bluuebunny/crossref_metadata_2025_split huggingface dataset:
A High-Resolution Landscape of Mutations in the BCL6 Super-Enhancer in Normal Human B-Cells
Authors: Shen Jiang-Cheng , Kamath-Loeb Ashwini S. , Kohrn Brendan F. , Loeb Keith R. , Preston Bradley D. , Loeb Lawrence A. 
Published: September 2019

AbstractThe super-enhancers (SE) of lineage-specific genes in B-cells are off-target sites of somatic hypermutation. However, the inability to detect sufficient numbers of mutations in normal human B-cells has precluded the generation of a high-resolution mutational landscape of SEs. Here, we captured and sequenced 12 B-cell SEs at single-nucleotide resolution from ten healthy individuals across diverse ethnicities. We detected a total of ∼9000 subclonal mutations (allele frequencies <0.1%); of these, ∼8000 are present in the BCL6 SE alone. Within the BCL6 SE, we identified three regions of clustered mutations where the mutation frequency is ∼7X10-4. Mutational spectra show a predominance of C>T/G>A and A>G/T>C substitutions, consistent with the activities of activation-induced-cytidine deaminase (AID) and the A-T mutator, DNA Polymerase η, respectively, in mutagenesis in normal B-cells. Analyses of mutational signatures further corroborate the participation of these factors in this process. Single base substitution signature SBS85, SBS37, and SBS39 were found in the BCL6 SE. While SBS85 is a denoted signature of AID in lymphoid cells, the etiologies of SBS37 and SBS39 are still unknown. Our analysis suggests the contribution of error-prone DNA polymerases to the latter signatures. The high-resolution mutation landscape has enabled accurate profiling of subclonal mutations in B-cell SEs in normal individuals. By virtue of the fact that subclonal SE mutations are clonally expanded in B-cell lymphomas, our studies also offer the potential for early detection of neoplastic alterations.SignificanceWe used Duplex Sequencing to detect low-frequency mutations in the BCL6 super-enhancer locus in normal human B-cells. The landscape of pre-existing mutations is remarkably conserved across different ethnicities and reveals clustered mutational hotspots that correlate with reported sites of clonal mutations and translocation breakpoints in human B-cell lymphomas. This high-resolution genomic landscape revealed by Duplex Sequencing offers accurate and thorough profiling of low frequency, pre-existing mutations in normal individuals, and the potential for early detection of neoplastic alterations.
Local adaptation to abiotic and biotic stresses and phenotypic selection on flowering time in annual Brachypodium spp. along an aridity gradient
Authors: Penner Shira , Sapir Yuval 
Published: September 2019

SummaryPlants have diverse strategies to cope with stress, including early flowering to “escape” abiotic stress and late flowering to mitigate biotic stress. Plants are usually exposed to multiple stresses simultaneously, but little is known about the impact of multiple co-occurring stresses on plant evolution.We tested for adaptation to both aridity and interspecific competition of the model plant Brachypodium spp., collected along the aridity gradient in Israel. We recorded flowering time and estimated fitness in a controlled watering experiment, with treatments mimicking Mediterranean and arid precipitation, and in two common gardens located in the extremes of the gradient (i.e., desert and mesic Mediterranean). At the latter we also manipulated interspecific competition to examine the combined effect of competition and aridity.Plants from arid environments always flowered earlier, but we found no selection on flowering time in the watering experiment. In the common gardens, however, the direction of selection on flowering time differed between sites and competition treatments.We conclude that interactions between aridity and competition drive local adaptation of Brachypodium in the Eastern Mediterranean basin. Variation in flowering time is an important adaptive mechanism to aridity and multiple selection agents can have interactive effects on the evolution of this trait.
Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium
Authors: González-Pech Raúl A. , Stephens Timothy G. , Chen Yibi , Mohamed Amin R. , Cheng Yuanyuan , Burt David W. , Bhattacharya Debashish , Ragan Mark A. , Chan Cheong Xin 
Published: September 2019

AbstractSymbiodiniaceae are predominantly symbiotic dinoflagellates critical to corals and other reef organisms. Symbiodinium is a basal symbiodiniacean lineage and includes symbiotic and free-living taxa. However, the molecular mechanisms underpinning these distinct lifestyles remain little known. Here, we present high-quality de novo genome assemblies for the symbiotic Symbiodinium tridacnidorum CCMP2592 (genome size 1.3 Gbp) and the free-living Symbiodinium natans CCMP2548 (genome size 0.74 Gbp). These genomes display extensive sequence divergence, sharing only ~1.5% conserved regions (≥90% identity). We predicted 45,474 and 35,270 genes for S. tridacnidorum and S. natans, respectively; of the 58,541 homologous gene families, 28.5% are common to both genomes. We recovered a greater extent of gene duplication and higher abundance of repeats, transposable elements and pseudogenes in the genome of S. tridacnidorum than in that of S. natans. These findings demonstrate that genome structural rearrangements are pertinent to distinct lifestyles in Symbiodinium, and may contribute to the vast genetic diversity within the genus, and more broadly in Symbiodiniaceae. Moreover, the results from our whole-genome comparisons against a free-living outgroup support the notion that the symbiotic lifestyle is a derived trait in, and that the free-living lifestyle is ancestral to, Symbiodinium.
Age-related changes in human emotional egocentricity: evidence from multi-level neuroimaging
Authors: Riva Federica , Lenger Melanie , Kronbichler Martin , Lamm Claus , Silani Giorgia 
Published: September 2019

AbstractEmotional egocentric bias (EEB) occurs when, due to a partial failure in self-other distinction, empathy for another’s emotions is influenced by our own emotional state. Recent studies have demonstrated that this bias is higher in children, adolescents and older adults than in young adults. In the latter, overcoming emotional egocentrism has been associated with significant activity in the right supramarginal gyrus (rSMG), as well as increased connectivity between rSGM and somatosensory and visual cortices. Investigations on the neural correlates of EEB in adolescents and older adults are missing. We filled this gap, by asking female participants from three different age groups (adolescents, young adults and older adults, N=92) to perform a well-validated EEB task (Silani et al., 2013) in an MRI scanner. A multi-level analysis approach of MRI data including functional segregation, effective connectivity and structural analyses was adopted. Results revealed higher EEB in older compared to young adults and a comparable EEB in adolescents and young adults. Age-related differences in EEB were associated with differences in task-related rSMG connectivity with somatosensory cortices, especially with S2, which acted as a partial mediator between age and EEB. These findings provide further evidence for the crucial role of the rSMG in self-other distinction in the emotional domain, and suggest that the age-related decline in overcoming EEB is best explained by changes in rSMG connectivity rather than decreased regional activity in that area. This advocates a more systematic investigation of task-related connectivity in studies on aging and life-span development of social-cognitive phenomena.Significance StatementEmpathy comprises both the ability to identify and share another’s emotional state, and the ability to disentangle one’s own from the other’s emotional state. When self- and other-related emotions are conflicting, empathy might be negatively influenced by egocentric tendencies. This phenomenon is referred to as emotional egocentric bias (EEB), with previous research showing that its extent changes across the life-span. Here, we provide evidence that age-related differences in EEB are mainly associated with age-related changes in rSMG effective connectivity, and in particular that higher EEB in older adults is associated to lower rSMG effective connectivity with somatosensory cortices. These findings suggest the importance, particularly in aging, of intact functional connectivity for optimal socio-cognitive functioning.
SRSF2 regulation of MDM2 reveals splicing as a therapeutic vulnerability of the p53 pathway
Authors: Comiskey Daniel F. , Montes Matías , Khurshid Safiya , Singh Ravi K. , Chandler Dawn S. 
Published: September 2019

ABSTRACTMDM2 is an oncogene and critical negative regulator of tumor suppressor p53. Genotoxic stress causes alternative splicing of MDM2 transcripts, which leads to alterations in p53 activity and contributes to tumorigenesis. MDM2-ALT1 is one of transcripts predominantly produced in response to genotoxic stress and is comprised of terminal coding exons 3 and 12. Previously, we found that SRSF1 induces MDM2-ALT1 by promoting MDM2 exon 11 skipping. Here we report that splicing regulator SRSF2 antagonizes the regulation of SRSF1 by facilitating the inclusion of exon 11 through binding at two conserved exonic splicing enhancers. Overexpression of SRSF2 reduced the generation of MDM2-ALT1 in genotoxic stress condition, whereas knockdown induces the expression of MDM2-ALT1 in absence of genotoxic stress. Consistently, blocking the exon 11 SRSF2 binding sites using oligonucleotides promotes MDM2-ALT1. The regulation of MDM2 splicing by SRSF2 is also conserved in mouse as mutation of one SRSF2 binding site in Mdm2 exon 11, using CRISPR-Cas9, increases the expression MDM2-ALT1 homolog Mdm2-MS2 and proliferation of NIH 3T3 cells. Taken together, these findings underscore the relevance of MDM2 alternative splicing in cancer and suggest that p53 levels can be modulated by artificially regulating MDM2 splicing.
A prioritized planning algorithm of trajectory coordination based on time windows for multiple AGVs with delay disturbance
Authors: Tai Ruochen , Wang Jingchuan , Chen Weidong 
Published: September 2019

Purpose
In the running of multiple automated guided vehicles (AGVs) in warehouses, delay problems in motions happen unavoidably as there might exist some disabled components of robots, the instability of networks and the interference of people walking. Under this case, robots would not follow the designed paths and the coupled relationship between temporal and space domain for paths is broken. And there is no doubt that other robots are disturbed by the ones where delays happen. Finally, this brings about chaos or even breakdown of the whole system. Therefore, taking the delay disturbance into consideration in the path planning of multiple robots is an issue worthy of attention and research.

Design/methodology/approach
This paper proposes a prioritized path planning algorithm based on time windows to solve the delay problems of multiple AGVs. The architecture is a unity consisting of three components which are focused on scheduling AGVs under normal operations, delays of AGVs, and recovery of AGVs. In the components of scheduling AGVs under normal operations and recovery, this paper adopts a dynamic routing method based on time windows to ensure the coordination of multiple AGVs and efficient completion of tasks. In the component for scheduling AGVs under delays, a dynamical prioritized local path planning algorithm based on time windows is designed to solve delay problems. The introduced planning principle of time windows would enable the algorithm to plan new solutions of trajectories for multiple AGVs, which could lower the makespan. At the same time, the real-time performance is acceptable based on the planning principle which stipulates the parameters of local time windows to ensure that the computation of the designed algorithm would not be too large.

Findings
The simulation results demonstrate that the proposed algorithm is more efficient than the state-of-the-art method based on homotopy classes, which aims at solving the delay problems. What is more, it is validated that the proposed algorithm can achieve the acceptable real-time performance for the scheduling in warehousing applications.

Originality/value
By introducing the planning principle and generating delay space and local adjustable paths, the proposed algorithm in this paper can not only solve the delay problems in real time, but also lower the makespan compared with the previous method. The designed algorithm guarantees the scheduling of multiple AGVs with delay disturbance and enhances the robustness of the scheduling algorithm in multi-AGV system.
ACD3GPSO: automatic clustering-based algorithm for multi-robot task allocation using dynamic distributed double-guided particle swarm optimization
Authors: Ayari Asma , Bouamama Sadok 
Published: September 2019

Purpose
The multi-robot task allocation (MRTA) problem is a challenging issue in the robotics area with plentiful practical applications. Expanding the number of tasks and robots increases the size of the state space significantly and influences the performance of the MRTA. As this process requires high computational time, this paper aims to describe a technique that minimizes the size of the explored state space, by partitioning the tasks into clusters. In this paper, the authors address the problem of MRTA by putting forward a new automatic clustering algorithm of the robots' tasks based on a dynamic-distributed double-guided particle swarm optimization, namely, ACD3GPSO.

Design/methodology/approach
This approach is made out of two phases: phase I groups the tasks into clusters using the ACD3GPSO algorithm and phase II allocates the robots to the clusters. Four factors are introduced in ACD3GPSO for better results. First, ACD3GPSO uses the k-means algorithm as a means to improve the initial generation of particles. The second factor is the distribution using the multi-agent approach to reduce the run time. The third one is the diversification introduced by two local optimum detectors LODpBest and LODgBest. The last one is based on the concept of templates and guidance probability Pguid.

Findings
Computational experiments were carried out to prove the effectiveness of this approach. It is compared against two state-of-the-art solutions of the MRTA and against two evolutionary methods under five different numerical simulations. The simulation results confirm that the proposed method is highly competitive in terms of the clustering time, clustering cost and MRTA time.

Practical implications
The proposed algorithm is quite useful for real-world applications, especially the scenarios involving a high number of robots and tasks.

Originality/value
In this methodology, owing to the ACD3GPSO algorithm, task allocation's run time has diminished. Therefore, the proposed method can be considered as a vital alternative in the field of MRTA with growing numbers of both robots and tasks. In PSO, stagnation and local optima issues are avoided by adding assorted variety to the population, without losing its fast convergence.
Basel III in Africa: making it work
Authors: Ozili Peterson K. 
Published: September 2019

Purpose
Basel III is a framework to protect the global banking system. The purpose of this paper is to provide a policy discussion on Basel III in Africa.

Design/methodology/approach
The significance of Basel III is discussed, and some ideas to consider when implementing Basel III to make it work in Africa, are provided.

Findings
Under Basel III, the African banking industry should expect better capital quality, higher capital levels, minimum liquidity requirement for banks, reduced systemic risk and differences in Basel III transitional arrangements. This paper also emphasizes that there should be enough time for the transition to Basel III in Africa; a combination of micro and macro-prudential regulations is needed; and the need to repair the balance sheets of banks, in preparation for Basel III.

Originality/value
The discussions in this paper will benefit policymakers, academics and other stakeholders interested in financial regulation in Africa such as the World bank and the International Monetary Fund.
Numerical study of obstacle geometry effect on the vortex shedding suppression and aerodynamic characteristics
Authors: Fezai Salwa , Ben-Cheikh Nader , Ben-Beya Brahim , Lili Taieb 
Published: September 2019

PurposeTwo-dimensional incompressible fluid flows around a rectangular shape placed over a larger rectangular shape at low Reynolds numbers (Re) have been numerically analyzed in the present work. The vortex shedding is investigated at different arrangements of the two shapes allowing the investigation of three possible configurations. The calculations are carried out for several values of Re ranging from 1 to 200. The effect of the obstacle geometry on the vortex shedding is analyzed for crawling, steady and unsteady regimes. The analysis of the flow evolution shows that with increasing Re beyond a certain critical value, the flow becomes unstable and undergoes a bifurcation. This paper aims to observe that the transition of the unsteady regime is performed by a Hopf bifurcation. The critical Re beyond which the flow becomes unsteady is determined for each configuration. A special attention is paid to compute the drag and lift forces acting on the rectangular shapes, which allowed determining; the best configuration in terms of both drag and lift. The unsteady periodic wake is characterized by the Strouhal number, which varies with the Re and the obstacle geometry. Hence, the values of vortex shedding frequencies are calculated in this work.Design/methodology/approachThe dimensionless Navier–Stokes equations were numerically solved using the following numerical technique based on the finite volume method. The temporal discretization of the time derivative is performed by an Euler backward second-order implicit scheme. Non-linear terms are evaluated explicitly; while, viscous terms are treated implicitly. The strong velocity–pressure coupling present in the continuity and the momentum equations are handled by implementing the projection method.FindingsThe present paper aims to numerically study the effect of the obstacle geometry on the vortex shedding and on the drag and lift forces to analyze the flow structure around three configurations at crawling, steady and unsteady regimes.Originality/valueA special attention is paid to compute the drag and lift forces acting on the rectangular shapes, which allowed determining; the best shapes configuration in terms of both drag and lift.
Parallel two-step finite element algorithm based on fully overlapping domain decomposition for the time-dependent natural convection problem
Authors: Ping Yuan , Su Haiyan , Zhao Jianping , Feng Xinlong 
Published: September 2019

Purpose
This paper aims to propose two parallel two-step finite element algorithms based on fully overlapping domain decomposition for solving the 2D/3D time-dependent natural convection problem.

Design/methodology/approach
The first-order implicit Euler formula and second-order Crank–Nicolson formula are used to time discretization respectively. Each processor of the algorithms computes a stabilized solution in its own global composite mesh in parallel. These algorithms compute a nonlinear system for the velocity, pressure and temperature based on a lower-order element pair (P1b-P1-P1) and solve a linear approximation based on a higher-order element pair (P2-P1-P2) on the same mesh, which shows that the new algorithms have the same convergence rate as the two-step finite element methods. What is more, the stability analysis of the proposed algorithms is derived. Finally, numerical experiments are presented to demonstrate the efficacy and accuracy of the proposed algorithms.

Findings
Finally, numerical experiments are presented to demonstrate the efficacy and accuracy of the proposed algorithms.

Originality/value
The novel parallel two-step algorithms for incompressible natural convection problem are proposed. The rigorous analysis of the stability is given for the proposed parallel two-step algorithms. Extensive 2D/3D numerical tests demonstrate that the parallel two-step algorithms can deal with the incompressible natural convection problem for high Rayleigh number well.
A linearity-preserving vertex interpolation algorithm for cell-centered finite volume approximations of anisotropic diffusion problems
Authors: Yang Di , Gao Zhiming 
Published: September 2019

Purpose
A finite volume scheme for diffusion equations on non-rectangular meshes is proposed in [Deyuan Li, Hongshou Shui, Minjun Tang, J. Numer. Meth. Comput. Appl., 1(4)(1980)217–224 (in Chinese)], which is the so-called nine point scheme on structured quadrilateral meshes. The scheme has both cell-centered unknowns and vertex unknowns which are usually expressed as a linear weighted interpolation of the cell-centered unknowns. The critical factor to obtain the optimal accuracy for the scheme is the reconstruction of vertex unknowns. However, when the mesh deformation is severe or the diffusion tensor is discontinuous, the accuracy of the scheme is not satisfactory, and the author hope to improve this scheme.

Design/methodology/approach
The authors propose an explicit weighted vertex interpolation algorithm which allows arbitrary diffusion tensors and does not depend on the location of discontinuity. Both the derivation of the scheme and that of vertex reconstruction algorithm satisfy the linearity preserving criterion which requires that a discretization scheme should be exact on linear solutions. The vertex interpolation algorithm can be easily extended to 3 D case.

Findings
Numerical results show that it maintain optimal convergence rates for the solution and flux on 2 D and 3 D meshes in case that the diffusion tensor is taken to be anisotropic, at times heterogeneous, and/or discontinuous.

Originality/value
This paper proposes a linearity preserving and explicit weighted vertex interpolation algorithm for cell-centered finite volume approximations of diffusion equations on general grids. The proposed finite volume scheme with the new interpolation algorithm allows arbitrary continuous or discontinuous diffusion tensors; the final scheme is applicable to arbitrary polygonal grids, which may have concave cells or degenerate ones with hanging nodes. The final scheme has second-order convergence rate for the approximate solution and higher than first-order accuracy for the flux on 2 D and 3 D meshes. The explicit weighted interpolation algorithm is easy to implement in three dimensions in case that the diffusion tensor is continuous or discontinuous.
Temperature identification of a heat source in conjugate heat transfer problems via an inverse analysis
Authors: Mayeli Peyman , Nikfar Mehdi 
Published: September 2019

Purpose
The present study aims to perform inverse analysis of a conjugate heat transfer problem including conduction and forced convection via the quasi-Newton method. The inverse analysis is defined for a heat source that is surrounded by a solid medium which is exposed to a free stream in external flow.

Design/methodology/approach
The objective of the inverse design problem is finding temperature distribution of the heat source as thermal boundary condition to establish a prescribed temperature along the interface of solid body and fluid. This problem is a simplified version of thermal-based ice protection systems in which the formation of ice is avoided by maintaining the interface of fluid and solid at a specified temperature.

Findings
The effects of the different pertinent parameters such as Reynolds number, interface temperature and thermal conductivity ratio of fluid and solid mediums are analyzed.

Originality/value
This paper fulfils the analysis to study how thermal based anti-icing system can be used with different heat source shapes.