Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions.

We introduce mvSuSiE, a multi-trait fine-mapping method for identifying putative causal variants from genetic association data (individual-level or summary data). mvSuSiE learns patterns of shared genetic effects from data, and exploits these patterns to improve power to identify causal SNPs. Comparisons on simulated data show that mvSuSiE is competitive in speed, power and precision with existing multi-trait methods, and uniformly improves on single-trait fine-mapping (SuSiE) in each trait separately. We applied mvSuSiE to jointly fine-map 16 blood cell traits using data from the UK Biobank. By jointly analyzing the traits and modeling heterogeneous effect sharing patterns, we discovered a much larger number of causal SNPs (>3,000) compared with single-trait fine-mapping, and with narrower credible sets. mvSuSiE also more comprehensively characterized the ways in which the genetic variants affect one or more blood cell traits; 68% of causal SNPs showed significant effects in more than one blood cell type.

Chunks, pauses, and holistic processing in Mandarin spontaneous speech.

Chunks are multiword sequences with independent meaning and function, or formulaic based on the intuition of native speakers, hypothesized to be holistically restored and retrieved in the mental lexicon. Previous studies suggest that pauses and intonational boundaries tend to occur at the boundaries of chunks, but less discussion was made on the influence of chunk categories over mental processing and on pause placement associated with intonational continuity. This study adopted spontaneous monologs of Mandarin natives in formal and informal settings. It examined the co-occurrence of chunks and pause-defined processing units and pause placement around chunks to explore to what extent chunks are holistically processed. The results showed that Mandarin chunks were likely to be situated within a single processing unit, indicating chunks as smaller units than processing units in spontaneous speech. Major chunk categories exhibited significantly different patterns in co-occurring with processing units, indicating the influence of chunk properties on the mental processing of chunks. In addition, chunks tended to be fluently processed in spontaneous speech production as fewer hesitations occurred before and during chunk production. Major chunk categories shared a similar threshold in encountering hesitations before chunk production and differed significantly in hesitation distribution during chunk production. Hesitations in the middle of chunks were more likely to be situated within intonation units compared to those before chunk production. Speakers' effort to maintain the intonational continuity of chunks when they encounter processing difficulties reveals the mental reality of the holistic nature of chunks. Furthermore, the co-occurrence of chunks and processing units differed significantly between the formal and informal speech genres, indicating genre influence on the mental processing of chunks. Altogether, the findings of this study have provided implications for theories on chunks and the syntactic-prosody interface and contributed to implications for the design of Mandarin instructions and teaching.

Recovery and facets for deformation twins in minerals and metals.

Type II and IV twins with irrational twin boundaries are studied by high-resolution transmission electron microscopy in two plagioclase crystals. The twin boundaries in these and in NiTi are found to relax to form rational facets separated by disconnections. The topological model (TM), amending the classical model, is required for a precise theoretical prediction of the orientation of the Type II/IV twin plane. Theoretical predictions also are presented for types I, III, V, and VI twins. The relaxation process that forms a faceted structure entails a separate prediction from the TM. Hence, faceting provides a difficult test for the TM. Analysis of the faceting by the TM is in excellent agreement with the observations.

Enhanced Electron Correlation and Significantly Suppressed Thermal Conductivity in Dirac Nodal-Line Metal Nanowires by Chemical Doping.

Enhancing electron correlation in a weakly interacting topological system has great potential to promote correlated topological states of matter with extraordinary quantum properties. Here, the enhancement of electron correlation in a prototypical topological metal, namely iridium dioxide (IrO2 ), via doping with 3d transition metal vanadium is demonstrated. Single-crystalline vanadium-doped IrO2 nanowires are synthesized through chemical vapor deposition where the nanowire yield and morphology are improved by creating rough surfaces on substrates. Vanadium doping leads to a dramatic decrease in Raman intensity without notable peak broadening, signifying the enhancement of electron correlation. The enhanced electron correlation is further evidenced by transport studies where the electrical resistivity is greatly increased and follows an unusual T $\sqrt T $ dependence on the temperature (T). The lattice thermal conductivity is suppressed by an order of magnitude via doping even at room temperature where phonon-impurity scattering becomes less important. Density functional theory calculations suggest that the remarkable reduction of thermal conductivity arises from the complex phonon dispersion and reduced energy gap between phonon branches, which greatly enhances phase space for phonon-phonon Umklapp scattering. This work demonstrates a unique system combining 3d and 5d transition metals in isostructural materials to enrich the system with various types of interactions.

A Novel Microshear Geometry for Exploring the Influence of Void Swelling on the Mechanical Properties Induced by MeV Heavy Ion Irradiation.

Small disks are often the specimen of choice for exposure in nuclear reactor environments, and this geometry invariably limits the types of mechanical testing that can be performed on the specimen. Recently, shear punch testing has been utilized to evaluate changes arising from neutron irradiation in test reactor environments on these small disk specimens. As part of a broader effort to link accelerated testing using ion irradiation and conventional neutron irradiation techniques, a novel microshear specimen geometry was developed for use with heavy-ion irradiated specimens. The technique was demonstrated in pure Cu irradiated to 11 and 110 peak dpa with 10 MeV Cu ions. At 11 peak dpa, the Cu specimen had a high density of small voids in the irradiated region, while at 110 peak dpa, larger voids with an average void swelling of ~20% were observed. Micropillar and microshear specimens both exhibited hardening at 11 dpa, followed by softening at 110 dpa. The close alignment of the new microshear technique and more conventional micropillar testing, and the fact that both follow intuition, is a good first step towards applying microshear testing to a wider range of irradiated materials.

Van der Waals Superstructure and Twisting in Self-Intercalated Magnet with Near Room-Temperature Perpendicular Ferromagnetism.

The emergence of van der Waals (vdW) magnets has created unprecedented opportunities to manipulate magnetism for advanced spintronics based upon all-vdW heterostructures. Among various vdW magnets, Cr1+δTe2 possesses high temperature ferromagnetism along with possible topological spin textures. As this system can support self-intercalation in the vdW gap, it is crucial to precisely pinpoint the exact intercalation to understand the intrinsic magnetism of the system. Here, we developed an iterative method to determine the self-intercalated structures and show evidence of vdW "superstructures" in individual Cr1+δTe2 nanoplates exhibiting magnetic behaviors distinct from bulk chromium tellurides. Among 26,332 possible configurations, we unambiguously identified the Cr-intercalated structure as 3-fold symmetry broken Cr1.5Te2 segmented by vdW gaps. Moreover, a twisted Cr-intercalated layered structure is observed. The spontaneous formation of twisted vdW "superstructures" not only provides insight into the diverse magnetic properties of intercalated vdW magnets but may also add complementary building blocks to vdW-based spintronics.

First-principles calculations for understanding microstructures and mechanical properties of co-sputtered Al alloys.

Recent experimental studies show that co-sputtering solutes with Al, together, can refine columnar grain size around few tens of nanometers and promote the formation and enhance the stability of planar defects such as stacking faults (SFs) and grain boundaries (GBs) in Al alloys. These crystal defects and fine columnar grains result in high strength, enhanced strain hardening and thermal stability of Al alloys. Using first-principles density-functional theory (DFT) calculations, we studied the role of eleven solutes in tailoring kinetics and energetics of adatoms and clusters on Al {111} surface, stable and unstable stacking fault energies, and kinetic energy barriers for the migration of defects. The calculations show that most solutes can effectively refine columnar grain size by decreasing the diffusivity of adatoms and surface clusters. These solutes do not necessarily decrease the stacking fault energy of Al alloys, but reduce the formation energy of faulted surface clusters and increase the energy barriers for the recovery of faulted surface clusters. Correspondingly, the formation of SFs is kinetically promoted during sputtering. Furthermore, solutes are segregated into the core of Shockley partial dislocations and play a pinning effect on SFs, SF arrays and twin boundaries, enhancing the thermal stability of these crystal defects. These findings provide insights into the design of high-strength Al alloys for high-temperature applications.

Near Degeneracy of Magnetic Phases in Two-Dimensional Chromium Telluride with Enhanced Perpendicular Magnetic Anisotropy.

The discovery of atomically thin van der Waals magnets (e.g., CrI3 and Cr2Ge2Te6) has triggered a renaissance in the study of two-dimensional (2D) magnetism. Most of the 2D magnetic compounds discovered so far host only one single magnetic phase unless the system is at a phase boundary. In this work, we report the near degeneracy of magnetic phases in ultrathin chromium telluride (Cr2Te3) layers with strong perpendicular magnetic anisotropy highly desired for stabilizing 2D magnetic order. Single-crystalline Cr2Te3 nanoplates with a trigonal structure (space group P3̅1c) were grown by chemical vapor deposition. The bulk magnetization measurements suggest a ferromagnetic (FM) order with an enhanced perpendicular magnetic anisotropy, as evidenced by a coercive field as large as ∼14 kOe when the field is applied perpendicular to the basal plane of the thin nanoplates. Magneto-optical Kerr effect studies confirm the intrinsic ferromagnetism and characterize the magnetic ordering temperature of individual nanoplates. First-principles density functional theory calculations suggest the near degeneracy of magnetic orderings with a continuously varying canting from the c-axis FM due to their comparable energy scales, explaining the zero-field kink observed in the magnetic hysteresis loops. Our work highlights Cr2Te3 as a promising 2D Ising system to study magnetic phase coexistence and switches for ultracompact information storage and processing.

A new sequence logo plot to highlight enrichment and depletion.

BACKGROUND: Sequence logo plots have become a standard graphical tool for visualizing sequence motifs in DNA, RNA or protein sequences. However standard logo plots primarily highlight enrichment of symbols, and may fail to highlight interesting depletions. Current alternatives that try to highlight depletion often produce visually cluttered logos. RESULTS: We introduce a new sequence logo plot, the EDLogo plot, that highlights both enrichment and depletion, while minimizing visual clutter. We provide an easy-to-use and highly customizable R package Logolas to produce a range of logo plots, including EDLogo plots. This software also allows elements in the logo plot to be strings of characters, rather than a single character, extending the range of applications beyond the usual DNA, RNA or protein sequences. And the software includes new Empirical Bayes methods to stabilize estimates of enrichment and depletion, and thus better highlight the most significant patterns in data. We illustrate our methods and software on applications to transcription factor binding site motifs, protein sequence alignments and cancer mutation signature profiles. CONCLUSIONS: Our new EDLogo plots and flexible software implementation can help data analysts visualize both enrichment and depletion of characters (DNA sequence bases, amino acids, etc.) across a wide range of applications.