Rice University Research Repository
The Rice Research Repository (R-3) provides access to research produced at Rice University, including theses and dissertations, journal articles, research center publications, datasets, and academic journals. Managed by Fondren Library, R-3 is indexed by Google and Google Scholar, follows best practices for preservation, and provides DOIs to facilitate citation. Woodson Research Center collections, including Rice Images and Documents and the Task Force on Slavery, Segregation, and Racial Injustice, have moved here.
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The GIAB genomic stratifications resource for human reference genomes
(Springer Nature, 2024) Dwarshuis, Nathan; Kalra, Divya; McDaniel, Jennifer; Sanio, Philippe; Alvarez Jerez, Pilar; Jadhav, Bharati; Huang, Wenyu (Eddy); Mondal, Rajarshi; Busby, Ben; Olson, Nathan D.; Sedlazeck, Fritz J.; Wagner, Justin; Majidian, Sina; Zook, Justin M.
Despite the growing variety of sequencing and variant-calling tools, no workflow performs equally well across the entire human genome. Understanding context-dependent performance is critical for enabling researchers, clinicians, and developers to make informed tradeoffs when selecting sequencing hardware and software. Here we describe a set of “stratifications,” which are BED files that define distinct contexts throughout the genome. We define these for GRCh37/38 as well as the new T2T-CHM13 reference, adding many new hard-to-sequence regions which are critical for understanding performance as the field progresses. Specifically, we highlight the increase in hard-to-map and GC-rich stratifications in CHM13 relative to the previous references. We then compare the benchmarking performance with each reference and show the performance penalty brought about by these additional difficult regions in CHM13. Additionally, we demonstrate how the stratifications can track context-specific improvements over different platform iterations, using Oxford Nanopore Technologies as an example. The means to generate these stratifications are available as a snakemake pipeline at https://github.com/usnistgov/giab-stratifications. We anticipate this being useful in enabling precise risk-reward calculations when building sequencing pipelines for any of the commonly-used reference genomes.
What drives perceptions of partisan cooperation?
(Cambridge University Press, 2024) Santoso, Lie Philip; Stevenson, Randolph T.; Weschle, Simon
What drives voters' perceptions of partisan cooperation? In this note, we investigate whether voters have accurate beliefs about which parties regularly cooperate with one another, and whether these beliefs follow the real-time portrait of cooperation and conflict between parties that is reported in the news. We combine original survey data of voters' perceptions of party cooperation in four countries over two time periods with a measure of parties' public relationships as reported by the media. We find that voters' perceptions of cooperation and conflict among parties do reflect actual patterns of interactions. This pattern holds even after controlling for policy differences between parties as well as joint cabinet membership. Furthermore, we show that the impact of contemporary events on cooperation perceptions is most pronounced for voters who monitor the political news more carefully. Our findings have important implications for partisan cooperation and mass–elite linkages. Specifically, we find that contrary to the usual finding that voters are generally uninformed about politics, voters hold broadly accurate beliefs about the patterns of partisan cooperation, and importantly, these views track changes in relevant news. This reflects positively on the masses' capacities to infer parties' behaviors.
Persistent flat band splitting and strong selective band renormalization in a kagome magnet thin film
(Springer Nature, 2024) Ren, Zheng; Huang, Jianwei; Tan, Hengxin; Biswas, Ananya; Pulkkinen, Aki; Zhang, Yichen; Xie, Yaofeng; Yue, Ziqin; Chen, Lei; Xie, Fang; Allen, Kevin; Wu, Han; Ren, Qirui; Rajapitamahuni, Anil; Kundu, Asish K.; Vescovo, Elio; Kono, Junichiro; Morosan, Emilia; Dai, Pengcheng; Zhu, Jian-Xin; Si, Qimiao; Minár, Ján; Yan, Binghai; Yi, Ming; Smalley-Curl Institute
Magnetic kagome materials provide a fascinating playground for exploring the interplay of magnetism, correlation and topology. Many magnetic kagome systems have been reported including the binary FemXn (X = Sn, Ge; m:n = 3:1, 3:2, 1:1) family and the rare earth RMn6Sn6 (R = rare earth) family, where their kagome flat bands are calculated to be near the Fermi level in the paramagnetic phase. While partially filling a kagome flat band is predicted to give rise to a Stoner-type ferromagnetism, experimental visualization of the magnetic splitting across the ordering temperature has not been reported for any of these systems due to the high ordering temperatures, hence leaving the nature of magnetism in kagome magnets an open question. Here, we probe the electronic structure with angle-resolved photoemission spectroscopy in a kagome magnet thin film FeSn synthesized using molecular beam epitaxy. We identify the exchange-split kagome flat bands, whose splitting persists above the magnetic ordering temperature, indicative of a local moment picture. Such local moments in the presence of the topological flat band are consistent with the compact molecular orbitals predicted in theory. We further observe a large spin-orbital selective band renormalization in the Fe $${{{{\rm{d}}}}}_{{xy}}+{{{{\rm{d}}}}}_{{x}^{2}-{y}^{2}}$$spin majority channel reminiscent of the orbital selective correlation effects in the iron-based superconductors. Our discovery of the coexistence of local moments with topological flat bands in a kagome system echoes similar findings in magic-angle twisted bilayer graphene, and provides a basis for theoretical effort towards modeling correlation effects in magnetic flat band systems.
Ecological shifts underlie parallels between ontogenetic and evolutionary allometries in parrotfishes
(Royal Society, 2024) Neves, Mayara P.; Hugi, April; Chan, Howan; Arnold, Kaleigh; Titus, Kara; Westneat, Mark W.; Zelditch, Miriam L.; Brandl, Simon; Evans, Kory M.
During ontogeny, animals often undergo significant shape and size changes, coinciding with ecological shifts. This is evident in parrotfishes (Eupercaria: Labridae), which experience notable ecological shifts during development, transitioning from carnivorous diets as larvae and juveniles to herbivorous and omnivorous diets as adults, using robust beaks and skulls for feeding on coral skeletons and other hard substrates. These ontogenetic shifts mirror their evolutionary history, as parrotfishes are known to have evolved from carnivorous wrasse ancestors. Parallel shifts at ontogenetic and phylogenetic levels may have resulted in similar evolutionary and ontogenetic allometric trajectories within parrotfishes. To test this hypothesis, using micro-computed tomography (μCT) scanning and three-dimensional geometric morphometrics, we analyse the effects of size on the skull shape of the striped parrotfish Scarus iseri and compare its ontogenetic allometry to the evolutionary allometries of 57 parrotfishes and 162 non-parrotfish wrasses. The young S. iseri have skull shapes resembling non-parrotfish wrasses and grow towards typical adult parrotfish forms as they mature. There was a significant relationship between size and skull shapes and strong evidence for parallel ontogenetic and evolutionary slopes in parrotfishes. Our findings suggest that morphological changes associated with the ecological shift characterizing interspecific parrotfish evolution are conserved in their intraspecific ontogenies.
Transcriptional responses to direct and indirect TGFB1 stimulation in cancerous and noncancerous mammary epithelial cells
(Springer Nature, 2024) Janus, Patryk; Kuś, Paweł; Jaksik, Roman; Vydra, Natalia; Toma-Jonik, Agnieszka; Gramatyka, Michalina; Kurpas, Monika; Kimmel, Marek; Widłak, Wiesława
Transforming growth factor beta (TGFβ) is important for the morphogenesis and secretory function of the mammary gland. It is one of the main activators of the epithelial–mesenchymal transition (EMT), a process important for tissue remodeling and regeneration. It also provides cells with the plasticity to form metastases during tumor progression. Noncancerous and cancer cells respond differently to TGFβ. However, knowledge of the cellular signaling cascades triggered by TGFβ in various cell types is still limited.