Extracting multi-way chromatin contacts from Hi-C data

There is a growing realization that multi-way chromatin contacts formed in chromosome structures are fundamental units of gene regulation. However, due to the paucity and complexity of such contacts, it is challenging to detect and identify them using experiments. Based on an assumption that chromosome structures can be mapped onto a network of Gaussian polymer, here we derive analytic expressions for n-body contact probabilities (n > 2) among chromatin loci based on pairwise genomic contact frequencies available in Hi-C, and show that multi-way contact probability maps can in principle be extracted from Hi-C. The three-body (triplet) contact probabilities, calculated from our theory, are in good correlation with those from measurements including Tri-C, MC-4C and SPRITE. Maps of multi-way chromatin contacts calculated from our analytic expressions can not only complement experimental measurements, but also can offer better understanding of the related issues, such as cell-line dependent assemblies of multiple genes and enhancers to chromatin hubs, competition between long-range and short-range multi-way contacts, and condensates of multiple CTCF anchors.

Extracting multi-way chromatin contacts from Hi-C data

There is a growing realization that multi-way chromatin contacts formed in chromosome structures are fundamental units of gene regulation. However, due to the paucity and complexity of such contacts, it is challenging to detect and identify them using experiments. Based on an assumption that chromosome structures can be mapped onto a network of Gaussian polymer, here we derive analytic expressions for n-body contact probabilities (n > 2) among chromatin loci based on pairwise genomic contact frequencies available in Hi-C, and show that multi-way contact probability maps can in principle be extracted from Hi-C. The three-body (triplet) contact probabilities, calculated from our theory, are in good correlation with those from measurements including Tri-C, MC-4C and SPRITE. Maps of multi-way chromatin contacts calculated from our analytic expressions can not only complement experimental measurements, but also can offer better understanding of the related issues, such as cell-line dependent assemblies of multiple genes and enhancers to chromatin hubs, competition between long-range and short-range multi-way contacts, and condensates of multiple CTCF anchors.

Examining data visualization pitfalls in scientific publications

Data visualization blends art and science to convey stories from data via graphical representations. Considering different problems, applications, requirements, and design goals, it is challenging to combine these two components at their full force. While the art component involves creating visually appealing and easily interpreted graphics for users, the science component requires accurate representations of a large amount of input data. With a lack of the science component, visualization cannot serve its role of creating correct representations of the actual data, thus leading to wrong perception, interpretation, and decision. It might be even worse if incorrect visual representations were intentionally produced to deceive the viewers. To address common pitfalls in graphical representations, this paper focuses on identifying and understanding the root causes of misinformation in graphical representations. We reviewed the misleading data visualization examples in the scientific publications collected from indexing databases and then projected them onto the fundamental units of visual communication such as color, shape, size, and spatial orientation. Moreover, a text mining technique was applied to extract practical insights from common visualization pitfalls. Cochran’s Q test and McNemar’s test were conducted to examine if there is any difference in the proportions of common errors among color, shape, size, and spatial orientation. The findings showed that the pie chart is the most misused graphical representation, and size is the most critical issue. It was also observed that there were statistically significant differences in the proportion of errors among color, shape, size, and spatial orientation.

Large Hall and Nernst responses from thermally induced spin chirality in a spin-trimer ferromagnet

The long-range order of noncoplanar magnetic textures with scalar spin chirality (SSC) can couple to conduction electrons to produce an additional (termed geometrical or topological) Hall effect. One such example is the Hall effect in the skyrmion lattice state with quantized SSC. An alternative route to attain a finite SSC is via the spin canting caused by thermal fluctuations in the vicinity of the ferromagnetic ordering transition. Here, we report that for a highly conducting ferromagnet with a two-dimensional array of spin trimers, the thermally generated SSC can give rise to a gigantic geometrical Hall conductivity even larger than the intrinsic anomalous Hall conductivity of the ground state. We also demonstrate that the SSC induced by thermal fluctuations leads to a strong response in the Nernst effect. A comparison of the sign and magnitude of fluctuation–Nernst and Hall responses in fundamental units indicates the need for a momentum–space picture to model these thermally induced signals.

Individuals, Communities, and Groups in Thomas Kuhn’s Model of Scientific Development

In The Structure of Scientific Revolutions, Thomas Kuhn resorts to concepts from several disciplines in order to describe the general patterns of scientific development. This blend of disciplines can be explained in part by Kuhn's intellectual path, from physics to history and then to philosophy of science; but it also points to a deeper methodological problem, which is the question of what is the real unity of analysis in his model of science. The primary intention of this article is, thus, to give a solution to this difficulty. The answer, I believe, rests on identifying three fundamental units present in Kuhn's theory of scientific development. They are, respectively, the individual, responsible for producing evidence, spreading information, and choosing theories; the community, a set of scientists investigating a series of phenomena; and the groups, individuals with similar behavior but with looser institutional or social ties — a usually neglected category in Kuhnian literature, but equally fundamental for the final outcome of scientific debates. After investigating these categories in detail, I propose a way of integrating them into a general model for explaining the resolution of scientific controversies. Finally, I try to resolve the apparent conflict among disciplinary vocabularies by offering an account of the function of sociological, psychological, and epistemological concepts for describing controversies, and some of the methodologies appropriate for each of these tasks.

Assessment of Spatial Distribution of Waste Bins in Karachi Through GIS Techniques

Karachi has been facing various issues of municipal solid waste management. In the early 1960s, Karachi was the centre of leisure, now it has stretched out due to its increasing population. However, due to insufficient facilities and ineffective strategies, issues related to waste management are also increasing. For the problems related to waste management, the fundamental units available are municipal trash bins. In this study, 409 GPS point data of collection points of waste have been assembled from various areas of Karachi for assessment of the spatial distribution of waste bins. A spatial variation of distance between the trash bins is also identified through ArcGIS 10.3.1 cartography tool of generalization, which aggregates the points of trash bins by making polygon shape of the same distance. Globally, Geospatial techniques are used for changing the system of waste management. This is the first study that assessed the suitable distance of bins placement in the area under focus. The results revealed that there are no principles acquired by the government for the placement of trash bins with appropriate distance. In many towns of Karachi like Landhi and Korangi, bins are absent which impels people to throw their trash anywhere in the city

Scaling up real networks by geometric branching growth

Real networks often grow through the sequential addition of new nodes that connect to older ones in the graph. However, many real systems evolve through the branching of fundamental units, whether those be scientific fields, countries, or species. Here, we provide empirical evidence for self-similar growth of network structure in the evolution of real systems—the journal-citation network and the world trade web—and present the geometric branching growth model, which predicts this evolution and explains the symmetries observed. The model produces multiscale unfolding of a network in a sequence of scaled-up replicas preserving network features, including clustering and community structure, at all scales. Practical applications in real instances include the tuning of network size for best response to external influence and finite-size scaling to assess critical behavior under random link failures.

Standardized nuclear markers advance metazoan taxonomy

Species are the fundamental units of life and their recognition is essential for science and society. DNA barcoding, the use of a single and often mitochondrial gene, has been increasingly employed as a universal approach for the identification of animal species. However, this approach faces several challenges. Here, we demonstrate with empirical data from a number of metazoan animal lineages that multiple nuclear-encoded markers, so called universal single-copy orthologs (USCOs) performs much better than the single barcode gene to discriminate closely related species. Overcoming the general shortcomings of mitochondrial DNA barcodes, USCOs also accurately assign samples to higher taxonomic levels. These loci thus provide a powerful and unifying framework for species delimitation which considerably improves the DNA-based inference of animal species.

Notion-Concept-Term. Interpretations

There are various interpretations of the fundamental notions used in the study of terminology. This article is a comparative study of their definitions, conducted in the process of establishing benchmarks in the study of editorial-printing terminology. It presents a research of the theoretical foundations of terminology, a study of various interpretations of linguistic meanings of key notions of terminology: „notion”, „concept” and „term”. One of the fundamental units of terminology is the „notion”, which is characterized as an abstract object of knowledge. Another fundamental unit, the „concept”, represents classes of objects of knowledge, of perceptible phenomena. Concepts are called abstractions, mental constructions or units of thought that ensure the connection between objects and their definitions. They have an essential role in human knowledge, communication not being possible if we do not have a codification of concepts in linguistic signs (terms). The concepts ensure the connection between the objects and the designations that correspond to them. And the „term” is the material form, expressed through linguistic means, of a notion specialized in a certain field of knowledge.