A unified view of LCRs across species

Low complexity regions (LCRs) in proteins play a major role in the higher order assemblies of organisms, such as the nucleolus and extracellular matrix. Despite recent focus on how certain features affect the function of LCRs in intracellular higher order assemblies, the relationships between LCRs within proteins, captured by their type and copy number, has yet to be systematically studied. Furthermore, we still lack a unified view of how the sequences, features, relationships and functions of LCRs relate to each other. Here, we developed a systematic and comprehensive approach using dotplot matrices and dimensionality reduction to define LCR relationships proteome-wide and to create a map of LCR sequences capable of integrating any LCR features. As a proof of concept of the importance of LCR relationships, we demonstrate the biological significance of LCR copy number for higher order assembly of the nucleolar protein RPA43 both in vitro and in vivo. Using the LCR map, we revealed the boundaries and connections between regions of sequence space occupied by LCRs, and that LCRs of certain higher order assemblies populated specific regions of sequence space. The integration of LCR relationships and the LCR map provided a unified view of LCRs which uncovered the distribution, distinguishing features, and conserved prevalence of glutamic acid-rich LCRs among nucleolar proteins. When applied across multiple species, this approach highlights how differential occupancy of certain regions of LCR sequence space corresponds to the conservation and emergence of higher order assemblies, such as the plant cell wall or metazoan extracellular matrix. Additionally, we identified previously undescribed regions of LCR sequence space, including a teleost-specific threonine/histidine-rich cluster which exhibits signatures of higher order assemblies. By providing this unified view of LCRs, our approach enables discovery of how LCRs encode higher order assemblies of organisms.

Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin

Chromosome organization and dynamics are involved in regulating many fundamental processes such as gene transcription and DNA repair. Experiments unveiled that chromatin motion is highly heterogeneous inside cell nuclei, ranging from a liquid-like, mobile state to a gel-like, rigid regime. Using polymer modeling, we investigate how these different physical states and dynamical heterogeneities may emerge from the same structural mechanisms. We found that the formation of topologically associating domains (TADs) is a key driver of chromatin motion heterogeneity. In particular, we showed that the local degree of compaction of the TAD regulates the transition from a weakly compact, fluid state of chromatin to a more compact, gel state exhibiting anomalous diffusion and coherent motion. Our work provides a comprehensive study of chromosome dynamics and a unified view of chromatin motion enabling interpretation of the wide variety of dynamical behaviors observed experimentally across different biological conditions, suggesting that the “liquid” or “solid” state of chromatin are in fact two sides of the same coin.

Uncertain Portfolio Optimization based on Dempster-Shafer Theory

Nowadays, the selection and management of the optimal portfolio are the most primary fields of financial decision-making. Thereby, selecting a portfolio capable of providing the highest efficiency and, at the same time, the lowest investment risk has been turned into one of the most critical concerns among financial activists. However, in this selection, the two factors above are not the only determining ones. Various factors are affecting financial markets' behavior under different possible scenarios, which should be identified. In this paper, we examine the high sensitivity of the Iranian capital market to the exchange rate fluctuations in the different scenarios due to the lack of a unified view of the value of that rate among experts as one of the mentioned factors and obtain its value using Dempster–Shafer theory (DST). Then, a portfolio selection model that prefers stocks with higher ranks is proposed. Representative results of the real-life case study reveal that the submitted approach is productive and practically applicable.

Future of Us – Transforming Healthcare With Intelligent Machines (Vol. 25, No. 12, Full Issue)

For the month of December 2021, APBN looks the applications of artificial intelligence and robotics in the healthcare space. In Features, we hear from Christopher Khang, President and CEO of GE Healthcare ASEAN, on how innovative technologies such as AI and automation are shaping a bright future for radiologists and their patients. Then, we have David Irecki from Boomi, who proposes that a unified view of patient data can enable holistic, coordinated services that will improve people'soverall quality of life, and an article contribution by Lewis Ho, Chief Executive Officer at Avalon SteriTech on innovative healthcare solutions and the future of smart cleaning. Shifting away from intelligent machines, we speak to Dr. Goh Choo Beng, Head of Medical Affairs at Takeda APAC, on unmet disease areas and learn more about the different treatments and trials currently in the pipeline at Takeda, and finally, we wrap up the year 2021 with Lu-Ching Lau, Director for External Affairs, Policy and Communications, Singapore and Malaysia, MSD, as she shares with us how we may navigate through current and future health challenges.

Same: structural sources of anaphora and relativization

This paper offers a unified view of the structures giving rise to anaphora and relativization within same-expressions. Taking as a point of departure the proposal that indices occupy syntactic positions in anaphoric DPs (Schwarz 2009, Simonenko 2014, a.o.), I examine the open issue of how anaphoric modifiers, particularly same, are predicted to interact with this proposed structural complexity. Based on the morphosyntactic behavior of definite descriptions with same, I argue that indices may be housed in DP structure in different ways. I argue moreover that the behavior of same in both anaphoric and non-anaphoric contexts supports the view that same is syntactically an equative degree head (Alrenga 2007, Oxford 2010), whose selectional properties are mirrored in a range of equative constructions. Finally, I propose an analysis of as-relatives selected by same that accounts for their alternation with anaphora, and offer a comparison with restrictive relatives.

The arts and their functions

In asking the question ‘What is art?’, four major conceptions of a work of art can be considered: an object; an indicator of beauty; an indicator of craftsmanship or creativity; and a process of performance. This chapter contends that the two principal functions of the arts are re-creation and interpersonal coordination. Re-creation reflects the inherently narrative and symbolic function of the arts, as conveyed through storytelling, acting, narrative dance, and figurative forms of visual art. Interpersonal coordination—as seen in artforms such as dance and music—occurs in the three domains of time, physical space (dance), and tonal pitch space (music). A unified view of the arts reveals not only the cognitive similarities among artforms, but the widespread ability of artforms to combine with one another to form syntheses, as seen in songs with words and dances choreographed to music. A comparative analysis of the arts provides greater insight into each artform than is possible by looking at artforms in isolation.