bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental Electron Microscopy of Determining B. subtilis Alpha-Amylase Crystals
Authors: Zhang Jingqiang , Qiaozhen Ye , Xinying Lu , Suiwen Zhou , Jinxian Luo
Published: June 2020

The structure determination of unstained biological molecules by electron microscopy would be straightforward but for two factors: One is their high sensitivity to electron damage and the other is the loss of three-dimensional order that generally takes place when the specimen's natural aqueous environment is replaced by the high vacuum of the electron microscope. In order to surmounting these difficulties, following methods would be used: (i) Phase contrast; (ii) For vacuum preservation the aqueous medium is replaced by glucose; (iii) Low dose (le/Å2.S) electron microscopy is used to prevent specimen from electron damage. However, a low dose image will not display the projected structure of a molecule or unit cell directly, because contrast and S/N are very low. Nenertheless, provided that the object is comprised of a large enough number of unit cells and that the periodicities are precisely maintained, all the information need to reconstruct the “average” molecule or unit cell will be available by computer. In order to recontrast the object, one needs to determine the Fourier amplitude and phase for each reflection. Fourier analysis of the micrograph data provide the phase and the measurement of the electron diffraction pattern provide the amplitudes. In this paper an experimental method of determining molecular structure of B. subtilis alpha-amylase crystal is discussed.
Electron Microscopy of Alcohol Oxidase Crystals from Pichia Pastoris
Authors: Vonck Janet , van Bruggen Ernst F.J.
Published: June 2020

Several yeast species are able to grow on methanol. When they are grown in a methanol-restricted culture, their peroxisomes contain large crystalline inclusions, consisting of alcohol oxidase (AOX). A monomer of AOX has a molecular weight of ca. 74,000. Inside the peroxisome, AOX occurs as octamers.

Electron microscopic studies of AOX from Hansenula polymorpha have revealed that the eight subunits are slightly elongated and form two layers of four, which are twisted relative to each other. The molecule measures ca. 12 nm in all directions.

Recently, crystals suitable for x-ray diffraction have been formed of AOX from Pichia pastoris . The space group is P21, with unit cell dimensions a=157.3Å, b=171.45Å, c=231.6Å, β=94°. These dimensions indicate that the unit cell contains four octamers, too much to solve by x-ray crystallography alone. Therefore, we have started an EM study of the crystals, to get information about the organization of the molecules in the crystal lattice.
High-Resolution Cryo-Electron Microscopy of Biological Macromolecules
Authors: Fujiyoshi Yoshinori
Published: June 2020

The resolution of direct images of biological macromolecules is normally restricted to far less than 0.3 nm. This is not due instrumental resolution, but irradiation damage. The damage to biological macromolecules may expect to be reduced when they are cooled to a very low temperature. We started to develop a new cryo-stage for a high resolution electron microscopy in 1983, and successfully constructed a superfluid helium stage for a 400 kV microscope by 1986, whereby chlorinated copper-phthalocyanine could be photographed to a resolution of 0.26 nm at a stage temperature of 1.5 K. We are continuing to develop the cryo-microscope and have developed a cryo-microscope equipped with a superfluid helium stage and new cryo-transfer device.

The New cryo-microscope achieves not only improved resolution but also increased operational ease. The construction of the new super-fluid helium stage is shown in Fig. 1, where the cross sectional structure is shown parallel to an electron beam path. The capacities of LN2 tank, LHe tank and the pot are 1400 ml, 1200 ml and 3 ml, respectively. Their surfaces are placed with gold to minimize thermal radiation. Consumption rates of liquid nitrogen and liquid helium are 170 ml/hour and 140 ml/hour, respectively. The working time of this stage is more than 7 hours starting from full LN2 and LHe tanks. Instrumental resolution of our cryo-stage cooled to 4.2 K was confirmed to be 0.20 nm by an optical diffraction pattern from the image of a chlorinated copper-phthalocyanine crystal. The image and the optical diffraction pattern are shown in Fig. 2 a, b, respectively.
High Resolution Electron Microscopy in Organic Chemistry: 1-MEV Electron Microscope in Kyoto
Authors: Moriguchi Sakumi , Kurata Hiroki , Isoda Seiji , Kobayashi Takashi
Published: June 2020

Since the epock-making results of 1.5 Å point-to-point resolution obtained with the 500 kV HREM in Kyoto in 1978, we are convinced of the validty of the high voltage electron microscope for the high resolution. However, in order to attain the higher resolution of about 1.3 Å, which is required to resolve a carbon-carbon distance in an aromatic hydrocarbon, there remain so many problems to be solved. In 1990 a new 1 MeV microscope with twin-tank (JE0L-ARM1000) in top-entry type has been installed in Kyoto university aiming to achieve such high resolution.

The stability of high voltage is especially important for high resolution because the energy spread of the incident electron beam attenuates the phase transfer function and reduces the image contrast in higher spatial frequencies region. In order to suppress the high voltage fluctuation lower than 1 p. p. m. at 1 MeV and to monitor it, the twin-tank system is adopted, which has produced also satisfactory results in the previous high voltage electron microscopes in Kyoto. Fig. 1 shows the stability of the high tension measured at the top of the accerelating column of the new 1 MeV microscope. The fluctuation is evidently suppressed to less than 1 × 10-6 for five minutes long. The ripple monitored on a sincroscope is also less than 1 p.p.m. The chromatic abberation constant Cc is 3.6mm.
Computer-Assisted High-Re Solution TEM
Authors: Ponce F.A. , Hikashi H.
Published: June 2020

The determination of the atomic positions from HRTEM micrographs is only possible if the optical parameters are known to a certain accuracy, and reliable through-focus series are available to match the experimental images with calculated images of possible atomic models. The main limitation in interpreting images at the atomic level is the knowledge of the optical parameters such as beam alignment, astigmatism correction and defocus value. Under ordinary conditions, the uncertainty in these values is sufficiently large to prevent the accurate determination of the atomic positions. Therefore, in order to achieve the resolution power of the microscope (under 0.2nm) it is necessary to take extraordinary measures. The use of on line computers has been proposed [e.g.: 2-5] and used with certain amount of success.

We have built a system that can perform operations in the range of one frame stored and analyzed per second. A schematic diagram of the system is shown in figure 1. A JEOL 4000EX microscope equipped with an external computer interface is directly linked to a SUN-3 computer. All electrical parameters in the microscope can be changed via this interface by the use of a set of commands. The image is received from a video camera. A commercial image processor improves the signal-to-noise ratio by recursively averaging with a time constant, usually set at 0.25 sec. The computer software is based on a multi-window system and is entirely mouse-driven. All operations can be performed by clicking the mouse on the appropiate windows and buttons. This capability leads to extreme friendliness, ease of operation, and high operator speeds. Image analysis can be done in various ways. Here, we have measured the image contrast and used it to optimize certain parameters. The system is designed to have instant access to: (a) x- and y- alignment coils, (b) x- and y- astigmatism correction coils, and (c) objective lens current. The algorithm is shown in figure 2. Figure 3 shows an example taken from a thin CdTe crystal. The image contrast is displayed for changing objective lens current (defocus value). The display is calibrated in angstroms. Images are stored on the disk and are accessible by clicking the data points in the graph. Some of the frame-store images are displayed in Fig. 4.
Profile Imaging of Surfaces
Authors: Smith David J. , Lu Ping , McCartney M. R.
Published: June 2020

Profile imaging is a method whereby the atomic resolution capabilities of the modern electron microscope can be harnessed to provide direct information about the topography of particular types of surfaces. However, several prerequisites must be satisfied before the surface features visible in the profile image can be considered as genuinely representative of the specific material. The microscope must be properly adjusted (i.e. focus, alignment and astigmatism), the surface in profile must be thin (typically 100Å or less), and it should be free of contaminants or surface reaction products. In the absence of contamination or other amorphous specimen regions, however, correct operating conditions are difficult to establish. Moreover, it is not obvious that any surface reactions or reconstructions that occur along the thin profile edge of the sample are related to bulk surface morphology. Finally, facilities forin situsurface treatment must be considered as essential for materials with reactive surfaces. In this paper, recent progress in surface profile imaging is briefly reviewed, keeping in mind these diverse requirements. The possibility for dynamic image viewing and recording without loss of performance levels should also be appreciated.

OxidesClean fracture surfaces of many maximally valent oxides can be obtained by the simple expedient of crushing under a clean solvent with a mortar and pestle, and the ubiquitous holey carbon support film solves the problem of a means for microscope adjustment. Alternative techniques of specimen preparation such as ion-milling or chemical thinning may be required in order to obtain extended areas of a specific surface and orientation, but care is then required to avoid surface, or near-surface, modifications. Typical projected cation spacings in the major low-index zones are such that it is possible to resolve individual cation columns, and profile images such as the [001] SnO2 crystal shown in Fig. 1 clearly reveal the atomic (re-)arrangements at the surface. Several electron-beam-induced processes during extended observations of oxide surfaces have been documented. These include surface diffusion, as well as surface, and near-surface, reduction due to electron-stimulated desorption (ESD) of oxygen. In some maximally-valent transition metal oxides, the epitaxial development of a lower (metallic) oxide takes place, but a variety of end-products can in general be anticipated depending on such factors as the initial surface cleanliness, the residual microscope vacuum and the degree of covalency/ionicity of the original oxide.
UHV-Sem Observation of Si(111) Surface Partially Covered with Surface Structure Induced by Au or Ag
Authors: Endo Akira , Daimon Hiroshi , Ino Shozo
Published: June 2020

It is well known from LEED (low energy electron diffraction) and RHEED (reflection high energy electron diffraction) studies that when Au or Ag is deposited onto a clean Si (111) surface, many surface superstructures, for example 5×2-Au, √3 × √3-Ag etc. are formed depending upon the substrate temperatures and the coverages of the metals. Applying REM (reflection electron Microscopy) method. Osakabe et al. observed domains of these surface structures in real space, but detailed domain structures are not clear because the method cannot obtain high resolution due to the foreshortening effect. We have developed a SEM (scanning electron microscope) apparatus which have very high resolution and can be operated in UHV (ultra high vacuum). Using this UHV-SEM detecting the secondary electron, the clear domain structures of the two dimensional surface superstructures have been observed for the first time.

This UHV-SEM can obtain 2.2×l0-8 Pa by baking all parts related to the vacuum. The lattice image of Au(11O) has been clearly observed with STEM (scanning transmission electron microscope) mode, thus the resolution of 0.143 nm has been obtained. In the secondary electron imaging mode, the resolution of 0.5-0.7 nm has been obtained for the Au particles evaporated on a thin carbon film. This UHV-SEM apparatus has a sample preparation chamber equipped with a RHEED system and Au or Ag evaporation source, in which samples are cleaned, formed into the aimed structures and transferred into the UHV-SEM apparatus.
The Surface of α-Al2O3(0001) Studied with the REM Method
Authors: Kim Yootaek , Hsu Tung
Published: June 2020

Reflection electron microscopy (REM) and reflection high energy electron diffraction (RHEED) techniques[1] are applied to the study of single crystal α-Al203 surfaces [2,3,4,5] .

Specimens were prepared by polishing and 1400°C annealing in air and microscopy was done on a JEOL JEM-200CX and a Philips 400T microscopes operated at 100KV. Most of the REM images were recorded in the mutually perpendicular azimuths.

We found that the surface smoothness over a 1 mm2 specimen is not uniform. In some areas the surface steps follow the directions (Fig. 1a. The scale in this figure also applies to all other figures.) while in other areas the steps are continuously curved (Fig. lb). The steps have a rather wide range of heights, probably from one atomic layer to several nm. There is no definite evidence on the smallest steps being one atom high, we have observed steps terminating at a dislocation (Fig. 2) and the weak contrast indicates that the step is only one or two atoms high. But we cannot determine the projection of the Burger's vector in the surface normal [6]. Consequently, we cannot determine the exact height of the step.
Low-Profile Microchannel-Plate Electron Detector System for SEM
Authors: Postek Michael T. , Keery William J. , Frederick Nolan V.
Published: June 2020

One main impetus of present-day scanning electron microscopy is in the low accelerating voltage mode. This mode of operation is useful for nondestructive inspection especially in the on-line inspection and metrology of semiconductor samples. Today, the majority of the scanning electron microscopes used in nondestructive inspection utilize the standard Ever-hart/Thornley (E/T) detector or a modification of this detector as the main detection system. The E/T detector although extremely efficient, suffers from poor signal to noise ratio at low accelerating voltages. This type of detector also suffers from alignment difficulties especially where linewidth measurement for semiconductor applications is concerned because of the uneven distribution of the collection field which is possible, especially if the detector is not located in a plane of symmetry of the specimen and electron beam. These limitations and others have recently led investigators to reconsider the design of secondary electron detection systems especially for low accelerating voltage and metrological applications.

A unique situation developed at the National Institute of Standards and Technology (NIST) where a high efficiency electron detector with an exceptionally low profile was needed for the highly customized scanning electron microscope based metrology instrument under development. This instrument incorporates a large laser interferometer stage in the sample chamber which is used for traceability to the national length standard. The large interferometer stage and the restrictive size and shape of the specimen chamber required the development of a lower-profile electron detector than the standard E/T detector and one which does not interfere with the stage motions and interferometry. It was decided that, since the microchan-nel-plate-type electron detector fulfilled the fundamental requirements imposed by the space restrictions, and since this type of detector is also highly efficient at low accelerating voltages, this type of detector system would be used.
On the Correction Possibilities of the Topo and Compo Signals in SEM
Authors: Mulak Andrzej , Kaczmarek Danuta
Published: June 2020

The present paper deals solely BSE signals. Murata has determined approximately the angular BSE charakteristic by assuming scattering law of Rutherford, the Everhart’s model and the Thomson - Whidding-ton losses law. Then we have

For the sake of simplicity we assume a specimen the single - dimensioned topography of which changes solely in the scanning direction. Angular characteristic BSE in the system of primary beam is obtained from (l) by substitutingθ=θ' +αWhile scanning the specimen and taking into account of the Lambert law the current of detector of solid angle dΩ placed at angles θ and φ, takes the form
A Biological Cryosystem for the Scanning Electron Microscope
Authors: zhaohua Zhang , Dong Luo , Yisong Guo
Published: June 2020

Since early 1970's the use of cold stage on SEM for observation of hydrated samples in their natural state has become more and more popular despite its high cost. Experiences gained from earlier experiments indicate that a successful design should incorporate the

following features:

1. The specimen temperature should be below −135°C (the recrystallization point of water), lower the temperature, better the results.

2. The frozen specimen, the cold block in the specimen preparation chamber, as well as the cold stage should be kept under vacuum at all times to keep them frost free.

3. Different specimen preparation processes such as fracturing, coating and sublimation should be possible in one compact preparation chamber .
Accuracy of Stereoscopic Technique in S.E.M.
Authors: Wang D. , Feng Y. , Lu H.
Published: June 2020

The principle of 3-D reconstrution for SEM image is not so conplex, ie. the SEM image of polar project is treated with a rectangular coordinate, however,it accuracy is an attractatble topic.The accuracy of a stereopair is effected by following factors:

(1) Sample's position:

Image’s field depth of SEM is determined by
Development of a New Digital Fe SEM
Authors: Ohi M. , Harasawa K. , Niikura T. , Okazaki H. , Ishimori Y. , Miyokawa T. , Nakagawa S.
Published: June 2020

By combining a conical type field emission gun and an auto gain controlled noise cancelling system, we have developed three types of digital FESEMs equipped with a digital imaging processor and three different sized specimen chambers each with a stage.

It is known that when a cold field emission gun (C-FEG) with a W (310) single crystal tip is used at a vacuum pressure of 10-10 torr, the emission current constantly fluctuates by 5 to 10% due to the adsorbed gas, etc. on the tip surface.

Since the probe current in an FESEM equipped with this C-FEG fluctuates to the same extent, the noise caused by emission current fluctuation (emission noise) appears on secondary electron images (SEI) and backscattered electron images (BEI).

In order to eliminate emission noise, an aperture (noise cancelling aperture or N/C aperture) installed under the C-FEG detects emission current fluctuation and inputs it to the differential amplifier of the video amplifier system for SEI or BEI on conventional FESEMs.

With FESEMs, however, when the accelerating voltage is change in the range from 0.5 to 30 kV, the virtual source of an FEG using Butler type electrodes moves several tens of centimeters on the optical axis. Moreover, the probe current is changed from 10-13 to 10-10 A by changing the excitation current of the condenser lens. For these two reasons, there have been adopted such methods as installing an N/C aperture in two positions (under the C-FEG and at the objective lens aperture position) and controlling the amplifier value of the noise cancelling system and condenser lens excitation by ROM data.
The Advantages of Cryotechniques: Application To Bioluminescent Cells
Authors: Nicolas Gisèle , Bassot Jean-Marie , Nicolas Marie-Thérèse
Published: June 2020

The use of fast-freeze fixation (FFF) followed by freeze-substitution (FS) brings substantial advantages which are due to the extreme rapidity of this fixation compared to the conventional one. The initial step, FFF, physically immobilizes most molecules and therefore arrests the biological reactions in a matter of milliseconds. The second step, FS, slowly removes the water content still in solid state and, at the same time, chemically fixes the other cell components in absence of external water. This procedure results in an excellent preservation of the ultrastructure, avoids osmotic artifacts,maintains in situ most soluble substances and keeps up a number of cell activities including antigenicities. Another point of interest is that the rapidity of the initial immobilization enables the capture of unstable structures which, otherwise, would slip towards a more stable state. When combined with electrophysiology, this technique arrests the ultrastructural modifications at a well defined state, allowing a precise timing of the events.

We studied the epithelium of the elytra of the scale-worm, Harmothoe lunulata which has excitable, conductible and bioluminescent properties. The intracellular sites of the light emission are paracrystals of endoplasmic reticulum (PER), named photosomes (Fig.1). They are able to flash only when they are coupled with plasma membrane infoldings by dyadic or triadic junctions (Fig.2) basically similar to those of the striated muscle fibers. We have studied them before, during and after stimulation. FFF-FS showed that these complexes are labile structures able to diffentiate and dedifferentiate within milliseconds. Moreover, a transient network of endoplasmic reticulum was captured which we have named intermediate endoplasmic reticulum (IER) surrounding the PER (Fig.1). Numerous gap junctions are found in the membranous infoldings of the junctional complexes (Fig.3). When cryofractured, they cleave unusually (Fig.4-5). It is tempting to suggest that they play an important role in the conduction of the excitation.
On-the-Grid Processing and Time-Resolved Cryo-TEM: The Extension of the Thin Liquid Film Vitrification Method
Authors: Talmon Y. , Burns J. L. , Chestnut M. H. , Siegel D. P.
Published: June 2020

The thin vitrified liquid film technique was pioneered by Dubochet and co-workers. The technique is based on forming a thin liquid film of the system to be examined over a holey carbon film, and plunging it, using a mechanical plunger, into liquid ethane at its freezing point. Talmon and co-workers have developed the controlled environment vitrification system (CEVS), that makes it possible to prepare the sample under controlled conditions of temperature and saturation with volatiles. This has extended the applicability of the technique to labile systems that are sensitive to temperature and concentration changes, and to the study of microstructures that exist above (up to 95 °C), and below (down to −20 °C) room temperature. Here we discuss two extensions to cryo-TEM specimen preparation by thin fluid film vitrification, both based on specimen preparation in the CEVS: on-the-grid processing and time-resolved cryo-transmission electron microscopy.
Selection of Em Analysis Points Using the Euclidian Distance Map
Authors: Bright David S.
Published: June 2020

An image with morphological information, such as a backscatter electron image, can be acquired quickly to provide points for spectroscopic analyses that usually take more instrument time. It is desirable to have the analysis points be in the interior of the particles or objects of interest. The Euclidian distance map is applied directly to this problem to maximize the distance of the analysis sites from any part of the object perimeter.

The first step in using an electron image to select points for spectroscopic analysis is often to make a binary image of the original, in which picture elements (pixels) corresponding to particles, or the crystalline phase of interest, for example, are white, while all other pixels, corresponding to background, are black. The second step is to select analysis points for each particle or ‘blob’ (group of contiguous pixels) in the binary image. The centroid or center of area (at tips of arrows, Fig. 1) is used when one analysis point is desired and the blob is sufficiently convex or straight (upper left arrow, Fig. 1). However, if the blobs are curved or have indentations or holes, the centroid may actually lie in the background rather than in the area to be analyzed (middle and lower arrows, Fig. 1).
A Computer Graphic Method to Enhance the Display and Interpretation of Three-Dimensional Data
Authors: Dryden Kelly A.
Published: June 2020

Three-dimensional density information derived from electron micrographs may reveal complex structural features which are difficult to interpret from one or more two-dimensional views. Displaying a series of static views on a graphics device in quick succession provides an effective means to examine the structure dynamically and in a way which enhances the depth perception.

Digital images derived from three-dimensional models are transfered to the memory of a 1280x1024 resolution (8-bit pixel) color raster graphics device (Lexidata 3400, Adage Inc., Billerica, MA) and displayed on a 19 in. color monitor at a 25-30 Hz interlaced refresh rate. Individual pixels are displayed as one of 256 different colors or grey levels from a palette of up to 224—1 combinations. An entire series of images is loaded into the graphics memory in a sequential order, usually in rows. The displayed series is zoomed up to focus on a single frame and separate frames are displayed in appropriate sequence by panning to different regions of the graphics memory. The frequency at which each frame can be displayed is adjustable and only limited by the refresh rate of the monitor. Such dynamic image sequences can be photographed with a standard video camera and replayed on a television monitor with a video cassette recorder. The programs for displaying image data are written in FORTRAN and have been implemented on a VAX/VMS 8550 minicomputer (Digital Equipment Corp., Maynard, MA).
A Photoelectron Microscope for Applications in the Biological Sciences
Authors: Griffith O. Hayes , Rempfer Gertrude F. , Skoczylas Walter P.
Published: June 2020

A photoelectron microscope (photoemission electron microscope, PEM or PEEM) has been developed for the study of organic and biological surfaces. The basic experiment is illustrated in Figure 1A. The specimen is placed on a solid conductive surface, inserted in the PEM, and subjected to UV light (rather than an electron beam as in TEM or SEM). A simplified diagram of the PEM is shown in Figure 2B (note the specimen mount is inverted). The emitted electrons are accelerated by the electric field between the specimen (at -30 kV) and the anode (at ground potential). After passing through the anode aperture, the electrons are focused by electron lenses resembling those of a transmission electron microscope.

An engineering drawing of the instrument is shown in Figure 1C. It differs from the earlier metallurgical instruments in several respects. This is an oil-free ultra high vacuum instrument to minimize contamination of specimen surfaces. The objective, intermediate and projector lenses are unipotential electrostatic lenses, and are described elsewhere. The theoretical resolution limit of this instrument is on the order of 5 nm for representative energy current densities and energy distributions encountered with threshold illumination (i.e. Hg short arc lamps). The experimental resolution is presently within a factor of two of this figure. Additional improvements in resolution can, in principle, be made with a corrected electron optical system. Magnifications up to 250,000X have been recently achieved with this instrument in combination with an image processor.
Simulation and Contrast Analysis of tem Images of Cracks
Authors: Goyal D. , H. King A.
Published: June 2020

TEM images of cracks have been found to give rise to a moiré fringe type of contrast. It is apparent that the moire fringe contrast is observed because of the presence of a fault in a perfect crystal, and is characteristic of the fault geometry and the diffracting conditions in the TEM. Various studies have reported that the moire fringe contrast observed due to the presence of a crack in an otherwise perfect crystal is distinctive of the mode of crack. This paper describes a technique to study the geometry and mode of the cracks by comparing the images they produce in the TEM because of the effect that their displacement fields have on the diffraction of electrons by the crystal (containing a crack) with the corresponding theoretical images. In order to formulate a means of matching experimental images with theoretical ones, displacement fields of dislocations present (if any) in the vicinity of the crack are not considered, only the effect of the displacement field of the crack is considered.

The theoretical images are obtained using a computer program based on the two beam approximation of the dynamical theory of diffraction contrast for an imperfect crystal. The procedures for the determination of the various parameters involved in these computations have been well documented. There are three basic modes of crack. Preliminary studies were carried out considering the simplest form of crack geometries, i. e., mode I, II, III and the mixed modes, with orthogonal crack geometries. It was found that the contrast obtained from each mode is very distinct. The effect of variation of operating conditions such as diffracting vector (), the deviation parameter (ω), the electron beam direction () and the displacement vector were studied. It has been found that any small change in the above parameters can result in a drastic change in the contrast. The most important parameter for the matching of the theoretical and the experimental images was found to be the determination of the geometry of the crack under consideration. In order to be able to simulate the crack image shown in Figure 1, the crack geometry was modified from a orthogonal geometry to one with a crack tip inclined to the original crack front. The variation in the crack tip direction resulted in the variation of the displacement vector also. Figure 1 is a cross-sectional micrograph of a silicon wafer with a chromium film on top, showing a crack in the silicon.
Theoretical Study of Weak-Beam Images of Stacking Faults Decorated with Impurities
Authors: Anstis G. R.
Published: June 2020

Weak—beam dark—field images of stacking faults in silicon vary in an interesting way as the angle of inclination of a fault to the beam changes. It is observed that the contrast of images formed with beam +g varies with angle of inclination at a rate different from that associated with beam −g. For the case of an extrinsic fault it was found that this variation can be calculated using the kinematical theory of scattering and by modelling the fault as two discontinuous changes to the crystal potential across neighbouring (111) plane. Thus the weak—beam imaging technique is sensitive to some of the details of atomic arrangements near the fault. To explain the contrast variation of intrinsic faults it is necessary to model the smooth transition of the crystal potential from one side of the fault to the other. While such a model gives a qualitatative description of experimental studies it is not able to account for the large differences in contrast between +g images and −g images that have been observed experimentally. In this paper it is postulated that the presence of impurity atoms near the plane of the fault accounts for some of the features of experimental observations.

The theory is based on the kinematical theory of scattering and the rigid ion model of the crystal potential. A crystal containing a stacking fault consists of a unit which repeats indefinitely in directions parallel to the plane of the fault. Along a line perpendicular to the fault the repeat unit is displaced by a vector R across the plane of the fault. The impurity atoms are assumed to be distributed periodically on planes parallel to the fault.
Off-pump ascending aorta or aortic arch to descending aorta bypass with a pericardial roll for the treatment of critically ill infants with interrupted aortic arch
Authors: Oztas Didem M. , Meric Mert , Beyaz Metin O. , Coban Senay , Sari Gizem , Yildiz Yahya , Ulukan Mustafa O. , Unal Orcun , Rodoplu Orhan , Sungur Zerrin , Yozgat Yilmaz , Saritas Turkay , Erdem Abdullah , Ugurlucan Murat , Tireli Emin , Turkoglu Halil
Published: June 2020

Aim:

Standard surgical treatment of the interrupted aortic arch with the use of cardiopulmonary bypass is risky especially in critically ill babies. In this manuscript, we present the results of off-pump pericardial roll bypass for the treatment of aortic interruption.

Material and methods:

The technique was applied in nine critically ill infants between July 2011 and December 2019. Data were reviewed retrospectively. There were four girls and five boys. The types of the interruption were type B in six cases and type A in three babies. Additional cardiovascular anomalies were ventricular septal defect in all, atrial septal defect or patent foramen ovale in all, single-ventricle pathologies in two and bicuspid aortic valve in three cases. All the patients were in critical situations such as intubated, having symptoms of infection, congestive heart failure or ischaemia and malperfusion leading visceral organ dysfunction.

Results:

All patients underwent off-pump ascending aorta or aortic arch to descending aorta bypass with a pericardial roll. Post-operative early mortality occurred in one patient with severe mitral regurgitation due to cardio-septic shock. One patient who had single-ventricle pathology underwent bidirectional Glenn and was lost on the post-operative 26th day due to sepsis 2 years after operation. Two patients presented with dilatation of the pericardial tube 18 and 24 months after the operations and one underwent reconstruction of the neo-arch. The remaining patients are asymptomatic, active and within normal limits of body and mental growth.

Conclusion:

Treatment of interrupted aortic arch with a bypass with an autologous pericardial roll treated with gluteraldehyde without cardiopulmonary bypass seems a safe and reliable technique especially for the treatment of critically ill infants.
Flux Ropes Are Born in Pairs: An Outcome of Interlinked, Reconnecting Flux Tubes
Authors: Russell C. T. , Qi Yi
Published: June 2020

Flux transfer events are transient magnetized plasma structures that are self‐balancing, rope‐like phenomena that can appear at the Earth's magnetopause when the interplanetary magnetic field is southward. The formation of this type of flux rope has been unclear. Using measurements of particles and magnetic fields on the MMS spacecraft, we find that rope‐like structures containing magnetospheric energetic electrons have exactly the same occurrence rate as those without magnetospheric electrons, independent of solar wind properties and location of observation. This equality is consistent with a pair of flux bundles being generated at the same time but displaced from each other as an outcome of their collision and resultant entanglement and reconnection. This entanglement reconnection produces one flux rope with two ends connected to the magnetosphere and the other connected on both ends to the shocked solar wind. Away from the subsolar entanglement zone, reconnection transports magnetic flux from the “closed” magnetosphere to the “open” tail lobes, as predicted by Dungey (1961, https://doi.org/10.1103/PhysRevLett.6.47).
Reversing abnormal hole localization in high-Al-content AlGaN quantum well to enhance deep ultraviolet emission by regulating the orbital state coupling
Authors: Chen Li , Lin Wei , Wang Huiqiong , Li Jinchai , Kang Junyong
Published: June 2020

AlGaN has attracted considerable interest for ultraviolet (UV) applications. With the development of UV optoelectronic devices, abnormal carrier confinement behaviour has been observed for c-plane-oriented AlGaN quantum wells (QWs) with high Al content. Because of the dispersive crystal field split-off hole band (CH band) composed of pz orbitals, the abnormal confinement becomes the limiting factor for efficient UV light emission. This observation differs from the widely accepted concept that confinement of carriers at the lowest quantum level is more pronounced than that at higher quantum levels, which has been an established conclusion for conventional continuous potential wells. In particular, orientational pz orbitals are sensitive to the confinement direction in line with the conducting direction, which affects the orbital intercoupling. In this work, models of Al0.75Ga0.25N/AlN QWs constructed with variable lattice orientations were used to investigate the orbital intercoupling among atoms between the well and barrier regions. Orbital engineering of QWs was implemented by changing the orbital state confinement, with the well plane inclined from 0° to 90° at a step of 30° (referred to the c plane). The barrier potential and transition rate at the band edge were enhanced through this orbital engineering. The concept of orbital engineering was also demonstrated through the construction of inclined QW planes on semi- and nonpolar planes implemented in microrods with pyramid-shaped tops. The higher emission intensity from the QWs on the nonpolar plane compared with those on the polar plane was confirmed via localized cathodoluminescence (CL) maps.
Mini-LED, Micro-LED and OLED displays: present status and future perspectives
Authors: Huang Yuge , Hsiang En-Lin , Deng Ming-Yang , Wu Shin-Tson
Published: June 2020

Presently, liquid crystal displays (LCDs) and organic light-emitting diode (OLED) displays are two dominant flat panel display technologies. Recently, inorganic mini-LEDs (mLEDs) and micro-LEDs (μLEDs) have emerged by significantly enhancing the dynamic range of LCDs or as sunlight readable emissive displays. “mLED, OLED, or μLED: who wins?” is a heated debatable question. In this review, we conduct a comprehensive analysis on the material properties, device structures, and performance of mLED/μLED/OLED emissive displays and mLED backlit LCDs. We evaluate the power consumption and ambient contrast ratio of each display in depth and systematically compare the motion picture response time, dynamic range, and adaptability to flexible/transparent displays. The pros and cons of mLED, OLED, and μLED displays are analysed, and their future perspectives are discussed.
Daily estimates of clinical severity of symptoms in bipolar disorder from smartphone-based self-assessments
Authors: Busk Jonas , Faurholt-Jepsen Maria , Frost Mads , Bardram Jakob E. , Kessing Lars Vedel , Winther Ole
Published: June 2020

Currently, the golden standard for assessing the severity of depressive and manic symptoms in patients with bipolar disorder (BD) is clinical evaluations using validated rating scales such as the Hamilton Depression Rating Scale 17-items (HDRS) and the Young Mania Rating Scale (YMRS). Frequent automatic estimation of symptom severity could potentially help support monitoring of illness activity and allow for early treatment intervention between outpatient visits. The present study aimed (1) to assess the feasibility of producing daily estimates of clinical rating scores based on smartphone-based self-assessments of symptoms collected from a group of patients with BD; (2) to demonstrate how these estimates can be utilized to compute individual daily risk of relapse scores. Based on a total of 280 clinical ratings collected from 84 patients with BD along with daily smartphone-based self-assessments, we applied a hierarchical Bayesian modelling approach capable of providing individual estimates while learning characteristics of the patient population. The proposed method was compared to common baseline methods. The model concerning depression severity achieved a mean predicted R2 of 0.57 (SD = 0.10) and RMSE of 3.85 (SD = 0.47) on the HDRS, while the model concerning mania severity achieved a mean predicted R2 of 0.16 (SD = 0.25) and RMSE of 3.68 (SD = 0.54) on the YMRS. In both cases, smartphone-based self-reported mood was the most important predictor variable. The present study shows that daily smartphone-based self-assessments can be utilized to automatically estimate clinical ratings of severity of depression and mania in patients with BD and assist in identifying individuals with high risk of relapse.
Specificity of end resection pathways for double-strand break regions containing ribonucleotides and base lesions
Authors: Daley James M. , Tomimatsu Nozomi , Hooks Grace , Wang Weibin , Miller Adam S. , Xue Xiaoyu , Nguyen Kevin A. , Kaur Hardeep , Williamson Elizabeth , Mukherjee Bipasha , Hromas Robert , Burma Sandeep , Sung Patrick
Published: June 2020

DNA double-strand break repair by homologous recombination begins with nucleolytic resection of the 5’ DNA strand at the break ends. Long-range resection is catalyzed by EXO1 and BLM-DNA2, which likely have to navigate through ribonucleotides and damaged bases. Here, we show that a short stretch of ribonucleotides at the 5’ terminus stimulates resection by EXO1. Ribonucleotides within a 5’ flap are resistant to cleavage by DNA2, and extended RNA:DNA hybrids inhibit both strand separation by BLM and resection by EXO1. Moreover, 8-oxo-guanine impedes EXO1 but enhances resection by BLM-DNA2, and an apurinic/apyrimidinic site stimulates resection by BLM-DNA2 and DNA strand unwinding by BLM. Accordingly, depletion of OGG1 or APE1 leads to greater dependence of DNA resection on DNA2. Importantly, RNase H2A deficiency impairs resection overall, which we attribute to the accumulation of long RNA:DNA hybrids at DNA ends. Our results help explain why eukaryotic cells possess multiple resection nucleases.
Graph theory approach to determine configurations of multidentate and high coverage adsorbates for heterogeneous catalysis
Authors: Deshpande Siddharth , Maxson Tristan , Greeley Jeffrey
Published: June 2020

Heterogeneous catalysts constitute a crucial component of many industrial processes, and to gain an understanding of the atomic-scale features of such catalysts, ab initio density functional theory is widely employed. Recently, growing computational power has permitted the extension of such studies to complex reaction networks involving either high adsorbate coverages or multidentate adsorbates, which bind to the surface through multiple atoms. Describing all possible adsorbate configurations for such systems, however, is often not possible based on chemical intuition alone. To systematically treat such complexities, we present a generalized Python-based graph theory approach to convert atomic scale models into undirected graph representations. These representations, when combined with workflows such as evolutionary algorithms, can systematically generate high coverage adsorbate models and classify unique minimum energy multidentate adsorbate configurations for surfaces of low symmetry, including multi-elemental alloy surfaces, steps, and kinks. Two case studies are presented which demonstrate these capabilities; first, an analysis of a coverage-dependent phase diagram of absorbate NO on the Pt3Sn(111) terrace surface, and second, an investigation of adsorption energies, together with identifying unique minimum energy configurations, for the reaction intermediate propyne (CHCCH3*) adsorbed on a PdIn(021) step surface. The evolutionary algorithm approach reproduces high coverage configurations of NO on Pt3Sn(111) using only 15% of the number of simulations required for a brute force approach. Furthermore, the screening of potentially hundreds of multidentate adsorbates is shown to be possible without human intervention. The strategy presented is quite general and can be applied to a spectrum of complex atomic systems.
Personalized early detection and prevention of breast cancer: ENVISION consensus statement
Authors: Pashayan Nora , Antoniou Antonis C. , Ivanus Urska , Esserman Laura J. , Easton Douglas F. , French David , Sroczynski Gaby , Hall Per , Cuzick Jack , Evans D. Gareth , Simard Jacques , Garcia-Closas Montserrat , Schmutzler Rita , Wegwarth Odette , Pharoah Paul , Moorthie Sowmiya , De Montgolfier Sandrine , Baron Camille , Herceg Zdenko , Turnbull Clare , Balleyguier Corinne , Rossi Paolo Giorgi , Wesseling Jelle , Ritchie David , Tischkowitz Marc , Broeders Mireille , Reisel Dan , Metspalu Andres , Callender Thomas , de Koning Harry , Devilee Peter , Delaloge Suzette , Schmidt Marjanka K. , Widschwendter Martin
Published: June 2020

The European Collaborative on Personalized Early Detection and Prevention of Breast Cancer (ENVISION) brings together several international research consortia working on different aspects of the personalized early detection and prevention of breast cancer. In a consensus conference held in 2019, the members of this network identified research areas requiring development to enable evidence-based personalized interventions that might improve the benefits and reduce the harms of existing breast cancer screening and prevention programmes. The priority areas identified were: 1) breast cancer subtype-specific risk assessment tools applicable to women of all ancestries; 2) intermediate surrogate markers of response to preventive measures; 3) novel non-surgical preventive measures to reduce the incidence of breast cancer of poor prognosis; and 4) hybrid effectiveness–implementation research combined with modelling studies to evaluate the long-term population outcomes of risk-based early detection strategies. The implementation of such programmes would require health-care systems to be open to learning and adapting, the engagement of a diverse range of stakeholders and tailoring to societal norms and values, while also addressing the ethical and legal issues. In this Consensus Statement, we discuss the current state of breast cancer risk prediction, risk-stratified prevention and early detection strategies, and their implementation. Throughout, we highlight priorities for advancing each of these areas.
Molecular approaches underlying the oogenic cycle of the scleractinian coral, Acropora tenuis
Authors: Tan Ee Suan , Izumi Ryotaro , Takeuchi Yuki , Isomura Naoko , Takemura Akihiro
Published: June 2020

This study aimed to elucidate the physiological processes of oogenesis in Acropora tenuis. Genes/proteins related to oogenesis were investigated: Vasa, a germ cell marker, vitellogenin (VG), a major yolk protein precursor, and its receptor (LDLR). Coral branches were collected monthly from coral reefs around Sesoko Island (Okinawa, Japan) for histological observation by in situ hybridisation (ISH) of the Vasa (AtVasa) and Low Density Lipoprotein Receptor (AtLDLR) genes and immunohistochemistry (IHC) of AtVasa and AtVG. AtVasa immunoreactivity was detected in germline cells and ooplasm, whereas AtVG immunoreactivity was detected in ooplasm and putative ovarian tissues. AtVasa was localised in germline cells located in the retractor muscles of the mesentery, whereas AtLDLR was localised in the putative ovarian and mesentery tissues. AtLDLR was detected in coral tissues during the vitellogenic phase, whereas AtVG immunoreactivity was found in primary oocytes. Germline cells expressing AtVasa are present throughout the year. In conclusion, Vasa has physiological and molecular roles throughout the oogenic cycle, as it determines gonadal germline cells and ensures normal oocyte development, whereas the roles of VG and LDLR are limited to the vitellogenic stages because they act in coordination with lipoprotein transport, vitellogenin synthesis, and yolk incorporation into oocytes.