bluuebunny/crossref_metadata_2025_split huggingface dataset:
Signal standardization of the secondary ion mass spectrometry (SIMS) microscope for quantification of halogens and calcium in biological applications
Authors: JEUSSET J. , STELLY N. , BRIANÇON C. , HALPERN S. , ROSHANI M. , FRAGU P. 
Published: August 2011

SummaryThe secondary ion mass spectrometry (SIMS) microscope is able to map chemical elements in tissue sections. Although absolute quantification of an element remains difficult, a relative quantitative approach is possible for soft tissue by using carbon (12C) as an internal reference present at large homogeneous and constant concentration in specimen and embedding resin. In this study, this approach is used to standardize the signal of an SIMS microscope for the quantification of halogens (19F—, 35Cl— and 79Br—) and calcium (40Ca+). Standard preparation was determined based on homogeneity and stability criteria by molecular incorporation (halogens) or mixing (calcium) in methacrylate resin. Standard measurements were performed by depth analysis on areas of 8 μm (halogens) and 150 μm (calcium) in diameter for 10–30 min, under Cs+ (halogens) or O2+ (calcium) bombardment. Results obtained from 100–120 measurements for each standard dilution show that the relationship between the signal intensity measured and the elemental concentration (μg/mg of wet tissue or mm) is linear in the range of biological concentrations. This quantitative approach was applied firstly to bromine of the 5‐bromo‐2′‐deoxyuridine (BrdU) used as nuclear marker of rat hepatocytes in proliferation. The second model concerns depletion of calcium concentration in cortical compartment in Paramecium tetraurelia during exocytosis. Then signal standardization in SIMS microscopy allows us to correlate quantitative results with those obtained from other methods.
Easily prepared holey films for use in cryo‐electron microscopy
Authors: JAHN W. 
Published: August 2011

SummaryHoley films or nets may be produced from an emulsion of glycerol/water in a solution of a mixture of Formvar® and Triafol® in dichloromethane, spread on mica. After being floated off the mica support the films may be treated with ethyl acetate to transform ‘pseudoholes' into holes or nets.
Observation by TEM of spontaneous alloying in nanometre‐sized atom clusters in the Au‐Al system
Authors: MORI H. , YASUDA H. 
Published: August 2011

SUMMARYCluster‐size dependence of alloying behaviour in nanometre‐sized atom clusters has been studied by transmission electron microscopy, using clusters in the Au‐Al system, which forms several intermetallic compounds in the phase diagram. In gold clusters of approximately 6–12 nm mean size, rapid dissolution of aluminium atoms took place and Au2Al or AuAl2 clusters were formed. When the size of gold clusters was increased to approximately 40 nm, no such rapid spontaneous alloying occurred. These observations suggest that there exists a critical size of initial gold clusters below which aluminide clusters are successfully formed by spontaneous alloying.
Quantification of the modulated structures in TiPdCr alloys
Authors: SCHWARTZ A. J. , PACIORNIK S. , KILAAS R. , TANNER L. E. 
Published: August 2011

SUMMARYTi50Pd(50‐x)Crxβ2 alloys (B2, CsCl‐type crystal structure) have been investigated as part of an overall study of the systematics of phase transformation behaviour and also for the commercial applicability of the shape memory effect at elevated temperatures. The phase transformations are unique in the sense that electron diffraction and high‐resolution transmission electron microscopy of Ti50Pd(50‐x)Crx alloys with x between 6 and 10 at.% reveal {110}B2 modulated structures with periodicities between 3 and 4·5 planes that vary linearly with composition. Satellites along certain <110>* lying at incommensurate positions are observed in electron diffraction patterns and are consistent with transverse lattice displacements. High‐resolution transmission electron microscopy (HRTEM) imaging usually reveals sinusoidal displacements; however, a few images appear ‘banded’ at three‐ and four‐plane intervals suggesting the possibility that three‐ and four‐plane commensurate packets combine to give the overall incommensurate satellite spacing. With the use of a newly developed technique for quantifying atomic displacements from HRTEM images, modulated phases in Ti50Pd43Cr7 and Ti50Pd42Cr8 alloys, where atoms are shifted from the cubic lattice sites by a transverse lattice displacement wave, have been studied. The real space displacements of the modulated structures were determined and compared to truly incommensurate and varying three‐ and four‐plane wave packet combinations by examination of the goodness of fit as assessed by the correlation coefficient for a least‐squares fit. In the cases of the Ti50Pd43Cr7 and Ti50Pd42Cr8 alloys, the incommensurate sine wave exhibited much better matching than the commensurate packets, indicating that these modulations are probably incommensurate.
New mechanism for field‐induced anisotropy of cobalt‐rich amorphous alloys
Authors: KIM C. K. , O'HANDLEY R. C. 
Published: August 2011

SUMMARYIt is generally assumed that amorphous magnetic alloys respond to field annealing by a process of local directional ordering which leaves the amorphous structure intact. We have made a comparative microstructural study of field‐annealed Co95‐xFe5(BSi)x amorphous alloys using transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) with thin sections parallel to the ribbon surface. Field annealing response was measured from anisotropy in low‐field hysteresis loops. These alloys show appreciable surface crystallization for annealing as much as 80 K below the bulk crystallization temperature. The surface crystallization proceeds by a known mechanism (selective oxidation) to which we have added a more detailed understanding. Three steps are involved: (1) formation of an amorphous borosilicate surface oxide layer during annealing; (2) depletion of glass stabilizing elements (boron and silicon) from the underlying amorphous metal substrate; (3) primary crystallization of the destabilized, metal‐enriched subsurface layer to an fee or hep cobalt‐rich phase. Striking differences in the microstructural morphology were revealed for different glass former ratios B/Si. For high B/Si ratios, the surface crystallites are predominantly fee Co and show a high density of oxygen faults. For low B/Si ratios, the surface crystallites are predominantly hep Co and almost free of faults. Response to field annealing is proportional to the B/Si ratio and correlates with the presence of oxygen faults in surface crystallites. Electron diffraction and microprobe analysis indicate that the surface oxide in silicon‐rich alloys is a dense silica glass which appears to be an effective diffusion barrier to oxygen. The surface oxide in boron‐rich alloys is a more porous oxide richer in B2O3. These observations appear to be related to those from perminvar alloys where oxygen was found to be necessary for field annealing to be effective.
Stimulated emission on microscopic scale: Light quenching of Pyridine 2 using a Ti:sapphire laser
Authors: HELL S. W. , SCHRADER M. , BAHLMANN K. , MEINECKE F. , LAKOWICZ J. R. , GRYCZYNSKI I. 
Published: August 2011

SummaryWe report the realization of stimulated emission on a microscopic scale. An experiment is presented describing significant depopulation of the excited state of the fluorophore Pyridine 2 with a mode‐locked Ti: Sapphire laser. Stimulated emission is performed at 750 nm and excitation at the frequency doubled wavelength of 375 nm. The pulses are synchronized so that the stimulating pulse follows the excitation pulse after 5 ps. The set‐up is a modified 4Pi‐confocal microscope employing one of the objective lenses for excitation and the opposing one for stimulated emission.
X‐ray microanalysis of ion distribution in frozen salt/dextran droplets after freeze‐substitution and embedding in anhydrous conditions
Authors: ORLOVICH D. A. , ASHFORD A. E. 
Published: August 2011

SummaryA model system using dextran droplets of different salt solutions either frozen together, or sandwiched together after freezing and then freeze‐substituted, embedded and dry sectioned has been investigated by X‐ray microanalysis. X‐ray maps and spot measur ements taken in transects through the interface of both droplets have shown that the P, K and Ca remain well localized in their original droplet. This validates freeze‐substitution as a method for localization of these elements in biological samples. Results with Na were more variable and not always explainable. Success was achieved by the use of super‐dry solvents and maintenance of a dry environment at all stages. We emphasize the need to avoid water contamination not only during freeze‐substitution but also during sectioning, storage and section transfer to the electron microscope.
Polarized light microscopy of weakly birefringent biological specimens
Authors: NEWTON R. H. , HAFFEGEE J. P. , HO M. W. 
Published: August 2011

SummaryA simple, but little known technique for producing marked colour contrast in images of weakly birefringent biological samples obtained with a polarized light microscope is investigated. The technique involves inserting a full wave plate at a small angle of horizontal rotation with respect to the analyser or polarizer, rather than at the conventional angle of 45° commonly employed in the field of mineralogy for examining strongly birefringent specimens. Inserting the full wave plate at a small angle (typically less than 10°) enhances the contrast between regions of tissue having different optical path differences and, in particular, different orientations of optic axes; improving the detection of structures of interest with the polarized light microscope.
Determination of localized diffusion coefficients in gels using confocal scanning laser microscopy
Authors: CUTTS L. S. , ROBERTS P. A. , ADLER J. , DAVIES M. C. , MELIA C. D. 
Published: August 2011

SummaryThe development of a photobleaching technique, CFMM (continuous fluorescence multipoint microphotolysis), to measur e diffusion coefficients in gel systems using a confocal scanning laser microscope is described. Diffusion coefficients (D) were determined for fluorescently labelled dextrans of varying molecular weight in agarose gels, and the results compared with two other methods. CFMM enabled diffusion coefficients to be rapidly determined from the profile across an irradiated area within a defined microscopic location of the gel. The technique was experimentally simple and produced values of D that corresponded well with classical double‐diffusion cell methods.
Stereo representation of atomic force micrographs: Optimizing the view
Authors: SHAO Z. , SOMLYO A. P. 
Published: August 2011

SummaryThe usefulness of stereographs for atomic force microscopy (AFM) is discussed and illustrated with AFM stereo images of biological macromolecules. The three‐dimensional nature of AFM data makes such display particularly appropriate, as it contains the information in an optimal format for creating stereographs suitable for direct evaluation by the human observer. We describe a simple procedure that employs standard functions in a commercial AFM for creating such stereographs.
Near‐atomic‐resolution EELS in silicon‐germanium alloys
Authors: BATSON P. E. 
Published: August 2011

SUMMARYRecent advances in instrumental capabilities now allow us to combine spatially resolved EELS with annular darkfield (ADF) imaging to relate the electronic or bonding behaviour of a small region to its atomic structure. Although still limited to projections of structures at the 0·2 nm level, the ADF imaging gives excellent information about the structure and composition of crystalline interfaces and defects. Spatially resolved EELS can then obtain the local bonding and electronic structure, with a similar spatial resolution. Using the silicon 2p core excitation as a probe of the conduction band density of states, it is possible to follow changes of these bands as a function of composition and defect structure in the Ge‐Si alloy system. Effects due to local strain are also observable.
Quantification of the EELS near‐edge structures to study Mn doping in oxides
Authors: BOTTON G. A. , APPEL C. C. , HORSEWELL A. , STOBBS W. M. 
Published: August 2011

SUMMARYThe L3 to L2 white‐line intensity ratios of Mn in solid solution in yttria‐stabilized zirconia and in Mn oxide standards are measured using different approaches. We show that the L3/L2 ratio alone cannot be used as a means of deducing the oxidation state and that a combined analysis of this ratio and the normalized white‐line intensity is required to retrieve the ionicity and magnetic state of the Mn dopant with respect to reference standards. Changes as a function of composition are measured and these are discussed in terms of variations in crystal field parameters associated with possible vacancy interaction. From the oxygen near‐edge structure we analyse the localization of the extra electron charge introduced by the dopant and discuss the possible effects of the association of this extra charge with oxygen vacancies in relation to the macroscopic ion conductivity.
Atomic‐resolution electron energy‐loss spectroscopy in the scanning transmission electron microscope
Authors: BROWNING N. D. , PENNYCOOK S. J. 
Published: August 2011

SUMMARYRecent developments in the dedicated scanning transmission electron microscope (STEM) now permit probe sizes of atomic dimensions to be obtained (0·22 nm FWHM at 100 kV). When coupled with an efficient parallel detector for electron energy‐loss spectroscopy (EELS), there now exists the potential to obtain EELS with atomic resolution. This potential is further enhanced by the Z‐contrast imaging technique in the STEM, which can produce incoherent, atomic‐resolution images of crystalline structures. The Z‐contrast image, being formed from only the high‐angle thermal diffuse scattering, can thus be acquired simultaneously with the energy‐loss spectrum and used to position the probe with atomic precision. However, to obtain an atomic‐resolution energy‐loss spectrum the range of the inelastic scattering must be less than the atomic spacing. Additionally, to enable a direct correlation between the spectrum and the Z‐contrast image, i.e. a description of the spatial resolution of the spectrum in terms of a convolution of a probe intensity profile and an object function, we need to determine the conditions for incoherent imaging with inelastically scattered electrons. In this paper, a theorem for the spatial resolution of the inelastic signal first proposed by Ritchie and Howie and a hydrogenic model for the object function developed by Maslen and Rossouw are combined to calculate the object functions for several characteristic K‐edges. More generally, the collection conditions, energy range and detectability for atomic‐resolution spectra are discussed. Finally, atomic‐resolution spectroscopy is demonstrated with a cobalt L‐edge profile of an atomically abrupt CoSi2/Si (111) interface.
Probing the local structure and bonding at interfaces and defects using EELS in the TEM
Authors: BRYDSON R. 
Published: August 2011

SUMMARYIn monolithic materials the presence of, and structure associated with, defects and grain boundaries often control the overall macroscopic properties of the bulk material. Similarly in composite materials the interfaces between the various constituents may also be property‐determining. Clearly it is desirable to be able to determine the structure and chemistry of such isolated, nonperiodic features using a spectroscopic technique capable of resolving chemical‐state information from areas of atomic dimensions. Electron energy‐loss spectroscopy (EELS) conducted in the (scanning) transmission electron microscope ((S)TEM) constitutes such a spatially resolved tool. When combined with atomic‐resolution imaging and appropriate surface‐sensitive spectroscopic techniques, important information about elemental distributions, local coordinations and valence states of atomic species at interfaces and defects may be derived. Examples drawn from studies of grain boundaries, interfaces in ceramic and metal matrix composites and investigations of defects in diamond are highlighted in order to illustrate this methodology.
Energy‐filtered Fresnel contrast analysis of Fe/Cu multilayers
Authors: DUNIN‐BORKOWSKI R. E. , BOOTHROYD C. B. , LLOYD S. J. , STOBBS W. M. 
Published: August 2011

SUMMARYEnergy‐filtered imaging in the transmission electron microscope is applied to the Fresnel contrast exhibited by a fine‐period Fe/Cu multilayer. Comparisons of filtered and unfiltered image series demonstrate the effects of inelastic scattering, and it is shown that the use of energy filtering allows improved confidence in the physical origins of the contrast for a specimen, such as that described, for which the structure is still uncertain.
Spatial resolution in EFTEM elemental maps
Authors: KRIVANEK O. L. , KUNDMANN M. K. , KIMOTO K. 
Published: August 2011

SUMMARYImaging filters developed over the last few years permit rapid elemental mapping by energy‐filtering transmission electron microscopy (EFTEM), with resolution and sensitivity limited primarily by the sample and by the TEM. We explore the attainable spatial resolution in the elemental maps theoretically and experimentally, and suggest optimized set‐up procedures for maximizing the resolution. The chromatic aberration of the objective lens of the microscope is shown to be a major limit. Its influence can be minimized by using small energy intervals and limited collection angles, but this is done at the cost of decreased collection efficiency. Resolution of better than 1 nm and sensitivities to less than a monolayer of elements with favourable edges are readily attainable in elemental maps obtained with acquisition times of 40 s total and less. Resolution better than 0·5 nm should be attainable with further optimization of the acquisition parameters.
Segregation‐induced hole drilling at grain boundaries
Authors: ÖZKAYA D. , YUAN J. , BROWN L. M. , FLEWITT P. E. J. 
Published: August 2011

SUMMARYGrain boundaries in metals provide preferential sites for impurity atoms to segregate, forming an area of the metal with different chemical and physical properties compared to the bulk. This also means that the electron beam damage characteristics of the grain boundary might be different from that of the bulk. Segregation can be expected to make grain boundaries particularly vulnerable to electron‐beaminduced hole drilling and beam damage, if the segregation produces a near two‐dimensional compound with increased ionicity. Here we report preferential hole drilling at grain boundaries in an Fe‐0–4 wt%P alloy. Such a phenomenon confirms evidence from energy‐loss spectroscopy that charge transfer occurs between P and Fe at the grain boundary. It also explains why it is easier to detect phosphorus using EDX compared to PEELS, and suggests that the electron beam damage may be a major limiting factor in grain‐boundary studies.
The Prion‐like Protein Doppel Enhances Ovine Spermatozoa Fertilizing Ability
Authors: Pimenta J , Dias FMV , Marques CC , Baptista MC , Vasques MI , Horta AEM , Barbas JP , Soares R , Mesquita P , Cabrita E , Fontes CMGA , Prates JA , Pereira RM 
Published: August 2011

ContentsThe function of prion‐like protein Doppel was suggested to be related to male fertility. In this study, the importance of ovine Doppel polypeptide on spermatozoa capacitation and fertilization was evaluated. After refolding, recombinant Doppel (rDpl) was supplemented with different concentrations (40, 80 or 190 ng/ml) to ovine spermatozoa during the capacitation process. In experiment 1, post‐thawed ovine spermatozoa were incubated with different concentrations of rDpl during 1 h for swim‐up, and changes in sperm motility, concentration, vigour, viability and capacitation were monitored (10 replicates). In experiment 2, the fertilization ability of post‐swim‐up spermatozoa incubated as above was tested through heterologous fertilization of bovinein vitromatured oocytes (n = 423, three replicates). Regardless of dosage, rDpl improved (p ≤ 0.03) spermatozoa viability. Sperm individual motility and vigour were the highest (p ≤ 0.04) for the group receiving 190 ng/ml rDpl. Sperm supplemented with the highest doses of rDpl achieved higher (p = 0.02) fertilization rates (56.0 ± 3.0%) than control (39.1 ± 2.2%) and 40 ng/ml rDpl (39.8 ± 2.7%). Preliminary data suggest that Doppel protein may enhancein vitrospermatozoa fertilizing ability.
Correlation between transient tachypnea of the newborn and wheezing attack
Authors: Çakan Mustafa , Nalbantoğlu Burçin , Nalbantoğlu Ayşin , Demırsoy Uğur , Say Aysu 
Published: August 2011

AbstractBackground:  Transient tachypnea of the newborn (TTN) is the most common cause of respiratory distress in newborns. Although associated with some morbidity, it is generally believed that once TTN resolves, there is no further increased risk for respiratory disease. However, in limited studies frequency of wheezing attacks is found to be increased in patients who had TTN diagnosis during the newborn period, in comparison to patients who had no respiratory problem. Thus, the question arises as to whether TTN is an innocent disease.Methods:  This study was done retrospectively. We recorded the demographic characteristics of 103 infants born between 17 October 2003 and 17 October 2004 at Zeynep Kamil Hospital and hospitalized because of TTN in the neonatal intensive care unit. In the second phase, we telephoned the parents of the 103 infants and asked about wheezing attacks. A total of 103 other infants, born during the same period, with no health problems during the newborn period, were included in the study as the control group and the same procedures were applied to them.Results:  The rate of wheezing attack among patients with TTN diagnosis was found to be significantly higher than that in patients who had no TTN diagnosis (P < 0.01). TTN was found to be an independent risk factor for wheezing attack (OR, 2.378; 95% CI, 1.20–4.70).Conclusion:  In conclusion, we established that TTN is an independent risk factor for wheezing. In addition we also hypothesized that genetic and environmental interactions synergistically predisposed these children for future wheezing.
Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea
Authors: Lloyd Karen G. , Alperin Marc J. , Teske Andreas 
Published: August 2011

SummaryUncultured ANaerobic MEthanotrophic (ANME) archaea are often assumed to be obligate methanotrophs that are incapable of net methanogenesis, and are therefore used as proxies for anaerobic methane oxidation in many environments in spite of uncertainty regarding their metabolic capabilities. Anaerobic methane oxidation regulates methane emissions in marine sediments and appears to occur through a reversal of a methane‐producing metabolism. We tested the assumption that ANME are obligate methanotrophs by detecting and quantifying gene transcription of ANME‐1 across zones of methane oxidation versus methane production in sediments from the White Oak River estuary, North Carolina. ANME‐1 consistently transcribe 16S rRNA and mRNA of methyl coenzyme M reductase (mcrA), the key gene for methanogenesis, up to 45 cm into methanogenic sediments. CARD‐FISH shows that ANME‐1 exist as single rod‐shaped cells or pairs of cells. Integrating normalized depth distributions of 16S rDNA and rRNA (measured with qPCR and RT‐qPCR respectively) shows that 26–77% of the rDNA (a proxy for ANME‐1 cell numbers), and 18–76% of the rRNA (a proxy for ANME‐1 activity) occurs within methane‐producing sediments. These results, along with a re‐assessment of the published Iiterature, change the perspective to ANME‐1 as methanogens that are also capable of methane oxidation.