Studying Organisational Topology with Simple Computational Models

The behaviour of many complex systems is influenced by the underlying network topology. In particular, this applies to social systems in which people or organisational units collaboratively solve problems. Network rewiring processes are one useful tool in understanding the relationship between network topology and behaviour. Here we use the Kawachi network rewiring process, together with three simple simulation models of organisational collaboration, to investigate the network characteristics that influence performance. The simulation models are based on the Assignment Problem, the Kuramoto Model from physics, and a novel model of collaborative problem-solving which involves finding numbers with certain characteristics, the existence of which is guaranteed by Lagrange\'s Theorem. For all three models, performance is best when the underlying organisational network has a low average distance between nodes. In addition, the third model identified long-range connectivity between nodes as an important predictor of performance. The commonly-used clustering coefficient, which is a measure of short-range connectivity, did not affect performance. We would expect that long-range network connectivity would also influence the behaviour of other complex systems displaying global self-synchronization. The paper also demonstrates the utility of simple computational models in studying issues of organisational topology.Network Rewiring, Small World Networks, Self-Synchronization, Agent Simulation, Collaboration, Problem Solving

Synchronisation Properties of Trees in the Kuramoto Model

We consider the Kuramoto model of coupled oscillators, specifically the case of tree networks, for which we prove a simple closed-form expression for the critical coupling. For several classes of tree, and for both uniform and Gaussian vertex frequency distributions, we provide tight closed form bounds and empirical expressions for the expected value of the critical coupling. We also provide several bounds on the expected value of the critical coupling for all trees. Finally, we show that for a given set of vertex frequencies, there is a rearrangement of oscillator frequencies for which the critical coupling is bounded by the spread of frequencies.Comment: 21 pages, 19 Figure

ASTRO Journals' Data Sharing Policy and Recommended Best Practices.

Transparency, openness, and reproducibility are important characteristics in scientific publishing. Although many researchers embrace these characteristics, data sharing has yet to become common practice. Nevertheless, data sharing is becoming an increasingly important topic among societies, publishers, researchers, patient advocates, and funders, especially as it pertains to data from clinical trials. In response, ASTRO developed a data policy and guide to best practices for authors submitting to its journals. ASTRO's data sharing policy is that authors should indicate, in data availability statements, if the data are being shared and if so, how the data may be accessed

Pengembangan Buku Ajar Mata Kuliah Bahasa Indonesia Untuk Mahasiswa STMIK Palangka Raya

Penelitian ini bertujuan mendeskripsikan proses perkuliahan Bahasa Indonesia di STMIK Palangka Raya, mengembangkan buku ajar mata kuliah Bahasa Indonesia yang sesuai dengan capaian kompetensi lulusan STMIK Palangka Raya, dan mengevaluasi validitas, efektivitas, serta kepraktisan buku ajar tersebut. Metode yang digunakan adalah Research and Development dengan menganalisis kebutuhan kemudian mengembangkan produk dan diuji validitas, efektivitas, dan kepraktisanya hingga diperoleh produk final. Produk yang dikembangkan adalah buku ajar mata kuliah Bahasa Indonesia untuk mahasiswa STMIK Palangka Raya. Hasil analisis menunjukkan buku ajar validitas sebesar 93%, efektif kerena sebesar 92,67% mahasiswa tuntas KKM, dan praktis karena mahasiswa sebesar 87,33% merespon keterterapan produk dengan baik, serta 89,60% praktisi merespon dengan baik saat diterapkan. Buku ajar ini memiliki keterterapan yang tinggi karena memiliki validitas yang tinggi pula. Buku ajar yang dikembangkan juga memiliki efektivitas yang baik, karena memiliki validitas yang tinggi dan kepraktisan yang tinggi pula. Dengan kepraktisan buku ajar yang tinggi, maka belajar materi Bahasa Indonesia akan lebih mudah.Disarankan agar dosen dapat menerapkan buku ajar Bahasa Indonesia untuk mahasiswa STMIK Palangka Raya guna membekali mahasiswa untuk cakap menerapkan kaidah-kaidah Bahasa Indonsia yang baik dan benar, dalam bidang ilmu pengetahuan dan teknologi maupun dalam kehidupan sehari-hari

Spectroscopy of Broad Line Blazars from 1LAC

We report on optical spectroscopy of 165 Flat Spectrum Radio Quasars (FSRQs) in the Fermi 1LAC sample, which have helped allow a nearly complete study of this population. Fermi FSRQ show significant evidence for non-thermal emission even in the optical; the degree depends on the gamma-ray hardness. They also have smaller virial estimates of hole mass than the optical quasar sample. This appears to be largely due to a preferred (axial) view of the gamma-ray FSRQ and non-isotropic (H/R ~ 0.4) distribution of broad-line velocities. Even after correction for this bias, the Fermi FSRQ show higher mean Eddington ratios than the optical population. A comparison of optical spectral properties with Owens Valley Radio Observatory radio flare activity shows no strong correlation.Comment: Accepted for publication in Ap

Trophic cascades in 3D: network analysis reveals how apex predators structure ecosystems

© 2016 The Authors. Methods in Ecology and Evolution © 2016 British Ecological Society Trophic cascade theory predicts that apex predators structure ecosystems by regulating mesopredator and herbivore abundance and behaviour. Studies on trophic cascades have typically focused on short linear chains of species interactions. A framework that integrates more realistic and complex interactions is needed to make broader predictions on ecosystem structuring. Network analysis is used to study food webs and other types of species interaction networks. These often comprise large numbers of species but rarely account for multiple interaction types and strengths. Here, we develop an intermediate complexity theoretical framework that allows specification of multiple interaction types and strengths for the study of trophic cascades. This ecological network is designed to suit data typically derived from field-based studies. The trophic cascade network contains fewer nodes than food webs, but provides semi-weighted directional links that enable different types of interactions to be included in a single model. We use this trophic cascade network model to explore how an apex predator shapes ecosystem structure in an Australian arid ecosystem. We compared two networks that contrasted in the dominance of an apex predator, the dingo (Canis dingo), using published results ranking the direction and strength of key interactions. Nodes and links interacted dynamically to shape these networks. We examined how changes to an apex predator population affect ecosystem structure through their direct and indirect influences on different components of this ecological community. Under strong apex predator influence, the network structure was denser and more complex, even and top-down driven; and dingo predation and soil commensalism formed denser interactive modules. Under weak apex predator influence (e.g. reflecting predator control), the resulting network structure was frayed, with mesopredator predation and grazing forming modules. Our study demonstrates that networks of intermediate complexity can provide a powerful tool for elucidating potential ecosystem-wide effects of apex predators and predicting the consequences of management interventions such as predator control. Integrating trophic cascades, with their array of complex interactions, with the three-dimensional structure of ecological networks, has the potential to reveal ‘ecological architecture’ that neither captures on its own

Review: Placental mitochondrial function and structure in gestational disorders

The aetiology of many gestational disorders is still unknown. However, insufficient trans-placental nutrient and oxygen transfer due to abnormal placentation is characteristic of several pathologies, and may alter the function of placental mitochondria. Mitochondria are multifunctional organelles that respond to a wide range of stimuli - such as physiological changes in cellular energy demands or various pathologies - by reshaping via fusion or fission, increasing/decreasing in number, altering oxidative phosphorylation, and signalling cellular functions such as apoptosis. Mitochondrial function is integral to tissue functions including energy production, metabolism, and regulation of various cellular responses including response to oxidative stress. This review details the functions of placental mitochondria and investigates mitochondrial function and structure in gestational disorders including preeclampsia, intrauterine growth restriction, diabetes mellitus, and obesity. Placental mitochondrial dysfunction may be critical in a range of gestational disorders which have important implications for maternal and fetal/offspring health

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells

The packaging of DNA into chromatin plays an important role in transcriptional regulation and nuclear processes. Brahma-related gene-1 SMARCA4 (also known as BRG1), the essential ATPase subunit of the mammalian SWI/SNF chromatin remodeling complex, uses the energy from ATP hydrolysis to disrupt nucleosomes at target regions. Although the transcriptional role of SMARCA4 at gene promoters is well-studied, less is known about its role in higher-order genome organization. SMARCA4 knockdown in human mammary epithelial MCF-10A cells resulted in 176 up-regulated genes, including many related to lipid and calcium metabolism, and 1292 down-regulated genes, some of which encode extracellular matrix (ECM) components that can exert mechanical forces and affect nuclear structure. ChIP-seq analysis of SMARCA4 localization and SMARCA4-bound super-enhancers demonstrated extensive binding at intergenic regions. Furthermore, Hi-C analysis showed extensive SMARCA4-mediated alterations in higher-order genome organization at multiple resolutions. First, SMARCA4 knockdown resulted in clustering of intra- and inter-subtelomeric regions, demonstrating a novel role for SMARCA4 in telomere organization. SMARCA4 binding was enriched at topologically associating domain (TAD) boundaries, and SMARCA4 knockdown resulted in weakening of TAD boundary strength. Taken together, these findings provide a dynamic view of SMARCA4-dependent changes in higher-order chromatin organization and gene expression, identifying SMARCA4 as a novel component of chromatin organization

Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

BACKGROUND: Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin organization during tumorigenesis have not been fully explored. To probe the differences in higher-order chromatin structure between mammary epithelial and breast cancer cells, we performed Hi-C analysis on MCF-10A mammary epithelial and MCF-7 breast cancer cell lines. RESULTS: Our studies reveal that the small, gene-rich chromosomes chr16 through chr22 in the MCF-7 breast cancer genome display decreased interaction frequency with each other compared to the inter-chromosomal interaction frequency in the MCF-10A epithelial cells. Interestingly, this finding is associated with a higher occurrence of open compartments on chr16-22 in MCF-7 cells. Pathway analysis of the MCF-7 up-regulated genes located in altered compartment regions on chr16-22 reveals pathways related to repression of WNT signaling. There are also differences in intra-chromosomal interactions between the cell lines; telomeric and sub-telomeric regions in the MCF-10A cells display more frequent interactions than are observed in the MCF-7 cells. CONCLUSIONS: We show evidence of an intricate relationship between chromosomal organization and gene expression between epithelial and breast cancer cells. Importantly, this work provides a genome-wide view of higher-order chromatin dynamics and a resource for studying higher-order chromatin interactions in two cell lines commonly used to study the progression of breast cancer

The Age-Activity-Rotation Relationship in Solar-Type Stars

Measured from high-resolution spectra, we present Ca II K line chromospheric fluxes in 35 G dwarf stars of 5 open clusters to determine the age-activity-rotation relationship from the young Hyades and Praesepe (0.6 Gyr) to the old M 67 (~ 4.5 Gyr) through the two intermediate age clusters IC 4651 and NGC 3680 (~ 1.7 Gyr). Our data show that a dramatic decrease in chromospheric activity takes place among solar stars between the Hyades and the IC4651 age, in about 1 Gyr. Afterwards, activity remains virtually constant for more than 3 Gyr. We briefly investigate the impact of this result on the age determinations of field G dwarfs in the solar neighborhood; the two main conclusions are that a consistent group of 'young' stars (i.e. as active as Hyades stars) is present, and that it is virtually impossible to give accurate chromospheric ages for stars older than ~ 2 Gyr. The observed abrupt decline in activity explains very well the Vaughan-Preston gap.Comment: 17 pages, 10 figures. Accepted for publication in Astronomy & Astrophysic