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The frozen phonon technique is introduced as a means of including the effects of thermal vibrations in multislice calculations of CBED patterns. This technique produces a thermal diffuse background, Kikuchi bands and a Debye-Waller factor, all of which are neglected in the standard multislice calculation. The frozen phonon calculations match experimental silicon (100) CBED patterns for specimen 0108-7673/91/030267-12503.00© 1991 International Union of Crystallography THERMAL VIBRATIONS IN CONVERGENT-BEAM ELECTRON DIFFRACTIONthicknesses of up to at least 550 A. The best-fit silicon r.m.s, vibration amplitude at near room temperature was determined to be 0.085(5)/~. As an independent check of validity, a comparison of calculated CBED, experimental CBED and electron energy loss spectroscopy (EELS) data was also performed. The frozen phonon technique provides an improved theoretical basis for the simulation of CBED and therefore annular dark field scanning transmission electron microscope imaging.( 1) IntroductionConvergent-beam electron diffraction (CBED) is widely used for microcharacterization (Steeds, 1983; Eades, 1988). The most common application is to identify known structures and their orientations, but CBED has also been used to determine accurate unit-cell dimensions (Jones, Rackham & Steeds, 1977), structure symmetries (Goodman, 1975;Tanaka, Saito & Sekii, 1983) and even atomic positions (Vincent, Bird & Steeds, 1984). Strain fields around defects (Fung, 1985;Carpenter & Spence, 1982), specimen thicknesses (Kelly, Jostsons, Blake & Napier, 1975;Kirkland, Loane, Xu & Silcox, 1989), ionicity (Zuo, Spence & O'Keeffe, 1988) and the phase of complex atomic structure factors (Zuo, Spence & H¢ier, 1989;Bird, James & Preston, 1987) have also been determined. The sum of the large-angle scattering in the CBED pattern produces the annular dark field (ADF) scanning transmission electron microscope (STEM) image (Langmore, Wall & Isaacson, 1973), which has recently proven capable of resolving atomic structures with Z contrast (Pennycook, 1989;Pennycook, Jesson & Chisholm, 1990) at better than 2,~ resolution (Xu, Kirkland, Silcox & Keyse, 1990; Shin, Kirkland & Silcox, 1989). Three major features of the large-angle scattering are Kikuchi bands (Kikuchi, 1928;Kainuma, 1955;Takagi, 1958), a thermal diffuse scattering (TDS) background (Hall & Hirsch, 1965) and a higher-order Laue zone (HOLZ) ring (Hirsch, Howie, Nicholson, Pashley & Whelan, 1977). Thermal vibrations generate the first two features and reduce the intensity of the third by a Debye-Waller factor (Debye, 1914). Since the intensity in the HOLZ ring may be a significant fraction of the ADF STEM signal (Spence, Zuo & Lynch, 1989), the signal may be sensitive to thermal vibration. There are suggestions that thermal vibrations can change the relative contrast of different elements in the ADF STEM signal (Wang & Cowley, 1989), which differs from the suggestion that the signal is simply related to the atomic cross sections . Accordingly, understanding the ...

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The multislice method, pioneered by Cowley and Moodie, has recently been adapted to simulate annular dark-field scanning transmission electronmicroscope (ADF STEM) images. This paper presents a series of calculations using this new approach with experimental parameters appropriate for a VG-HB501 STEM to investigate the visibility of single heavy adatoms on thin crystalline silicon membranes. The tendency for electrons to channel along columns of atoms in crystals can greatly increase the intensity incident on an adatom on the exit surface, thereby increasing the adatom visibility. The simulations indicate that an adatom on the exit surface on a column of crystal atoms is up to three times as visible as an adatom on the entrance surface, and that the adatom remains highly visible as the crystal thickness is increased. Tilting the specimen or displacing the adatom from the column appears to lower the visibility of the adatom dramatically. These calculations suggest that, with the appropriate imaging conditions, a single gold adatom may be visible on at least 235 of (111) silicon.

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This article describes the algorithms implemented in the Essie search engine that is currently serving several Web sites at the National Library of Medicine. Essie is a phrase-based search engine with term and concept query expansion and probabilistic relevancy ranking. Essie's design is motivated by an observation that query terms are often conceptually related to terms in a document, without actually occurring in the document text. Essie's performance was evaluated using data and standard evaluation methods from the 2003 and 2006 Text REtrieval Conference (TREC) Genomics track. Essie was the best-performing search engine in the 2003 TREC Genomics track and achieved results comparable to those of the highest-ranking systems on the 2006 TREC Genomics track task. Essie shows that a judicious combination of exploiting document structure, phrase searching, and concept based query expansion is a useful approach for information retrieval in the biomedical domain.

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BackgroundTrial registries were established to combat publication bias by creating a comprehensive and unambiguous record of initiated clinical trials. However, the proliferation of registries and registration policies means that a single trial may be registered multiple times (i.e., “duplicates”). Because unidentified duplicates threaten our ability to identify trials unambiguously, we investigate to what degree duplicates have been identified across registries globally.MethodsWe retrieved all records from the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) search portal and made a list of all records identified as duplicates by the ICTRP. To investigate how to discriminate duplicates from non-duplicates, we applied text-based similarity scoring to various registration fields of both ICTRP-identified duplicates and arbitrary pairs of trials. We then used the best similarity measure to identify the most similar pairs of records and manually assessed a random sample of pairs not identified as duplicates by the ICTRP to estimate the number of previously unidentified (or “hidden”) duplicates.ResultsTwo hundred eighty-five thousand unique records, or 271 thousand unique trials after accounting for known duplicates, were retrieved from the ICTRP portal in April 2015. We found that the title field best discriminated duplicates from non-duplicates. Out of 41 billion total pair-wise comparisons, we identified the 474,000 pairs of titles with the highest similarity scores (>0.5). After manually assessing a random sample of 434 pairs, we estimated that 45 % of all duplicate registrations currently go undetected and remain to be identified and confirmed as duplicates. Thus, the actual number of unique trials represented in this dataset is estimated to be approximately 258,000 (5 % less).ConclusionsThe ICTRP portal does not currently enable the unambiguous identification of trials across registries. Further research is needed to identify and verify the duplicates that currently go undetected. Sponsors, registries, and the ICTRP should consider actions to ensure duplicate registrations are easily identifiable.Electronic supplementary materialThe online version of this article (doi:10.1186/s13643-016-0283-8) contains supplementary material, which is available to authorized users.