The genotype-phenotype (GP) map of RNA secondary structure links each RNA sequence to its corresponding secondary structure. Previous research has shown that the large-scale structural properties of ...GP maps, such as the size of neutral sets in genotype space, can influence evolutionary outcomes. In order to use neutral set sizes, efficient and accurate computational methods are needed to compute them. Here, we propose a new method, which is based on free energy estimates and is much faster than existing sample-based methods. Moreover, this approach can give insight into the reasons behind neutral set size variations, for example, why structures with fewer stacks tend to have larger neutral set sizes. In addition, we generalize neutral set size calculations from the previously studied many-to-one framework, where each sequence folds into a single energetically preferred structure, to a fuller many-to-many framework, where several low-energy structures are included. We find that structures with high neutral sets in one framework also tend to have large neutral sets in the other framework for a range of parameters and thus the choice of GP map does not fundamentally affect which structures have the largest neutral set sizes.
Genotype-phenotype maps link genetic changes to their fitness effect and are thus an essential component of evolutionary models. The map between RNA sequences and their secondary structures is a key ...example and has applications in functional RNA evolution. For this map, the structural effect of substitutions is well understood, but models usually assume a constant sequence length and do not consider insertions or deletions. Here, we expand the sequence-structure map to include single nucleotide insertions and deletions by using the RNAshapes concept. To quantify the structural effect of insertions and deletions, we generalize existing definitions for robustness and non-neutral mutation probabilities. We find striking similarities between substitutions, deletions and insertions: robustness to substitutions is correlated with robustness to insertions and, for most structures, to deletions. In addition, frequent structural changes after substitutions also tend to be common for insertions and deletions. This is consistent with the connection between energetically suboptimal folds and possible structural transitions. The similarities observed hold both for genotypic and phenotypic robustness and mutation probabilities, i.e. for individual sequences and for averages over sequences with the same structure. Our results could have implications for the rate of neutral and non-neutral evolution.
Herein, we propose a novel indoor structure extraction (ISE) method that can reconstruct an indoor planar structure with a feature structure map (FSM) and enable indoor robot navigation using a ...navigation structure map (NSM). To construct the FSM, we first propose a two-staged region growing algorithm to segment the planar feature and to obtain the original planar point cloud. Subsequently, we simplify the planar feature using quadtree segmentation based on cluster fusion. Finally, we perform simple triangulation in the interior and vertex-assignment triangulation in the boundary to accomplish feature reconstruction for the planar structure. The FSM is organized in the form of a mesh model. To construct the NSM, we first propose a novel ground extraction method based on indoor structure analysis under the Manhattan world assumption. It can accurately capture the ground plane in an indoor scene. Subsequently, we establish a passable area map (PAM) within different heights. Finally, a novel-form NSM is established using the original planar point cloud and the PAM. Experiments are performed using three public datasets and one self-collected dataset. The proposed plane segmentation approach is evaluated on two simulation datasets and achieves a recall of approximately 99%, which is 5% higher than that of the traditional plane segmentation method. Furthermore, the triangulation performance of our method compared with the traditional greedy projection triangulation show that our method performs better in terms of feature representation. The experimental results reveal that our ISE method is robust and effective for extracting indoor structures.
The quaternary chalcogenide halides Ba3GaSe4Br and Ba3InSe4Br were prepared from reactions of binary selenides and bromides at 1073 K. Single-crystal X-ray diffraction analysis revealed that ...Ba3GaSe4Br adopts the Ba3GaS4Cl-type structure (orthorhombic, space group Pnma, Z = 4, a = 12.8248(6) Å, b = 9.9608(5) Å, c = 8.7690(4) Å) and Ba3InSe4Br adopts the K3SO4F-type structure (tetragonal, space group I4/mcm, Z = 4, a = 8.6888(16) Å, c = 14.950(3) Å). Both structures contain isolated MSe45– tetrahedral units separated by Ba2+ and Br− ions. A structure map based on radius ratios is able to demarcate the three structure types encountered for various members of the series of chalcogenide halides Ba3MCh4X (M = Al, Ga, In; Ch = S, Se; X = Cl, Br, I). Large band gaps in Ba3GaSe4Br and Ba3InSe4Br originate from the separation of Ga–Se or In–Se bonding and antibonding levels, as revealed by electronic structure calculations. The measured optical band gaps are 1.7 eV for Ba3GaSe4Br and 1.6 eV for Ba3InSe4Br.
A structure map demarcates three structure types adopted by chalcogenide halides Ba3MCh4X, including two new members. Display omitted
•Two new selenide bromides Ba3GaSe4Br and Ba3InSe4Br were prepared.•A structure map separates three structure types adopted by Ba3MCh4X compounds.•Ba3GaSe4Br and Ba3InSe4Br have optical band gaps of 1.6–1.7 eV.
The traditional methods for predicting the occurrence of deleterious topologically close-packed (TCP) phases in Ni-based superalloys have been based on the PHACOMP and newPHACOMP methodologies. These ...schemes use the average number of holes
N
¯
h
or the centre of gravity of the elemental d-bands
M
¯
d
to predict whether or not a given multicomponent alloy will be prone to TCP formation. However, as both these one-dimensional methodologies are well-known to fail with respect to new generations of alloys, a novel two-dimensional structure map
(
N
¯
,
Δ
V
/
V
¯
)
is introduced where
N
¯
is the average electron concentration and
Δ
V
/
V
¯
is a composition-dependent size-factor difference. This map is found to separate the experimental data on the TCP phases of binary A–B transition metal alloys into well-defined but sometimes overlapping regions corresponding to different structure types such as A15,
σ,
χ, R, P,
δ,
μ, M and Laves. Detailed investigations of ternary phase diagrams and multicomponent systems show that TCP phases, regardless of the number of constituents, are located in the same regions of the structure map that are favoured by the binary compounds of the same structure type. The structure map is then used in conjunction with CALPHAD computations of
σ phase stability to show that the predictive power of newPHACOMP for the seven component Ni–Co–Cr–Ta–W–Re–Al system studied recently by Reed et al.
24 is indeed poor. This supports a growing consensus that robust methods of TCP phase prediction in multicomponent alloys will require the inclusion of reliable first-principles thermodynamic databases within the semi-empirical CALPHAD scheme.
Twelve quaternary rare-earth selenides Ba2REGaSe5 and Ba2REInSe5 were prepared in the form of single crystals from reactions of BaSe, RE, M2Se3 (M = Ga, In), and Se at 1373 K. The compounds ...Ba2REGaSe5 fall into two separate series adopting an orthorhombic (RE = La, Ce; space group Pnma, Z = 4, a = 12.49–12.50 Å, b = 9.60–9.63 Å, c = 8.74 Å) or a triclinic structure (RE = Tb, Ho, Tm, Yb, Lu; space group P1¯, Z = 2, a = 7.28–7.31 Å, b = 8.61–8.72 Å, c = 9.37–9.43 Å, α = 103.4–103.5°, β = 103.0–103.1°, γ = 107.3–107.5°). The compounds Ba2REInSe5 adopt an orthorhombic structure (RE = Pr, Tb, Ho, Tm, Lu; space group Cmc21, Z = 4, a = 4.23–4.33 Å, b = 18.75–18.96 Å, c = 13.29–13.31 Å). All structures contain anionic M-centred tetrahedra, isolated Se2– anions, Ba2+ cations in eight-fold coordination, and RE3+ cations in either six- or seven-fold coordination. A structure map developed based on radius ratios involving the RE3+, M3+, and Ch2– ions is effective in segregating four structures (in space groups Cmc21, P1¯, Pnma, and I4/mcm) found for Ba2REMCh5 (M = Ga, In; Ch = S, Se, Te). Bond valence sum calculations reveal that the upper limit for the largest RE components that can be substituted within a given structural series is set by the need to avoid overbonding of the RE atoms. An optical band gap of 1.34(2) eV was measured for the compound Ba2LaGaSe5, slightly less than a value of 1.76 eV obtained from electronic band structure calculations, which suggest an indirect transition.
A structure map based on radius ratios segregates different structures adopted by Ba2REMCh5. Display omitted
•Twelve new quaternary chalcogenides Ba2REMSe5 (M = Ga, In) were prepared.•A structure map effectively separates different structures found in Ba2REMCh5.•The limits of formation are defined by avoidance of overbonding of RE atoms.•Ba2REGaSe5 separates into two structural branches depending on size of RE.
Fast multiscale reconstruction for Cryo-EM Donati, Laurène; Nilchian, Masih; Sorzano, Carlos Oscar S. ...
Journal of structural biology,
12/2018, Volume:
204, Issue:
3
Journal Article
Peer reviewed
Open access
We present a multiscale reconstruction framework for single-particle analysis (SPA). The representation of three-dimensional (3D) objects with scaled basis functions permits the reconstruction of ...volumes at any desired scale in the real-space. This multiscale approach generates interesting opportunities in SPA for the stabilization of the initial volume problem or the 3D iterative refinement procedure. In particular, we show that reconstructions performed at coarse scale are more robust to angular errors and permit gains in computational speed. A key component of the proposed iterative scheme is its fast implementation. The costly step of reconstruction, which was previously hindering the use of advanced iterative methods in SPA, is formulated as a discrete convolution with a cost that does not depend on the number of projection directions. The inclusion of the contrast transfer function inside the imaging matrix is also done at no extra computational cost. By permitting full 3D regularization, the framework is by itself a robust alternative to direct methods for performing reconstruction in adverse imaging conditions (e.g., heavy noise, large angular misassignments, low number of projections). We present reconstructions obtained at different scales from a dataset of the 2015/2016 EMDataBank Map Challenge. The algorithm has been implemented in the Scipion package.
The present study aims to understand better the structural elements controlling the hydrocarbon potentiality and productivity for the upper Cretaceous reservoirs in the Eastern flank of the Abu ...Gharadig Basin in the Western Desert of Egypt. The major sandstone reservoirs in this area are found within Abu Roash “G” Member and Upper Bahariya Formation, characterized by lateral facies changes with major structure uncertainty and unleashed hydrocarbon potential. Therefore, we aimed to identify the lateral distribution of the studied reservoirs regionally in Abrar, Ferdaus, Ganna, Rawda, Sidra, and Rayan fields at the North Bahariya Concession and Aqsa and Yamma-SE fields at the East Bahariya Concession through integrated geological and geophysical studies for further exploration activities in this area. As a result, we produced regional depth contour maps covering most of the producing fields with the lateral distribution of hydrocarbon occurrences through the area. Moreover, the petrophysical parameter maps for the Middle and Lower Abu Roash “G” reservoirs, such as net pay thickness, shale volume, effective porosity, and hydrocarbon saturation are prepared to understand the hydrocarbon potentiality. This, in turn, allowed us to determine nine promising structural traps for future exploration with high certainty.
Scores of researchers have paid attention to empirical and conceptual dimensions of Customer relationship management (CRM). A few studies summarise the research output of CRM focusing on a specific ...industry. Nevertheless, there is scant literature summarising the research output of CRM in contrast to the data mining-based CRM. This study presents a scientometric analysis that evaluates CRM research output with a special focus on data mining-based CRM. Bibliometric data were extracted for the period 2000–2020 from the Web of Science database to apply descriptive analysis and scientometric analysis to obtain the bibliometric profile of CRM research. Further, we generated the conceptual structure map using multiple correspondence analysis and clustering for CRM and data mining-based CRM research fields. Interestingly, the analysis revealed that the future trendfi of CRM research would be based on techniques associated with machine learning and artificial intelligence. The study provides extensive insight into the basic structure of the CRM and data mining-based CRM research domain and identifies future research areas.
PurposeThe purpose of this study is to map the conceptual structure of the body of knowledge linking digital technologies and auditing, with the aim of contributing to a better understanding of this ...research stream.Design/methodology/approachThis research develops a bibliometric analysis of 256 articles following two steps. The analysis of descriptive performance indicators identifies the main traits of the community of scholars debating audit and technology in terms of publications, productive countries and authors, as well as the publication’s impact of the target journals concerning specific fields, number of citations per country and most cited articles in the data set. To analyse the conceptual structure of the data set, the study performs a co-word analysis adopting social network analysis tools.FindingsThe results highlight a growing academic interest in the research topic, especially in the past few years. The bibliometric analysis reveals three main topics concerning the use and application of technology in the audit profession: the adoption of continuous auditing and continuous monitoring in the auditing profession; the use of software tools in the audit profession; the connections between information systems and audit.Originality/valueThis paper contributes to the field by providing an examination of the current state of the art of research on the use and application of technology in the audit profession as well as identifying the current gaps in the literature and, most importantly, propose a research agenda for the field.
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