiation and implantation with Ga+ ions induce highly localized modifications to the contact potential. The FET embedded on ToGoFET probe detected the surface electric field profile generated by schottky contact between the Pt tip and the sample surface. Experimentally, it was shown that significant differences of electric field due to the contact potential barrier in differently processed specimens were observed using ToGOFET probe. This result shows the potential that the local contact potential difference can be measured by simple working principle with high sensitivity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Berkovich Nanoindentation on AlN Thin Films.

PubMed

Jian, Sheng-Rui; Chen, Guo-Ju; Lin, Ting-Chun

2010-03-31

Berkovich nanoindentation-induced mechanical deformation mechanisms of AlN thin films have been investigated by using atomic force microscopy (AFM) and cross-sectional transmission electron microscopy (XTEM) techniques. AlN thin films are deposited on the metal-organic chemical-vapor deposition (MOCVD) derived Si-doped (2 × 1017 cm-3) GaN template by using the helicon sputtering system. The XTEM samples were prepared by means of focused ion beam (FIB) milling to accurately position the cross-section of the nanoindented area. The hardness and Young's modulus of AlN thin films were measured by a Berkovich nanoindenter operated with the continuous contact stiffness measurements (CSM) option. The obtained values of the hardness and Young's modulus are 22 and 332 GPa, respectively. The XTEM images taken in the vicinity regions just underneath the indenter tip revealed that the multiple "pop-ins" observed in the load-displacement curve during loading are due primarily to the activities of dislocation nucleation and propagation. The absence of discontinuities in the unloading segments of load-displacement curve suggests that no pressure-induced phase transition was involved. Results obtained in this study may also have technological implications for estimating possible mechanical damages induced by the fabrication processes of making the AlN-based devices.

Exsolution of Iron-Titanium Oxides in Magnetite in Miller Range (MIL) 03346 Nakhlite: Evidence for Post Crystallization Reduction in the Nakhlite Cumulate Pile

NASA Technical Reports Server (NTRS)

Righter, Kevin; Keller, L. P.; Rahman, Z.; Christoffersen, R.

2012-01-01

MIL 03346 is one of the most mesostasis-rich nakhlites [1] and thought to have equilibrated at oxygen fugacities near the fayalite-magnetite-quartz oxygen (FMQ) buffer ([2,3]). Studies of FeTi oxides in nakhlites have led to additional constraints on their equilibration temperatures and fO2s [4,5,6,7]. Comparison of these results to fO2s calculated for shergottites indicates that nakhlites are among the most oxidized samples from the martian meteorite suite [2]. The mesostasis of MIL 03346 contains skeletal titanomagnetite. Several scientists noticed several years ago (e.g. [8]) that this titanomagnetite contains very fine oxidation-driven exsolution lamellae (Figure 1). However, the lamellae are so small that they cannot be characterized by electron microprobe analysis (EMPA). Here we select several areas for focused ion beam (FIB) extraction, prepare transmission electron microscopy (TEM) foils, and identify and analyze the lamellae using TEM at the Johnson Space Center (JSC). The resulting analyses are combined with previous work on nakhlites to interpret the thermal and oxidation history of this meteorite group.

Accuracy of simple biochemical tests in identifying liver fibrosis in patients co-infected with human immunodeficiency virus and hepatitis C virus.

PubMed

Tural, Cristina; Tor, Jordi; Sanvisens, Arantza; Pérez-Alvarez, Núria; Martínez, Elisenda; Ojanguren, Isabel; García-Samaniego, Javier; Rockstroh, Juergen; Barluenga, Eva; Muga, Robert; Planas, Ramon; Sirera, Guillem; Rey-Joly, Celestino; Clotet, Bonaventura

2009-03-01

We assessed the ability of 3 simple biochemical tests to stage liver fibrosis in patients co-infected with human immunodeficiency virus (HIV) and hepatitis C virus (HCV). We analyzed liver biopsy samples from 324 consecutive HIV/HCV-positive patients (72% men; mean age, 38 y; mean CD4+ T-cell counts, 548 cells/mm(3)). Scheuer fibrosis scores were as follows: 30% had F0, 22% had F1, 19% had F2, 23% had F3, and 6% had F4. Logistic regression analyses were used to predict the probability of significant (>or=F2) or advanced (>or=F3) fibrosis, based on numeric scores from the APRI, FORNS, or FIB-4 tests (alone and in combination). Area under the receiver operating characteristic curves were analyzed to assess diagnostic performance. Area under the receiver operating characteristic curves analyses indicated that the 3 tests had similar abilities to identify F2 and F3; the ability of APRI, FORNS, and FIB-4 were as follows: F2 or greater: 0.72, 0.67, and 0.72, respectively; F3 or greater: 0.75, 0.73, and 0.78, respectively. The accuracy of each test in predicting which samples were F3 or greater was significantly higher than for F2 or greater (APRI, FORNS, and FIB-4: >or=F3: 75%, 76%, and 76%, respectively; >or=F2: 66%, 62%, and 68%, respectively). By using the lowest cut-off values for all 3 tests, F3 or greater was ruled out with sensitivity and negative predictive values of 79% to 94% and 87% to 91%, respectively, and 47% to 70% accuracy. Advanced liver fibrosis (>or=F3) was identified using the highest cut-off value, with specificity and positive predictive values of 90% to 96% and 63% to 73%, respectively, and 75% to 77% accuracy. Simple biochemical tests accurately predicted liver fibrosis in more than half the HIV/HCV co-infected patients. The absence and presence of liver fibrosis are predicted fairly using the lowest and highest cut-off levels, respectively.

Application of empirical predictive modeling using conventional and alternative fecal indicator bacteria in eastern North Carolina waters

USGS Publications Warehouse

Gonzalez, Raul; Conn, Kathleen E.; Crosswell, Joey; Noble, Rachel

2012-01-01

Coastal and estuarine waters are the site of intense anthropogenic influence with concomitant use for recreation and seafood harvesting. Therefore, coastal and estuarine water quality has a direct impact on human health. In eastern North Carolina (NC) there are over 240 recreational and 1025 shellfish harvesting water quality monitoring sites that are regularly assessed. Because of the large number of sites, sampling frequency is often only on a weekly basis. This frequency, along with an 18–24 h incubation time for fecal indicator bacteria (FIB) enumeration via culture-based methods, reduces the efficiency of the public notification process. In states like NC where beach monitoring resources are limited but historical data are plentiful, predictive models may offer an improvement for monitoring and notification by providing real-time FIB estimates. In this study, water samples were collected during 12 dry (n = 88) and 13 wet (n = 66) weather events at up to 10 sites. Statistical predictive models for Escherichiacoli (EC), enterococci (ENT), and members of the Bacteroidales group were created and subsequently validated. Our results showed that models for EC and ENT (adjusted R2 were 0.61 and 0.64, respectively) incorporated a range of antecedent rainfall, climate, and environmental variables. The most important variables for EC and ENT models were 5-day antecedent rainfall, dissolved oxygen, and salinity. These models successfully predicted FIB levels over a wide range of conditions with a 3% (EC model) and 9% (ENT model) overall error rate for recreational threshold values and a 0% (EC model) overall error rate for shellfish threshold values. Though modeling of members of the Bacteroidales group had less predictive ability (adjusted R2 were 0.56 and 0.53 for fecal Bacteroides spp. and human Bacteroides spp., respectively), the modeling approach and testing provided information on Bacteroidales ecology. This is the first example of a set of successful statistical predictive models appropriate for assessment of both recreational and shellfish harvesting water quality in estuarine waters.

The gamma-glutamyl transpeptidase to platelet ratio (GPR) predicts significant liver fibrosis and cirrhosis in patients with chronic HBV infection in West Africa.

PubMed

Lemoine, Maud; Shimakawa, Yusuke; Nayagam, Shevanthi; Khalil, Mustapha; Suso, Penda; Lloyd, Jo; Goldin, Robert; Njai, Harr-Freeya; Ndow, Gibril; Taal, Makie; Cooke, Graham; D'Alessandro, Umberto; Vray, Muriel; Mbaye, Papa Saliou; Njie, Ramou; Mallet, Vincent; Thursz, Mark

2016-08-01

Simple and inexpensive non-invasive fibrosis tests are highly needed but have been poorly studied in sub-Saharan Africa. Using liver histology as a gold standard, we developed a novel index using routine laboratory tests to predict significant fibrosis in patients with chronic HBV infection in The Gambia, West Africa. We prospectively assessed the diagnostic accuracy of the novel index, Fibroscan, aspartate transaminase-to-platelet ratio index (APRI), and Fib-4 in Gambian patients with CHB (training set) and also in French and Senegalese CHB cohorts (validation sets). Of 135 consecutive treatment-naïve patients with CHB who had liver biopsy, 39% had significant fibrosis (Metavir fibrosis stage ≥F2) and 15% had cirrhosis (F4). In multivariable analysis, gamma-glutamyl transpeptidase (GGT) and platelet count were independent predictors of significant fibrosis. Consequently, GGT-to-platelet ratio (GPR) was developed. In The Gambia, the area under the receiver operating characteristic curve (AUROC) of the GPR was significantly higher than that of APRI and Fib-4 to predict ≥F2, ≥F3 and F4. In Senegal, the AUROC of GPR was significantly better than Fib-4 and APRI for ≥F2 (0.73, 95% CI 0.59 to 0.86) and better than Fib-4 and Fibroscan for ≥F3 (0.93, 0.87 to 0.99). In France, the AUROC of GPR to diagnose ≥F2 (0.72, 95% CI 0.59 to 0.85) and F4 (0.87, 0.76 to 0.98) was equivalent to that of APRI and Fib-4. The GPR is a more accurate routine laboratory marker than APRI and Fib-4 to stage liver fibrosis in patients with CHB in West Africa. The GPR represents a simple and inexpensive alternative to liver biopsy and Fibroscan in sub-Saharan Africa. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Study on Platinum Coating Depth in Focused Ion Beam Diamond Cutting Tool Milling and Methods for Removing Platinum Layer.

PubMed

Choi, Woong Kirl; Baek, Seung Yub

2015-09-22

In recent years, nanomachining has attracted increasing attention in advanced manufacturing science and technologies as a value-added processes to control material structures, components, devices, and nanoscale systems. To make sub-micro patterns on these products, micro/nanoscale single-crystal diamond cutting tools are essential. Popular non-contact methods for the macro/micro processing of diamond composites are pulsed laser ablation (PLA) and electric discharge machining (EDM). However, for manufacturing nanoscale diamond tools, these machining methods are not appropriate. Despite diamond's extreme physical properties, diamond can be micro/nano machined relatively easily using a focused ion beam (FIB) technique. In the FIB milling process, the surface properties of the diamond cutting tool is affected by the amorphous damage layer caused by the FIB gallium ion collision and implantation and these influence the diamond cutting tool edge sharpness and increase the processing procedures. To protect the diamond substrate, a protection layer-platinum (Pt) coating is essential in diamond FIB milling. In this study, the depth of Pt coating layer which could decrease process-induced damage during FIB fabrication is investigated, along with methods for removing the Pt coating layer on diamond tools. The optimum Pt coating depth has been confirmed, which is very important for maintaining cutting tool edge sharpness and decreasing processing procedures. The ultra-precision grinding method and etching with aqua regia method have been investigated for removing the Pt coating layer. Experimental results show that when the diamond cutting tool width is bigger than 500 nm, ultra-precision grinding method is appropriate for removing Pt coating layer on diamond tool. However, the ultra-precision grinding method is not recommended for removing the Pt coating layer when the cutting tool width is smaller than 500 nm, because the possibility that the diamond cutting tool is damaged by the grinding process will be increased. Despite the etching method requiring more procedures to remove the Pt coating layer after FIB milling, it is a feasible method for diamond tools with under 500 nm width.

FIB Plan View Preparation and Electron Tomography of Ga-Containing Droplets Induced by Melt-Back Etching in Si.

PubMed

Gries, Katharina I; Werner, Katharina; Beyer, Andreas; Stolz, Wolfgang; Volz, Kerstin

2016-02-01

Melt-back etching is an effect that can occur for gallium (Ga) containing III/V semiconductors grown on Si. Since this effect influences interfaces between the two compounds and therefore the physical characteristics of the material composition, it is desirable to understand its driving forces. Therefore, we investigated Ga grown on Si (001) via metal organic chemical vapor deposition using trimethyl Ga as a precursor. As a result of the melt-back etching, Ga-containing droplets formed on the Si surface which reach into the Si wafer. The shape of these structures was analyzed by plan view investigation and cross sectional tomography in a (scanning) transmission electron microscope. For plan view preparation a focused ion beam was used to avoid damage to the Ga-containing structures, which are sensitive to the chemicals normally used during conventional plan view preparation. Combining the results of both investigation methods confirms that the Ga-containing structure within the Si exhibits a pyramid shape with facets along the Si {111} lattice planes.

Porous Aluminum Oxide and Magnesium Oxide Films Using Organic Hydrogels as Structure Matrices

PubMed Central

Chen, Zimei

2018-01-01

We describe the synthesis of mesoporous Al2O3 and MgO layers on silicon wafer substrates by using poly(dimethylacrylamide) hydrogels as porogenic matrices. Hydrogel films are prepared by spreading the polymer through spin-coating, followed by photo-cross-linking and anchoring to the substrate surface. The metal oxides are obtained by swelling the hydrogels in the respective metal nitrate solutions and subsequent thermal conversion. Combustion of the hydrogel results in mesoporous metal oxide layers with thicknesses in the μm range and high specific surface areas up to 558 m2∙g−1. Materials are characterized by SEM, FIB ablation, EDX, and Kr physisorption porosimetry. PMID:29565802

Effects of lead on oxidation behavior of Alloy 690TT within a high temperature aqueous environment

NASA Astrophysics Data System (ADS)

Hou, Qiang; Liu, Zhiyong; Li, Chengtao; Li, Xiaogang

2017-12-01

The chemical compositions, phases and structures of two oxide films on Alloy 690TT following exposure for 4400 h in pure water with and without lead at 320 °C were studied by surface analysis techniques. The analysis of a lead-doped oxide film prepared by a focused ion beam (FIB) demonstrated that both Cr-rich and Ni-rich oxides were alternatively distributed within the outer layer, whereas the inner layer was porous and poorly protected, causing severe corrosion of the alloy and a thicker film was formed. A duplex film model was proposed for the effects discussion of lead on the oxidation mechanism.

Application of Scanning-Imaging X-Ray Microscopy to Fluid Inclusion Candidates in Carbonates of Carbonaceous Chondrites

NASA Technical Reports Server (NTRS)

Tsuchiyama, Akira; Nakano, Tsukasa; Miyake, Akira; Akihisa, Takeuchi; Uesugi, Kentaro; Suzuki, Yoshio; Kitayama, Akira; Matsuno, Junya; Zolensky, Michael E.

2016-01-01

In order to search for such fluid inclusions in carbonaceous chondrites, a nondestructive technique using x-ray micro-absorption tomography combined with FIB sampling was developed and applied to a carbonaceous chondrite. They found fluid inclusion candidates in calcite grains, which were formed by aqueous alteration. However, they could not determine whether they are really aqueous fluids or merely voids. Phase and absorption contrast images can be simultaneously obtained in 3D by using scanning-imaging x-ray microscopy (SIXM). In refractive index, n=1-sigma+i(beta), in the real part, 1-sigma is the refractive index with decrement, sigma, which is nearly proportional to the density, and the imaginary part, beta, is the extinction coefficient, which is related to the liner attenuation coefficient, mu. Many phases, including water and organic materials as well as minerals, can be identified by SIXM, and this technique has potential availability for Hayabusa-2 sample analysis too. In this study, we examined quantitative performance of d and m values and the spatial resolution in SIXM by using standard materials, and applied this technique to carbonaceous chondrite samples. We used POM ([CH2O]n), silicon, quartz, forsterite, corundum, magnetite and nickel as standard materials for examining the sigma and mu values. A fluid inclusion in terrestrial quartz and bi-valve shell (Atrina vexillum), which are composed of calcite and organic layers with different thickness, were also used for examining the spatial resolution. The Ivuna (CI) and Sutter's Mill (CM) meteorites were used as carbonaceous chondrite samples. Rod- or cube-shaped samples 20-30 micron in size were extracted by using FIB from cross-sectional surfaces of the standard materials or polished thin sections of the chondrites, which was previously observed with SEM. Then, the sample was attached to a thin W-needle and imaged by SIXM system at beamline BL47XU, SPring-8, Japan. The slice thickness was 109.3 nm and the pixel size was mostly 100 nm.

Routine Laboratory Blood Tests May Diagnose Significant Fibrosis in Liver Transplant Recipients with Chronic Hepatitis C: A 10 Year Experience.

PubMed

Sheen, Victoria; Nguyen, Heajung; Jimenez, Melissa; Agopian, Vatche; Vangala, Sitaram; Elashoff, David; Saab, Sammy

2016-03-28

The aims of our study were to determine whether routine blood tests, the aspartate aminotransferase (AST) to Platelet Ratio Index (APRI) and Fibrosis 4 (Fib-4) scores, were associated with advanced fibrosis and to create a novel model in liver transplant recipients with chronic hepatitis C virus (HCV). We performed a cross sectional study of patients at The University of California at Los Angeles (UCLA) Medical Center who underwent liver transplantation for HCV. We used linear mixed effects models to analyze association between fibrosis severity and individual biochemical markers and mixed effects logistic regression to construct diagnostic models for advanced fibrosis (METAVIR F3-4). Cross-validation was used to estimate a receiving operator characteristic (ROC) curve for the prediction models and to estimate the area under the curve (AUC). The mean (± standard deviation [SD]) age of our cohort was 55 (±7.7) years, and almost three quarter were male. The mean (±SD) time from transplant to liver biopsy was 19.9 (±17.1) months. The mean (±SD) APRI and Fib-4 scores were 3 (±12) and 7 (±14), respectively. Increased fibrosis was associated with lower platelet count and alanine aminotransferase (ALT) values and higher total bilirubin and Fib-4 scores. We developed a model that takes into account age, gender, platelet count, ALT, and total bilirubin, and this model outperformed APRI and Fib-4 with an AUC of 0.68 (p < 0.001). Our novel prediction model diagnosed the presence of advanced fibrosis more reliably than APRI and Fib-4 scores. This noninvasive calculation may be used clinically to identify liver transplant recipients with HCV with significant liver damage.

Comparison of non-invasive assessment to diagnose liver fibrosis in chronic hepatitis B and C patients.

PubMed

Stibbe, Krista J M; Verveer, Claudia; Francke, Jan; Hansen, Bettina E; Zondervan, Pieter E; Kuipers, Ernst J; de Knegt, Robert J; van Vuuren, Anneke J

2011-07-01

Chronic viral hepatitis B and C cause liver fibrosis, leading to cirrhosis. Fibrosis assessment is essential to establish prognosis and treatment indication. We compared seven non-invasive tests, separately and in combination, in chronic hepatitis patients to detect early stages of fibrosis according to the Metavir score in liver biopsy. Galactose and methacetin breath tests (GBT and MBT), biomarkers (hyaluronic acid (HA), aspartate aminotransferase platelet ratio index (APRI), FibroTest, and Fib-4) and transient elastography (TE) were evaluated in 89 patients. Additionally, 31 healthy controls were included for evaluation of breath tests and biomarkers. Serum markers (HA, APRI, FibroTest, and Fib-4) and elastography significantly distinguished non-cirrhotic (F0123) from cirrhotic (F4) patients (p < 0.001, p = 0.015, p < 0.001, p = 0.005, p = 0.006, respectively). GBT, HA, APRI, FibroTest, Fib-4, and TE detected F01 from F234 (p = 0.04, p = 0.011, p = 0.009, p < 0.001, p < 0.001, and p < 0.001, respectively). A combination of different tests (TE, HA, and FibroTest) improved the performance statistically, area under the curve (AUC) = 0.87 for F234, 0.92 for F34, and 0.90 for F4. HA, APRI, FibroTest, Fib-4, and TE reliably distinguish non-cirrhotic and cirrhotic patients. Except for MBT, all tests discriminate between mild and moderate fibrosis. As single tests: FibroTest, Fib-4, and TE were the most accurate for detecting early fibrosis; combining different non-invasive tests increased the accuracy for detection of liver fibrosis to such an extent and thus might be acceptable to replace liver biopsy.

Using Rapid Indicators for Enterococcus to Assess the Risk of Illness after Exposure to Urban Runoff Contaminated Marine Water

PubMed Central

Colford, John M.; Schiff, Kenneth C.; Griffith, John F.; Yau, Vince; Arnold, Benjamin F.; Wright, Catherine C.; Gruber, Joshua S.; Wade, Timothy J.; Burns, Susan; Hayes, Jacqueline; McGee, Charles; Gold, Mark; Cao, Yiping; Noble, Rachel T.; Haugland, Richard; Weisberg, Stephen B.

2012-01-01

Background Traditional fecal indicator bacteria (FIB) measurement is too slow (>18 hr) for timely swimmer warnings. Objectives Assess relationship of rapid indicator methods (qPCR) to illness at a marine-beach impacted by urban-runoff. Methods We measured baseline and two-week health in 9525 individuals visiting Doheny Beach 2007-08. Illness rates were compared (swimmers vs. non-swimmers). FIB measured by traditional (Enterococcus spp. by EPA Method 1600 or Enterolert™, fecal coliforms, total coliforms) and three rapid qPCR assays for Enterococcus spp. (Taqman, Scorpion-1, Scorpion-2) were compared to health. Primary bacterial source was a creek flowing untreated into ocean; the creek did not reach the ocean when a sand berm formed. This provided a natural experiment for examining FIB-health relationships under varying conditions. Results We observed significant increases in diarrhea (OR1.90, 95% CI 1.29-2.80 for swallowing water) and other outcomes in swimmers compared to non-swimmers. Exposure (body immersion, head immersion, swallowed water) was associated with increasing risk of gastrointestinal illness (GI). Daily GI incidence patterns were different: swimmers (2-day peak ) and non-swimmers (no peak). With berm-open, we observed associations between GI and traditional and rapid methods for Enterococcus; fewer associations occurred when berm status was not considered. Conclusions We found increased risk of GI at this urban-runoff beach. When FIB source flowed freely (berm-open), several traditional and rapid indicators were related to illness. When FIB source was weak (berm-closed) fewer illness-associations were seen. These different relationships under different conditions at a single beach demonstrate the difficulties using these indicators to predict health risk. PMID:22356828

Grazing Incidence Cross-Sectioning of Thin-Film Solar Cells via Cryogenic Focused Ion Beam: A Case Study on CIGSe

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

Sardashti, Kasra; Haight, Richard; Anderson, Ryan

2016-06-22

Cryogenic focused ion beam (Cryo-FIB) milling at near-grazing angles is employed to fabricate cross-sections on thin Cu(In,Ga)Se2 with >8x expansion in thickness. Kelvin probe force microscopy (KPFM) on sloped cross sections showed reduction in grain boundaries potential deeper into the film. Cryo Fib-KPFM enabled the first determination of the electronic structure of the Mo/CIGSe back contact, where a sub 100 nm thick MoSey assists hole extraction due to 45 meV higher work function. This demonstrates that CryoFIB-KPFM combination can reveal new targets of opportunity for improvement in thin-films photovoltaics such as high-work-function contacts to facilitate hole extraction through the backmore » interface of CIGS.« less

An AFM-SIMS Nano Tomography Acquisition System

NASA Astrophysics Data System (ADS)

Swinford, Richard William

An instrument, adding the capability to measure 3D volumetric chemical composition, has been constructed by me as a member of the Sanchez Nano Laboratory. The laboratory's in situ atomic force microscope (AFM) and secondary ion mass spectrometry systems (SIMS) are functional and integrated as one instrument. The SIMS utilizes a Ga focused ion beam (FIB) combined with a quadrupole mass analyzer. The AFM is comprised of a 6-axis stage, three coarse axes and three fine. The coarse stage is used for placing the AFM tip anywhere inside a (13x13x5 mm3) (xyz) volume. Thus the tip can be moved in and out of the FIB processing region with ease. The planned range for the Z-axis piezo was 60 microm, but was reduced after it was damaged from arc events. The repaired Z-axis piezo is now operated at a smaller nominal range of 18 microm (16.7 microm after pre-loading), still quite respectable for an AFM. The noise floor of the AFM is approximately 0.4 nm Rq. The voxel size for the combined instrument is targeted at 50 nm or larger. Thus 0.4 nm of xyz uncertainty is acceptable. The instrument has been used for analyzing samples using FIB beam currents of 250 pA and 5.75 nA. Coarse tip approaches can take a long time so an abbreviated technique is employed. Because of the relatively long thro of the Z piezo, the tip can be disengaged by deactivating the servo PID. Once disengaged, it can be moved laterally out of the way of the FIB-SIMS using the coarse stage. This instrument has been used to acquire volumetric data on AlTiC using AFM tip diameters of 18.9 nm and 30.6 nm. Acquisition times are very long, requiring multiple days to acquire a 50-image stack. New features to be added include auto stigmation, auto beam shift, more software automation, etc. Longer term upgrades to include a new lower voltage Z-piezo with strain-gauge feedback and a new design to extend the life for the coarse XY nano-positioners. This AFM-SIMS instrument, as constructed, has proven to be a great proof of concept vehicle. In the future it will be used to analyze micro fossils and it will also be used as a part of an intensive teaching curriculum.

Exploring Cryogenic Focused Ion Beam Milling as a Group III-V Device Fabrication Tool

DTIC Science & Technology

2013-09-01

boiling, triple , and critical points of the elements” in CRC Handbook of Chemistry and Physics, 92nd ed., Boca Raton, FL: CRC press, 2011-2012, p. 4...The most widely used ion source in FIB instruments is a gallium (Ga) liquid metal ion source (LMIS) [4]. Gallium is attractive as an ion source...Figure 3b. EDS spectra were captured at different points across the patterned region of the room temperature milled sample, as indicated in Figure 4

Differential Decay of Enterococci and Escherichia coli Originating from Two Fecal Pollution Sources

PubMed Central

Harwood, Valerie J.; Shanks, Orin C.; Fout, G. Shay; Ashbolt, Nicholas J.

2013-01-01

Using in situ subtropical aquatic mesocosms, fecal source (cattle manure versus sewage) was shown to be the most important contributor to differential loss in viability of fecal indicator bacteria (FIB), specifically enterococci in freshwater and Escherichia coli in marine habitats. In this study, sunlight exposure and indigenous aquatic microbiota were also important contributors, whose effects on FIB also differed between water types. PMID:23377944

Rapid Focused Ion Beam Milling Based Fabrication of Plasmonic Nanoparticles and Assemblies via "Sketch and Peel" Strategy.

PubMed

Chen, Yiqin; Bi, Kaixi; Wang, Qianjin; Zheng, Mengjie; Liu, Qing; Han, Yunxin; Yang, Junbo; Chang, Shengli; Zhang, Guanhua; Duan, Huigao

2016-12-27

Focused ion beam (FIB) milling is a versatile maskless and resistless patterning technique and has been widely used for the fabrication of inverse plasmonic structures such as nanoholes and nanoslits for various applications. However, due to its subtractive milling nature, it is an impractical method to fabricate isolated plasmonic nanoparticles and assemblies which are more commonly adopted in applications. In this work, we propose and demonstrate an approach to reliably and rapidly define plasmonic nanoparticles and their assemblies using FIB milling via a simple "sketch and peel" strategy. Systematic experimental investigations and mechanism studies reveal that the high reliability of this fabrication approach is enabled by a conformally formed sidewall coating due to the ion-milling-induced redeposition. Particularly, we demonstrated that this strategy is also applicable to the state-of-the-art helium ion beam milling technology, with which high-fidelity plasmonic dimers with tiny gaps could be directly and rapidly prototyped. Because the proposed approach enables rapid and reliable patterning of arbitrary plasmonic nanostructures that are not feasible to fabricate via conventional FIB milling process, our work provides the FIB milling technology an additional nanopatterning capability and thus could greatly increase its popularity for utilization in fundamental research and device prototyping.

Differences in end-point force trajectories elicited by electrical stimulation of individual human calf muscles

PubMed Central

Giordano, S B; Segal, R L; Abelew, T A

2009-01-01

The purpose of this study was to investigate the end-point force trajectories of the fibularis longus (FIB), lateral gastrocnemius (LG) and medial gastrocnemius (MG) muscles. Most information about individual muscle function has come from studies which use models based on electromyographic (EMG) recordings. In this study (N=20 subjects) we used electrical stimulation (20Hz) to elicit activity in individual muscles, recorded the end-point forces at the foot and verified the selectivity of stimulation by using magnetic resonance imaging. Unexpectedly, no significant differences were found between LG and MG force directions. Stimulation of LG and MG resulted in downward and medial or lateral forces depending on the subject. We found FIB end-point forces to be significantly different than those of LG and MG. In all subjects, stimulation of FIB resulted in downward and lateral forces. Based on our results, we suggest that there are multiple factors determining when and whether LG or MG will produce a medial or lateral force and FIB consistently plays a significant role in eversion/abduction and plantarflexion. We suggest that the inter-subject variability we found is not simply an artifact of experimental or technical error but is functionally relevant and should be addressed in future studies and models. PMID:20095454

FIB-SEM tomography of human skin telocytes and their extracellular vesicles

PubMed Central

Cretoiu, Dragos; Gherghiceanu, Mihaela; Hummel, Eric; Zimmermann, Hans; Simionescu, Olga; Popescu, Laurentiu M

2015-01-01

We have shown in 2012 the existence of telocytes (TCs) in human dermis. TCs were described by transmission electron microscopy (TEM) as interstitial cells located in non-epithelial spaces (stroma) of many organs (see www.telocytes.com). TCs have very long prolongations (tens to hundreds micrometers) named Telopodes (Tps). These Tps have a special conformation with dilated portions named podoms (containing mitochondria, endoplasmic reticulum and caveolae) and very thin segments (below resolving power of light microscopy), called podomers. To show the real 3D architecture of TC network, we used the most advanced available electron microscope technology: focused ion beam scanning electron microscopy (FIB-SEM) tomography. Generally, 3D reconstruction of dermal TCs by FIB-SEM tomography revealed the existence of Tps with various conformations: (i) long, flattened irregular veils (ribbon-like segments) with knobs, corresponding to podoms, and (ii) tubular structures (podomers) with uneven calibre because of irregular dilations (knobs) – the podoms. FIB-SEM tomography also showed numerous extracellular vesicles (diameter 438.6 ± 149.1 nm, n = 30) released by a human dermal TC. Our data might be useful for understanding the role(s) of TCs in intercellular signalling and communication, as well as for comprehension of pathologies like scleroderma, multiple sclerosis, psoriasis, etc. PMID:25823591

Nitrogen Gas Field Ion Source (GFIS) Focused Ion Beam (FIB) Secondary Electron Imaging: A First Look.

PubMed

Schmidt, Marek E; Yasaka, Anto; Akabori, Masashi; Mizuta, Hiroshi

2017-08-01

The recent technological advance of the gas field ion source (GFIS) and its successful integration into systems has renewed the interest in the focused ion beam (FIB) technology. Due to the atomically small source size and the use of light ions, the limitations of the liquid metal ion source are solved as device dimensions are pushed further towards the single-digit nanometer size. Helium and neon ions are the most widely used, but a large portfolio of available ion species is desirable, to allow a wide range of applications. Among argon and hydrogen, $${\\rm N}_{2}^{{\\plus}} $$ ions offer unique characteristics due to their covalent bond and their use as dopant for various carbon-based materials including diamond. Here, we provide a first look at the $${\\rm N}_{2}^{{\\plus}} $$ GFIS-FIB enabled imaging of a large selection of microscopic structures, including gold on carbon test specimen, thin metal films on insulator and nanostructured carbon-based devices, which are among the most actively researched materials in the field of nanoelectronics. The results are compared with images acquired by He+ ions, and we show that $${\\rm N}_{2}^{{\\plus}} $$ GFIS-FIB can offer improved material contrast even at very low imaging dose and is more sensitive to the surface roughness.

Titanium dioxide nanoparticles relieve silk gland damage and increase cocooning of Bombyx mori under phoxim-induced toxicity.

PubMed

Li, Bing; Yu, Xiaohong; Gui, Suxin; Xie, Yi; Hong, Jie; Zhao, Xiaoyang; Sheng, Lei; Sang, Xuezi; Sun, Qingqing; Wang, Ling; Shen, Weide; Hong, Fashui

2013-12-18

Organophosphate pesticides are applied widely in the world for agricultural purposes, and their exposures often resulted in non-cocooning of Bombyx mori in China. TiO2 nanoparticles have been demonstrated to increase pesticide resistance of Bombyx mori. While the toxicity of phoxim is well-documented, very limited information exists on the mechanisms of TiO2 nanoparticles improving the cocooning function of Bombyx mori following exposure to phoxim. The present study was, therefore, undertaken to determine whether TiO2 nanoparticles attenuate silk gland injury and elevate cocooning of B. mori following exposure to phoxim. The findings suggested that phoxim exposure resulted in severe damages of the silk gland structure and significantly decreased the cocooning in the silk gland of Bombyx mori. Furthermore, phoxim exposure significantly resulted in reductions of total protein concentrations and suppressed expressions of silk protein synthesis-related genes, including Fib-L, Fib-H, P25, Ser-2, and Ser-3, in the silk gland. TiO2 nanoparticle pretreatment, however, could significantly relieve silk gland injury of Bombyx mori. Importantly, TiO2 nanoparticles could remarkably elevate cocooning and total protein contents and promote expressions of Fib-L, Fib-H, P25, Ser-2, and Ser-3 in the silk gland following exposure to phoxim.

Tin Whisker Electrical Short Circuit Characteristics. Part 2

NASA Technical Reports Server (NTRS)

Courey, Karim J.; Asfour, Shihab S.; Onar, Arzu; Bayliss, Jon A.; Ludwig, Lawrence L.; Wright, Maria C.

2009-01-01

Existing risk simulations make the assumption that when a free tin whisker has bridged two adjacent exposed electrical conductors, the result is an electrical short circuit. This conservative assumption is made because shorting is a random event that has an unknown probability associated with it. Note however that due to contact resistance electrical shorts may not occur at lower voltage levels. In our first article we developed an empirical probability model for tin whisker shorting. In this paper, we develop a more comprehensive empirical model using a refined experiment with a larger sample size, in which we studied the effect of varying voltage on the breakdown of the contact resistance which leads to a short circuit. From the resulting data we estimated the probability distribution of an electrical short, as a function of voltage. In addition, the unexpected polycrystalline structure seen in the focused ion beam (FIB) cross section in the first experiment was confirmed in this experiment using transmission electron microscopy (TEM). The FIB was also used to cross section two card guides to facilitate the measurement of the grain size of each card guide's tin plating to determine its finish.

Sodium citrate vacuum tubes validation: preventing preanalytical variability in routine coagulation testing.

PubMed

Lima-Oliveira, Gabriel; Lippi, Giuseppe; Salvagno, Gian Luca; Montagnana, Martina; Picheth, Geraldo; Guidi, Gian Cesare

2013-04-01

Sometimes in-vitro diagnostic devices (e.g. blood collection tubes) are not validated before use or when the producer's brand is changed. The aim of this study was to validate five brands of sodium citrate vacuum tubes. Blood specimens from 50 volunteers were collected in five different tube brands (I: Venosafe, II: VACUETTE, III: BD Vacutainer, IV: LABOR IMPORT and V: S-Monovette). Routine coagulation tests [activated partial thromboplastin time (aPTT), prothrombin time (PT), and fibrinogen (FIB)] were performed on ACL TOP instrument using HemosIL reagents. The significance of the differences between samples was assessed by paired Student's t-test, set at P < 0.005. Significant differences were observed for: PT when comparing I vs. II, I vs. III, I vs. V, II vs. III, II vs. IV, II vs. V, III vs. IV, III vs. V and IV vs. V; aPTT when comparing I vs. II, I vs. III, I vs. IV, II vs. IV, III vs. IV and IV vs. V. No differences were observed among brands for FIB determination. We suggest that every laboratory management should both standardize the procedures and frequently evaluate the quality of in-vitro diagnostic devices.

Nanoscale Origins of the Size Effect in the Compression Response of Single Crystal Ni-Base Superalloy Micro-Pillars

PubMed Central

Ying, Siqi; Ma, Lifeng; Papadaki, Chrysanthi; Romano Brandt, Leon; Zhang, Hongjia

2018-01-01

Nickel superalloys play a pivotal role in enabling power-generation devices on land, sea, and in the air. They derive their strength from coherent cuboidal precipitates of the ordered γ’ phase that is different from the γ matrix in composition, structure and properties. In order to reveal the correlation between elemental distribution, dislocation glide and the plastic deformation of micro- and nano-sized volumes of a nickel superalloy, a combined in situ nanoindentation compression study was carried out with a scanning electron microscope (SEM) on micro- and nano-pillars fabricated by focused ion beam (FIB) milling of Ni-base superalloy CMSX4. The observed mechanical response (hardening followed by softening) was correlated with the progression of crystal slip that was revealed using FIB nano-tomography and energy-dispersive spectroscopy (EDS) elemental mapping. A hypothesis was put forward that the dependence of material strength on the size of the sample (micropillar diameter) is correlated with the characteristic dimension of the structural units (γ’ precipitates). By proposing two new dislocation-based models, the results were found to be described well by a new parameter-free Hall–Petch equation. PMID:29621189

Characterization and extraction of the synaptic apposition surface for synaptic geometry analysis

PubMed Central

Morales, Juan; Rodríguez, Angel; Rodríguez, José-Rodrigo; DeFelipe, Javier; Merchán-Pérez, Angel

2013-01-01

Geometrical features of chemical synapses are relevant to their function. Two critical components of the synaptic junction are the active zone (AZ) and the postsynaptic density (PSD), as they are related to the probability of synaptic release and the number of postsynaptic receptors, respectively. Morphological studies of these structures are greatly facilitated by the use of recent electron microscopy techniques, such as combined focused ion beam milling and scanning electron microscopy (FIB/SEM), and software tools that permit reconstruction of large numbers of synapses in three dimensions. Since the AZ and the PSD are in close apposition and have a similar surface area, they can be represented by a single surface—the synaptic apposition surface (SAS). We have developed an efficient computational technique to automatically extract this surface from synaptic junctions that have previously been three-dimensionally reconstructed from actual tissue samples imaged by automated FIB/SEM. Given its relationship with the release probability and the number of postsynaptic receptors, the surface area of the SAS is a functionally relevant measure of the size of a synapse that can complement other geometrical features like the volume of the reconstructed synaptic junction, the equivalent ellipsoid size and the Feret's diameter. PMID:23847474

Thermal annealing behavior of hydrogen and surface topography of H 2 + ion implanted tungsten

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

Zhang, Jiandong; Jiang, Weilin; Zhu, Zihua

2018-01-25

Tungsten (W) has been proposed as a plasma-facing material (PFM) in fusion reactors due to its outstanding properties. Degradation of the material properties is expected to occur as a result of hydrogen (H) isotope permeation and trapping in W. In this study, two polycrystalline W plates were implanted with 80 keV H 2 + ions to a fluence of 2E21 H+/m2 at room temperature (RT). Time-of-flight secondary ion mass spectrometry (ToF-SIMS), focused ion beam (FIB) and scanning electron microscopy (SEM) were used for sample characterization. The SIMS data shows that H atoms are distributed well beyond the ion projected range.more » Isochronal annealing appears to suggest two H release stages that might be associated with the reported activation energies. H release at RT was observed between days 10 and 70 following ion implantation, and the level was maintained over the next 60 days. In addition, FIB/SEM results exhibit H2 blister formation near the surface of the as-implanted W. The blister distribution remains unchanged after thermal annealing up to 600 °C.« less

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

Xu, C. Shan; Hayworth, Kenneth J.; Lu, Zhiyuan

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 10 6 ?m 3 . These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processesmore » and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.« less

The Myxococcus xanthus Spore Cuticula Protein C Is a Fragment of FibA, an Extracellular Metalloprotease Produced Exclusively in Aggregated Cells

PubMed Central

Lee, Bongsoo; Mann, Petra; Grover, Vidhi; Treuner-Lange, Anke; Kahnt, Jörg; Higgs, Penelope I.

2011-01-01

Myxococcus xanthus is a soil bacterium with a complex life cycle involving distinct cell fates, including production of environmentally resistant spores to withstand periods of nutrient limitation. Spores are surrounded by an apparently self-assembling cuticula containing at least Proteins S and C; the gene encoding Protein C is unknown. During analyses of cell heterogeneity in M. xanthus, we observed that Protein C accumulated exclusively in cells found in aggregates. Using mass spectrometry analysis of Protein C either isolated from spore cuticula or immunoprecipitated from aggregated cells, we demonstrate that Protein C is actually a proteolytic fragment of the previously identified but functionally elusive zinc metalloprotease, FibA. Subpopulation specific FibA accumulation is not due to transcriptional regulation suggesting post-transcriptional regulation mechanisms mediate its heterogeneous accumulation patterns. PMID:22174937

Evaluating focused ion beam patterning for position-controlled nanowire growth using computer vision

NASA Astrophysics Data System (ADS)

Mosberg, A. B.; Myklebost, S.; Ren, D.; Weman, H.; Fimland, B. O.; van Helvoort, A. T. J.

2017-09-01

To efficiently evaluate the novel approach of focused ion beam (FIB) direct patterning of substrates for nanowire growth, a reference matrix of hole arrays has been used to study the effect of ion fluence and hole diameter on nanowire growth. Self-catalyzed GaAsSb nanowires were grown using molecular beam epitaxy and studied by scanning electron microscopy (SEM). To ensure an objective analysis, SEM images were analyzed with computer vision to automatically identify nanowires and characterize each array. It is shown that FIB milling parameters can be used to control the nanowire growth. Lower ion fluence and smaller diameter holes result in a higher yield (up to 83%) of single vertical nanowires, while higher fluence and hole diameter exhibit a regime of multiple nanowires. The catalyst size distribution and placement uniformity of vertical nanowires is best for low-value parameter combinations, indicating how to improve the FIB parameters for positioned-controlled nanowire growth.

Investigation of properties of nanobridge Josephson junctions and superconducting tracks fabricated by FIB

NASA Astrophysics Data System (ADS)

Li, B.; Godfrey, T.; Cox, D.; Li, T.; Gallop, J.; Galer, S.; Nisbet, A.; Romans, Ed; Hao, L.

2018-02-01

An important requirement across a range of sensitive detectors is to determine accurately the energy deposited by the impact of a particle in a small volume. The particle may be anything from a visible photon through to an X-ray or massive charged particle. We have been developing nanobridge Josephson junctions based SQUIDs and nanoSQUID devices covering the entire range of particle detection energies from 1eV to MeV. In this paper we discuss some developments in nanobridge Josephson junctions fabrication using focussed ion beam (FIB) and how these developments impact future applications. We focus on tuning of the transition temperature of a superconducting thin-film absorber, with the aim to match the absorber Tc to the working temperature range of the SQUID and also on using a new Xe FIB to improve Josephson junction and superconducting film quality.

Application of focused ion beam for the fabrication of AFM probes

NASA Astrophysics Data System (ADS)

Kolomiytsev, A. S.; Lisitsyn, S. A.; Smirnov, V. A.; Fedotov, A. A.; Varzarev, Yu N.

2017-10-01

The results of an experimental study of the probe tips fabrication for critical-dimension atomic force microscopy (CD-AFM) using the focused ion beam (FIB) induced deposition are presented. Methods of the FIB-induced deposition of tungsten and carbon onto the tip of an AFM probe are studied. Based on the results obtained in the study, probes for the CD-AFM technique with a tip height about 1 μm and radius of 20 nm were created. The formation of CD-AFM probes by FIB-induced deposition allows creating a high efficiency tool for nanotechnology and nanodiagnostics. The use of modified cantilevers allows minimizing the artefacts of AFM images and increasing the accuracy of the relief measurement. The obtained results can be used for fabrication of AFM probes for express monitoring of the technological process in the manufacturing of the elements for micro- and nanoelectronics.

Accuracy of transient elastography-FibroScan®, acoustic radiation force impulse (ARFI) imaging, the enhanced liver fibrosis (ELF) test, APRI, and the FIB-4 index compared with liver biopsy in patients with chronic hepatitis C.

PubMed

Ragazzo, Taisa Grotta; Paranagua-Vezozzo, Denise; Lima, Fabiana Roberto; de Campos Mazo, Daniel Ferraz; Pessoa, Mário Guimarães; Oliveira, Claudia Pinto; Alves, Venancio Avancini Ferreira; Carrilho, Flair José

2017-10-01

Although liver biopsy is the gold standard for determining the degree of liver fibrosis, issues regarding its invasiveness and the small amount of liver tissue evaluated can limit its applicability and interpretation in clinical practice. Non-invasive evaluation methods for liver fibrosis can address some of these limitations. The aim of this study was to evaluate the accuracy of transient elastography-FibroScan®, acoustic radiation force impulse (ARFI), enhanced liver fibrosis (ELF), the aspartate aminotransferase-to-platelet ratio index (APRI), and the FIB-4 index compared with liver biopsy in hepatitis C. We evaluated chronic hepatitis C patients who were followed at the Division of Clinical Gastroenterology and Hepatology, Hospital das Clínicas, Department of Gastroenterology of University of São Paulo School of Medicine, São Paulo, Brazil, and who underwent liver biopsy. The accuracy of each method was determined by a receiver operating characteristic (ROC) curve analysis, and fibrosis was classified as significant fibrosis (≥F2), advanced fibrosis (≥F3), or cirrhosis (F4). The Obuchowski method was also used to determine the diagnostic accuracy of each method at the various stages of fibrosis. In total, 107 FibroScan®, 51 ARFI, 68 ELF, 106 APRI, and 106 FIB-4 analyses were performed. A total of 107 patients were included in the study. The areas under the ROC curve (AUROCs) according to fibrosis degree were as follows: significant fibrosis (≥F2): FibroScan®: 0.83, FIB-4: 0.76, ELF: 0.70, APRI: 0.69, and ARFI: 0.67; advanced fibrosis (≥F3): FibroScan®: 0.85, ELF: 0.82, FIB-4: 0.77, ARFI: 0.74, and APRI: 0.71; and cirrhosis (F4): APRI: 1, FIB-4: 1, FibroScan®: 0.99, ARFI: 0.96, and ELF: 0.94. The accuracies of transient elastography, ARFI, ELF, APRI and FIB-4 determined by the Obuchowski method were F0-F1: 0.81, 0.78, 0.44, 0.72 and 0.67, respectively; F1-F2: 0.73, 0.53, 0.62, 0.60, and 0.68, respectively; F2-F3: 0.70, 0.64, 0.77, 0.60, and 0.67, respectively; and F3-F4: 0.98, 0.96, 0.82, 1, and 1, respectively. Transient elastography remained the most effective method for evaluating all degrees of fibrosis. The accuracy of all methodologies was best at F4.

Approaching isotropy in the vortex system of SmFeAs(O,F) at extreme magnetic fields

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

Moll, Philip J.W.; Zhidadlo, Nikolai D.; Karpinski, J.

2014-01-07

The role of anisotropy in the iron-pnictides is one of the key questions in understanding their high-temperature superconductivity. The inherent layeredness of these systems, consisting of FeAs layers separated by various layers, gives rise to an upper critical field anisotropy γ(T c) ~ 3 in the “122” system (i.e. (Ba,K)Fe 2As 2) and up to 6-8 in the “1111” system (i.e. SmFeAs(O,F)). In the “122” compounds, this anisotropy is known to decrease upon cooling, converging to almost isotropic superconductivity at lowest temperatures[1]. This can be understood through a particular temperature dependence of the inter- and intra-band scattering. The “1111” classmore » is naturally more anisotropic due to the thicker SmO blocking layer, and the much higher upper critical fields (H c2, HIIab(0)>>100T) cannot be reached at low temperature. Despite this challenging field requirement, the aim of this project is to discern whether this emergent isotropy in the “122” materials is a property of all FeAs classes. Focused Ion Beam (FIB) micromachined samples have in the past proven to be particularly well suited for pulsed magnetic fields[2]. Employing the micrometer precision of the FIB, we fabricated three individual samples on a 2x2 mm chip and thus maximized the acquired transport data per pulse.« less

The Effect of Microstructure On Transport Properties of Porous Electrodes

NASA Astrophysics Data System (ADS)

Peterson, Serena W.

The goal of this work is to further understand the relationships between porous electrode microstructure and mass transport properties. This understanding allows us to predict and improve cell performance from fundamental principles. The investigated battery systems are the widely used rechargeable Li-ion battery and the non-rechargeable alkaline battery. This work includes three main contributions in the battery field listed below. Direct Measurement of Effective Electronic Transport in Porous Li-ion Electrodes. An accurate assessment of the electronic conductivity of electrodes is necessary for understanding and optimizing battery performance. The bulk electronic conductivity of porous LiCoO2-based cathodes was measured as a function of porosity, pressure, carbon fraction, and the presence of an electrolyte. The measurements were performed by delamination of thin-film electrodes from their aluminum current collectors and by use of a four-line probe. Imaging and Correlating Microstructure To Conductivity. Transport properties of porous electrodes are strongly related to microstructure. An experimental 3D microstructure is needed not only for computation of direct transport properties, but also for a detailed electrode microstructure characterization. This work utilized X-ray tomography and focused ion beam (FIB)/scanning electron microscopy (SEM) to obtain the 3D structures of alkaline battery cathodes. FIB/SEM has the advantage of detecting carbon additives; thus, it was the main tomography tool employed. Additionally, protocols and techniques for acquiring, processing and segmenting series of FIB/SEM images were developed as part of this work. FIB/SEM images were also used to correlate electrodes' microstructure to their respective conductivities for both Li-ion and alkaline batteries. Electrode Microstructure Metrics and the 3D Stochastic Grid Model. A detailed characterization of microstructure was conducted in this work, including characterization of the volume fraction, nearest neighbor probability, domain size distribution, shape factor, and Fourier transform coefficient. These metrics are compared between 2D FIB/SEM, 3D FIB/SEM and X-ray structures. Among those metrics, the first three metrics are used as a basis for SG model parameterization. The 3D stochastic grid (SG) model is based on Monte Carlo techniques, in which a small set of fundamental inter-domain parameters are used to generate structures. This allows us to predict electrode microstructure and its effects on both electronic and ionic properties.

Semi-quantitative evaluation of fecal contamination potential by human and ruminant sources using multiple lines of evidence

USGS Publications Warehouse

Stoeckel, D.M.; Stelzer, E.A.; Stogner, R.W.; Mau, D.P.

2011-01-01

Protocols for microbial source tracking of fecal contamination generally are able to identify when a source of contamination is present, but thus far have been unable to evaluate what portion of fecal-indicator bacteria (FIB) came from various sources. A mathematical approach to estimate relative amounts of FIB, such as Escherichia coli, from various sources based on the concentration and distribution of microbial source tracking markers in feces was developed. The approach was tested using dilute fecal suspensions, then applied as part of an analytical suite to a contaminated headwater stream in the Rocky Mountains (Upper Fountain Creek, Colorado). In one single-source fecal suspension, a source that was not present could not be excluded because of incomplete marker specificity; however, human and ruminant sources were detected whenever they were present. In the mixed-feces suspension (pet and human), the minority contributor (human) was detected at a concentration low enough to preclude human contamination as the dominant source of E. coli to the sample. Without the semi-quantitative approach described, simple detects of human-associated marker in stream samples would have provided inaccurate evidence that human contamination was a major source of E. coli to the stream. In samples from Upper Fountain Creek the pattern of E. coli, general and host-associated microbial source tracking markers, nutrients, and wastewater-associated chemical detections-augmented with local observations and land-use patterns-indicated that, contrary to expectations, birds rather than humans or ruminants were the predominant source of fecal contamination to Upper Fountain Creek. This new approach to E. coli allocation, validated by a controlled study and tested by application in a relatively simple setting, represents a widely applicable step forward in the field of microbial source tracking of fecal contamination. ?? 2011 Elsevier Ltd.

Effects of hemolysis and lipemia interference on kaolin-activated thromboelastography, and comparison with conventional coagulation tests.

PubMed

Tang, Ning; Jin, Xi; Sun, Ziyong; Jian, Cui

2017-04-01

The effects of hemolysis and lipemia on thromboelastography (TEG) analysis have been scarcely evaluated in human samples, and neglected in clinical practice. We aimed to investigate the effects of in vitro mechanical hemolysis and lipemia on TEG analysis and conventional coagulation tests. Twenty-four healthy volunteers were enrolled in the study. Besides the controls, three groups with slight, moderate and severe mechanical hemolysis were constituted according to free hemoglobin (Hb) concentrations of 0.5-1.0, 2.0-6.0 and 7.0-13.0 g/L, respectively; and three groups with mild, moderate and high lipemia were established according to triglyceride concentrations of ∼6.0, ∼12.0, and ∼18.0 mmol/L, respectively. Four TEG parameters, reaction time (R), coagulation time (K), angle (α), and maximum amplitude (MA), were measured alongside conventional plasma tests including prothrombin time (PT), activated partial thromboplastin time (APTT) and fibrinogen (FIB) by mechanical method, and platelet count by optical method. Results showed that the median R and MA values at moderate and severe hemolysis and K at severe hemolysis exceeded respective reference intervals, and were considered unacceptable. Median values of TEG parameters in lipemic samples were all within reference intervals. Bias values of conventional plasma tests PT, APTT and FIB in hemolyzed or lipemic samples were all lower than the Clinical Laboratory Improvement Amendments (CLIA) allowable limits. Bias values of platelet count at moderate to severe hemolysis and lipemia exceeded the CLIA allowable limits. In conclusion, the detection of TEG was in general more affected by mechanical hemolysis than plasma coagulation tests. Pre-analytical variables should be taken into account when unexpected TEG results are obtained.

An Investigation of the Electrical Short Circuit Characteristics of Tin Whiskers

NASA Technical Reports Server (NTRS)

Courey, Karim J.

2008-01-01

In this experiment, an empirical model to quantify the probability of occurrence of an electrical short circuit from tin whiskers as a function of voltage was developed. This model can be used to improve existing risk simulation models FIB and TEM images of a tin whisker confirm the rare polycrystalline structure on one of the three whiskers studied. FIB cross-section of the card guides verified that the tin finish was bright tin.

Three-dimensional analysis of somatic mitochondrial dynamics in fission-deficient injured motor neurons using FIB/SEM.

PubMed

Tamada, Hiromi; Kiryu-Seo, Sumiko; Hosokawa, Hiroki; Ohta, Keisuke; Ishihara, Naotada; Nomura, Masatoshi; Mihara, Katsuyoshi; Nakamura, Kei-Ichiro; Kiyama, Hiroshi

2017-08-01

Mitochondria undergo morphological changes through fusion and fission for their quality control, which are vital for neuronal function. In this study, we examined three-dimensional morphologies of mitochondria in motor neurons under normal, nerve injured, and nerve injured plus fission-impaired conditions using the focused ion beam/scanning electron microscopy (FIB/SEM), because the FIB/SEM technology is a powerful tool to demonstrate both 3D images of whole organelle and the intra-organellar structure simultaneously. Crossing of dynamin-related protein 1 (Drp1) gene-floxed mice with neuronal injury-specific Cre driver mice, Atf3:BAC Tg mice, allowed for Drp1 ablation specifically in injured neurons. FIB/SEM analysis demonstrated that somatic mitochondrial morphologies in motor neurons were not altered before or after nerve injury. However, the fission impairment resulted in prominent somatic mitochondrial enlargement, which initially induced complex morphologies with round regions and long tubular processes, subsequently causing a decrease in the number of processes and further enlargement of the round regions, which eventually resulted in big spheroidal mitochondria without processes. The abnormal mitochondria exhibited several degradative morphologies: local or total cristae collapse, vacuolization, and mitophagy. These suggest that mitochondrial fission is crucial for maintaining mitochondrial integrity in injured motor neurons, and multiple forms of mitochondria degradation may accelerate neuronal degradation. © 2017 Wiley Periodicals, Inc.

Strategies for gallium removal after focused ion beam patterning of ferroelectric oxide nanostructures

NASA Astrophysics Data System (ADS)

Schilling, A.; Adams, T.; Bowman, R. M.; Gregg, J. M.

2007-01-01

As part of a study into the properties of ferroelectric single crystals at nanoscale dimensions, the effects that focused ion beam (FIB) processing can have, in terms of structural damage and ion implantation, on perovskite oxide materials has been examined, and a post-processing procedure developed to remove such effects. Single crystal material of the perovskite ferroelectric barium titanate (BaTiO3) has been patterned into thin film lamellae structures using a FIB microscope. Previous work had shown that FIB patterning induced gallium impregnation and associated creation of amorphous layers in a surface region of the single crystal material some 20 nm thick, but that both recrystallization and expulsion of gallium could be achieved through thermal annealing in air. Here we confirm this observation, but find that thermally induced gallium expulsion is associated with the formation of gallium-rich platelets on the surface of the annealed material. These platelets are thought to be gallium oxide. Etching using nitric and hydrochloric acids had no effect on the gallium-rich platelets. Effective platelet removal involved thermal annealing at 700 °C for 1 h in a vacuum followed by 1 h in oxygen, and then a post-annealing low-power plasma clean in an Ar/O atmosphere. Similar processing is likely to be necessary for the full recovery of post FIB-milled nanostructures in oxide ceramic systems in general.

Effects of Achilles tendon vibration, surface and visual conditions on lower leg electromyography in young adults with and without recurrent ankle sprains.

PubMed

Lubetzky, Anat V; Price, Robert; McCoy, Sarah W

2016-07-01

Functional ankle instability is associated with decreased ankle muscle function. Compliant surfaces and eyes-closed training are commonly used for rehabilitation and prevention of ankle sprains. Brief Achilles tendon vibration is commonly used in the study of postural control. To test the level of activation of tibialis anterior (TIB) and fibularis longus (FIB), bilateral Achilles tendon vibration was applied for the middle 20 s in a series of 60-s trials, when 10 healthy young adults and 10 adults with history of repeated ankle sprains were standing bipedal: on floor, on memory foam, or on a Both Sides Up (BOSU) ball, with eyes open, and on floor and foam with eyes closed. Differences in Integrated surface electromyography (IEMG) of TIB and FIB were significant for both groups pre, during, and post vibration (Friedman Tests, p < 0.001 for all). In both groups, the highest IEMG for TIB was obtained during vibration when standing on foam with eyes closed, whereas the highest IEMG for FIB was obtained during vibration when standing on the BOSU. Bipedal stance on BOSU and brief Achilles tendon vibration may be a useful intervention when a session's goal is to facilitate lower leg muscles activation. Future research should explore training effects as well as the effect of FIB tendon vibration. Copyright © 2016 Elsevier Ltd. All rights reserved.

FIB-SEM tomography of human skin telocytes and their extracellular vesicles.

PubMed

Cretoiu, Dragos; Gherghiceanu, Mihaela; Hummel, Eric; Zimmermann, Hans; Simionescu, Olga; Popescu, Laurentiu M

2015-04-01

We have shown in 2012 the existence of telocytes (TCs) in human dermis. TCs were described by transmission electron microscopy (TEM) as interstitial cells located in non-epithelial spaces (stroma) of many organs (see www.telocytes.com). TCs have very long prolongations (tens to hundreds micrometers) named Telopodes (Tps). These Tps have a special conformation with dilated portions named podoms (containing mitochondria, endoplasmic reticulum and caveolae) and very thin segments (below resolving power of light microscopy), called podomers. To show the real 3D architecture of TC network, we used the most advanced available electron microscope technology: focused ion beam scanning electron microscopy (FIB-SEM) tomography. Generally, 3D reconstruction of dermal TCs by FIB-SEM tomography revealed the existence of Tps with various conformations: (i) long, flattened irregular veils (ribbon-like segments) with knobs, corresponding to podoms, and (ii) tubular structures (podomers) with uneven calibre because of irregular dilations (knobs) - the podoms. FIB-SEM tomography also showed numerous extracellular vesicles (diameter 438.6 ± 149.1 nm, n = 30) released by a human dermal TC. Our data might be useful for understanding the role(s) of TCs in intercellular signalling and communication, as well as for comprehension of pathologies like scleroderma, multiple sclerosis, psoriasis, etc. © 2015 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Lack of segregation of a Marfan-like phenotype associating marfanoie habitus and mitral valve disease with fibrillin gene on chromosome 15

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

VanMaldergen, L.; Hilbert, P.; Gillerot, Y.

1994-09-01

Apart from typical Marfan syndrome (MS), several Marfan-like conditions are known. One of those is the MASS syndrome (Mitral involvement, Aortic dilatation, Skin and Skeletal abnormalities) defined by Pyeritz et al. Among these, a dominantly inherited mitral valve prolapse with marfanoid habitus have also been reported. Until now, except for a Marfan-like condition described by Boileau et al., all Marfan families are linked to fib 15. A large Belgian pedigree with 25 affected patients among 62 at risk subjects spanning four generations is described. A syndrome including marfanoid skeletal dysplasia (tall stature, dolichostenomelia, arachnodactyly, pectus carinatum joint dislocation), prolapse and/ormore » myxomatous degeneration of the mitral valve, but without aortic dilatation of eye involvement was observed. Although the phenotype fulfills Berlin diagnostic criteria for MS, it closely resembles MASS syndrome. Preliminary linkage results show discordance aggregation insertion in the fib 15 gene, as evaluated by intragenic microsatellite fib 15. Since Dietz et al. described a similar patient with fib 15 gene, we suggest that this variant of Marfan syndrome is genetically heterogeneous and caused by mutations, some of which are allelic to classical Marfan syndrome plus a subtype, some of which are not. Linkage studies are under way to further characterize the gene involved in the present family.« less

Fossilization of Iron-Oxidizing Bacteria at Hydrothermal Vents: a Useful Biosignature on Mars?

NASA Astrophysics Data System (ADS)

Leveille, R. J.; Lui, S.

2009-05-01

Iron oxidizing bacteria are ubiquitous in marine and terrestrial environments on Earth, where they often display distinctive cell morphologies and are commonly encrusted by minerals, especially bacteriogenic iron oxides and silica. Putative microfossils of iron oxidizing bacteria have been found in jaspers as old as 490Ma and microbial iron oxidation may be an ancient metabolic pathway. In order to investigate the usefulness of mineralized iron oxidizing bacteria as a biosignature, we have examined mineral samples collected from relict hydrothermal systems along Explorer Ridge, NE Pacific Ocean. In addition, microaerophilic, neutrophilic iron oxidizing bacteria, isolated from Pacific hydrothermal vents, were grown in a Fe-enriched seawater medium at constant pH (6.5) and oxygen concentration (5 percent) in a controlled bioreactor system. Both natural samples and experimental products were examined with a combination of variable pressure scanning electron microscopy (SEM), field emission gun SEM, and in some cases by preparing samples with a focused ion beam (FIB) milling system. Natural seafloor samples display abundant filamentous forms often resembling, in both size and shape, the twisted stalks of Gallionella and the elongated filaments of Leptothrix. Generally, these filamentous features are 1-5 microns in diameter and up to several microns in length. Some samples consist entirely of low- density, porous masses of silica encrusted filamentous forms. Presumably, these masses were formed by a rapid precipitation by the influx of silica-rich fluids into a microbial mat dominated by bacteria with filamentous morphologies. The presence of rare, amorphous (unmineralized) filamentous matter rich in C and Fe suggests that these bacteria were iron oxidizers. There is no evidence that sulfur oxidizers were present. Filamentous features sectioned by FIB milling show internal material within semi-hollow tubular-like features. Silica encrustations also show pseudo-concentric growth bands. In the bioreactor cultures, constant conditions led to abundant microbial growth and formation of an iron oxyhydroxide precipitate, either in direct association with the cells or within the growth medium. This suggests that not all of the iron precipitation is biogenic in origin. Cells typically show a filamentous morphology reminiscent of the mineral-encrusted forms observed in the natural samples. Continuing work includes high-resolution TEM observations of cultured organisms, examination of 2-year long in situ seafloor incubation experiments, and bioreactor silicification experiments in order to better understand the roles of iron and silica in the fossilization process. Microaerophilic iron oxidation could have existed on the early Earth in environments containing small amounts of oxygen produced either by locally concentrated photosynthetic microorganisms (e.g., cyanobacteria) or abiotically, as proposed for the subsurface of the Fe-dominated Rio Tinto (Spain) basin system. By analogy, similar subsurface or near-surface microaerophilic environments could have existed on Mars in the past. The distinctive morphologies and mineralization patterns of iron oxidizing bacteria could be a useful biosignature to search for on Mars. Deposits and biogenic features similar to those described here could theoretically be identified on Mars with existing imaging and analytical technologies. Therefore, future missions to Mars should target ancient hydrothermal systems, some of which have been putatively identified already.

X-ray Photoelectron Spectroscopy as a tool to investigate silane-based coatings for the protection of outdoor bronze: The role of alloying elements

NASA Astrophysics Data System (ADS)

Masi, G.; Balbo, A.; Esvan, J.; Monticelli, C.; Avila, J.; Robbiola, L.; Bernardi, E.; Bignozzi, M. C.; Asensio, M. C.; Martini, C.; Chiavari, C.

2018-03-01

Application of a protective coating is the most widely used conservation treatment for outdoor bronzes (cast Cu-Sn-Zn-Pb-Sb alloys). However, improving coating protectiveness requires detailed knowledge of the coating/substrate chemical bonding. This is particularly the case for 3-mercapto-propyl-trimethoxy-silane (PropS-SH) applied on bronze, exhibiting a good protective behaviour in outdoor simulated conditions. The present work deals with X-Ray Photoelectron Spectroscopy (XPS) and Electron Microscopy (FEG-SEM + FIB (Focused Ion Beam)) characterization of a thin PropS-SH film on bronze. In particular, in order to better understand the influence of alloying elements on coating performance, PropS-SH was studied first on pure Cu and Sn substrates then on bronzes with increasing alloy additions: Cu8Sn as well as a quinary Cu-Sn-Zn-Pb-Sb bronze. Moreover, considering the real application of this coating on historical bronze substrates, previously artificially aged ("patinated") bronze samples were prepared and a comparison between bare and "patinated" quinary bronzes was performed. In the case of coated quinary bronze, the free surface of samples was analysed by High Resolution Photoelectron Spectroscopy using Synchrotron Radiation (HR-SRPES) at ANTARES (Synchrotron SOLEIL), which offers a higher energy and lateral resolution. By compiling complementary spectroscopic and imaging information, a deeper insight into the interactions between the protective coating and the bronze substrate was achieved.

Controlled delivery of SDF-1α and IGF-1: CXCR4(+) cell recruitment and functional skeletal muscle recovery.

PubMed

Rybalko, Viktoriya Y; Pham, Chantal B; Hsieh, Pei-Ling; Hammers, David W; Merscham-Banda, Melissa; Suggs, Laura J; Farrar, Roger P

2015-11-01

Therapeutic delivery of regeneration-promoting biological factors directly to the site of injury has demonstrated its efficacy in various injury models. Several reports describe improved tissue regeneration following local injection of tissue specific growth factors, cytokines and chemokines. Evidence exists that combined cytokine/growth factor treatment is superior for optimizing tissue repair by targeting different aspects of the regeneration response. The purpose of this study was to evaluate the therapeutic potential of the controlled delivery of stromal cell-derived factor-1alpha (SDF-1α) alone or in combination with insulin-like growth factor-I (SDF-1α/IGF-I) for the treatment of tourniquet-induced ischemia/reperfusion injury (TK-I/R) of skeletal muscle. We hypothesized that SDF-1α will promote sustained stem cell recruitment to the site of muscle injury, while IGF-I will induce progenitor cell differentiation to effectively restore muscle contractile function after TK-I/R injury while concurrently reducing apoptosis. Utilizing a novel poly-ethylene glycol PEGylated fibrin gel matrix (PEG-Fib), we incorporated SDF-1α alone (PEG-Fib/SDF-1α) or in combination with IGF-I (PEG-Fib/SDF-1α/IGF-I) for controlled release at the site of acute muscle injury. Despite enhanced cell recruitment and revascularization of the regenerating muscle after SDF-1α treatment, functional analysis showed no benefit from PEG-Fib/SDF-1α therapy, while dual delivery of PEG-Fib/SDF-1α/IGF-I resulted in IGF-I-mediated improvement of maximal force recovery and SDF-1α-driven in vivo neovasculogenesis. Histological data supported functional data, as well as highlighted the important differences in the regeneration process among treatment groups. This study provides evidence that while revascularization may be necessary for maximizing muscle force recovery, without modulation of other effects of inflammation it is insufficient.

Albumin-to-fibrinogen ratio as a promising biomarker to predict clinical outcome of non-small cell lung cancer individuals.

PubMed

Li, Shu-Qi; Jiang, Yu-Huan; Lin, Jin; Zhang, Jing; Sun, Fan; Gao, Qiu-Fang; Zhang, Lei; Chen, Qing-Gen; Wang, Xiao-Zhong; Ying, Hou-Qun

2018-04-01

Chronic inflammation is one of the critical causes to promote the initiation and metastasis of solid malignancies including lung cancer (LC). Here, we aimed to investigate the prognostic roles of albumin (Alb)-to-fibrinogen (Fib) ratio (AFR), Fib and Alb in LC and to establish a novel effective nomogram combined with AFR. Four hundred twelve LC patients diagnosed between February 2005 and December 2014 were recruited in this prospective study. The prognostic roles of AFR, Fib, Alb, neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR) and monocyte-to-lymphocyte ratio (MLR) were identified by X-tile software, Kaplan-Meier curve, Cox regression model, and time-dependent ROC. Pretreatment high circulating Fib, low AFR, and Alb were significantly associated with increased risk of death for LC patients, especially for non-small cell lung cancer (NSCLC) patients in all stages. The area under curves (AUCs) of AFR, Fib, and NLR were higher than them within Alb and PLR for predicting the survival of NSCLC patients. Moreover, we found that clinical outcome of high AFR patient with chemo-radiotherapy was superior to low AFR patient; overall survival rate of stage II-III NSCLC patients undergoing chemo-radiotherapy was significantly lower than the surgical patients with treatment of adjuvant chemo-radiotherapy(P = 0.001) in low AFR subgroup. On the contrary, clinical outcome of the patients receiving chemo-radiotherapy was the same to the patients undergoing surgery and adjuvant chemo-radiotherapy (P = 0.405) in high AFR subgroup. In addition, c-index of predicted nomogram including AFR (0.717) for NSCLC patients with treatment of chemo-radiotherapy was higher than that without AFR (0.707). Our findings demonstrated that circulating pretreatment AFR might be a potential biomarker to predict clinical efficacy of surgical resection and adjuvant chemo-radiotherapy and be a prognostic biomarker for NSCLC individuals. © 2018 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

The combination of liver stiffness measurement and NAFLD fibrosis score improves the noninvasive diagnostic accuracy for severe liver fibrosis in patients with nonalcoholic fatty liver disease.

PubMed

Petta, Salvatore; Vanni, Ester; Bugianesi, Elisabetta; Di Marco, Vito; Cammà, Calogero; Cabibi, Daniela; Mezzabotta, Lavinia; Craxì, Antonio

2015-05-01

The accuracy of noninvasive tools for the diagnosis of severe fibrosis in patients with nonalcoholic fatty liver disease(NAFLD) in clinical practice is still limited. We aimed at assessing the diagnostic performance of combined noninvasive tools in two independent cohorts of Italian NAFLD patients. We analysed data from 321 Italian patients(179 Sicilian-training cohort, and 142 northern Italy-validation cohort) with an histological diagnosis of NAFLD. Severe fibrosis was defined as fibrosis ≥ F3 according to Kleiner classification. The APRI, AST/ALT, BARD, FIB-4, and NFS scores were calculated according to published algorithms. Liver stiffness measurement(LSM) was performed by FibroScan. Cut-off points of LSM, NFS and FIB-4 for rule-in or rule-out F3-F4 fibrosis were calculated by the reported formulas. In the Sicilian cohort AUCs of LSM, NFS, FIB-4, LSM plus NFS, LSM plus FIB-4, and NFS plus FIB-4 were 0.857, 0.803, 0.790, 0.878, 0.888 and 0.807, respectively, while in the northern Italy cohort the corresponding AUCs were 0.848, 0.730, 0.703, 0.844, 0.850, and 0.733 respectively. In the training cohort, the combination of LSM plus NFS was the best performing strategy, providing false positive, false negative and uncertainty area rates of 0%,1.1% and 48% respectively. Similar results were obtained in the validation cohort with false positive, false negative and uncertainty area rates of 0%,7.3% and 40.8%. The combination of LSM with NFS, two complementary, easy-to-perform, and widely available tools, is able to accurately diagnose or exclude the presence of severe liver fibrosis, also reducing of about 50-60% the number of needed diagnostic liver biopsies. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Coupling a continuous watershed-scale microbial fate and transport model with a stochastic dose-response model to estimate risk of illness in an urban watershed.

PubMed

Liao, Hehuan; Krometis, Leigh-Anne H; Kline, Karen

2016-05-01

Within the United States, elevated levels of fecal indicator bacteria (FIB) remain the leading cause of surface water-quality impairments requiring formal remediation plans under the federal Clean Water Act's Total Maximum Daily Load (TMDL) program. The sufficiency of compliance with numerical FIB criteria as the targeted endpoint of TMDL remediation plans may be questionable given poor correlations between FIB and pathogenic microorganisms and varying degrees of risk associated with exposure to different fecal pollution sources (e.g. human vs animal). The present study linked a watershed-scale FIB fate and transport model with a dose-response model to continuously predict human health risks via quantitative microbial risk assessment (QMRA), for comparison to regulatory benchmarks. This process permitted comparison of risks associated with different fecal pollution sources in an impaired urban watershed in order to identify remediation priorities. Results indicate that total human illness risks were consistently higher than the regulatory benchmark of 36 illnesses/1000 people for the study watershed, even when the predicted FIB levels were in compliance with the Escherichia coli geometric mean standard of 126CFU/100mL. Sanitary sewer overflows were associated with the greatest risk of illness. This is of particular concern, given increasing indications that sewer leakage is ubiquitous in urban areas, yet not typically fully accounted for during TMDL development. Uncertainty analysis suggested the accuracy of risk estimates would be improved by more detailed knowledge of site-specific pathogen presence and densities. While previous applications of the QMRA process to impaired waterways have mostly focused on single storm events or hypothetical situations, the continuous modeling framework presented in this study could be integrated into long-term water quality management planning, especially the United States' TMDL program, providing greater clarity to watershed stakeholders and decision-makers. Copyright © 2016 Elsevier B.V. All rights reserved.