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  1. Feathers are arguably the most complex integumentary structures in the entire animal kingdom. The evolutionary origins of feathers are still debated, but growing evidence from both molecular studies in extinct theropods [1–8] and living birds (e.g., [9–18]), as well as numerous fossil discoveries of structures morphologically consistent with feathers (e.g., [4,19–25]) indicate that feathers arose from filamentous structures first identifed in some theropod dinosaurs and birds more than 160 million years ago (e.g., [2,26,27]). However, some data suggest that integumentary structures similar to those from which feathers derived may have been present at the base of Dinosauria [28,29] or perhaps, the base of Archosauria ([30,31] and references therein). Because modern feathers are not biomineralized in life (contra [32,33]) their persistence in the fossil record is counterintuitive, but critical. The impressions of feathers in sediments surrounding skeletal elements led to the identification of Archaeopteryx as the first bird [34,35], but there was no organic trace with this specimen to suggest that any original material remained. However, the first specimen attributed to Archaeopteryx was a single, isolated feather [36]. This specimen presented differently from feather impressions surrounding the skeletal remains, instead visualized as a carbonized trace clearly distinct from the embedding sediments,more »suggesting that taphonomic processes resulting in preservation differed between the isolated feather and the skeletal specimen. The environmental factors resulting in these different modes of preservation remain relatively unexplored.« less
    Free, publicly-accessible full text available April 1, 2023
  2. Abstract Gene Ontology (GO) is widely used in the biological domain. It is the most comprehensive ontology providing formal representation of gene functions (GO concepts) and relations between them. However, unintentional quality defects (e.g. missing or erroneous relations) in GO may exist due to the large size of GO concepts and complexity of GO structures. Such quality defects would impact the results of GO-based analyses and applications. In this work, we introduce a novel evidence-based lexical pattern approach for quality assurance of GO relations. We leverage two layers of evidence to suggest potentially missing relations in GO as follows. We first utilize related concept pairs (i.e. existing relations) in GO to extract relationship-specific lexical patterns, which serve as the first layer evidence to automatically suggest potentially missing relations between unrelated concept pairs. For each suggested missing relation, we further identify two other existing relations as the second layer of evidence that resemble the difference between the missing relation and the existing relation based on which the missing relation is suggested. Applied to the 15 December 2021 release of GO, this approach suggested a total of 866 potentially missing relations. Local domain experts evaluated the entire set of potentially missing relations,more »and identified 821 as missing relations and 45 indicate erroneous existing relations. We submitted these findings to the GO consortium for further validation and received encouraging feedback. These indicate that our evidence-based approach can be utilized to uncover missing relations and erroneous existing relations in GO.« less
    Free, publicly-accessible full text available May 1, 2023
  3. ABSTRACT

    Multiwavelength variability studies of active galactic nuclei can be used to probe their inner regions that are not directly resolvable. Dust reverberation mapping (DRM) estimates the size of the dust emitting region by measuring the delays between the infrared (IR) response to variability in the optical light curves. We measure DRM lags of Zw229-015 between optical ground-based and Kepler light curves and concurrent IR Spitzer 3.6 and 4.5 µm light curves from 2010 to 2015, finding an overall mean rest-frame lag of 18.3 ± 4.5 d. Each combination of optical and IR light curve returns lags that are consistent with each other within 1σ, which implies that the different wavelengths are dominated by the same hot dust emission. The lags measured for Zw229-015 are found to be consistently smaller than predictions using the lag–luminosity relationship. Also, the overall IR response to the optical emission actually depends on the geometry and structure of the dust emitting region as well, so we use Markov chain Monte Carlo modelling to simulate the dust distribution to further estimate these structural and geometrical properties. We find that a large increase in flux between the 2011–2012 observation seasons, which is more dramatic in the IR light curve, is notmore »well simulated by a single dust component. When excluding this increase in flux, the modelling consistently suggests that the dust is distributed in an extended flat disc, and finds a mean inclination angle of 49$^{+3}_{-13}$ deg.

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  4. Abstract We present multiwavelength observations of the Type II SN 2020pni. Classified at ∼1.3 days after explosion, the object showed narrow (FWHM intensity <250 km s −1 ) recombination lines of ionized helium, nitrogen, and carbon, as typically seen in flash-spectroscopy events. Using the non-LTE radiative transfer code CMFGEN to model our first high-resolution spectrum, we infer a progenitor mass-loss rate of M ̇ = ( 3.5 – 5.3 ) × 10 − 3 M ⊙ yr −1 (assuming a wind velocity of v w = 200 km s −1 ), estimated at a radius of R in = 2.5 × 10 14 cm. In addition, we find that the progenitor of SN 2020pni was enriched in helium and nitrogen (relative abundances in mass fractions of 0.30–0.40 and 8.2 × 10 −3 , respectively). Radio upper limits are also consistent with dense circumstellar material (CSM) and a mass-loss rate of M ̇ > 5 × 10 − 4 M ☉ yr − 1 . During the initial 4 days after first light, we also observe an increase in velocity of the hydrogen lines (from ∼250 to ∼1000 km s −1 ), suggesting complex CSM. The presence of dense and confinedmore »CSM, as well as its inhomogeneous structure, indicates a phase of enhanced mass loss of the progenitor of SN 2020pni during the last year before explosion. Finally, we compare SN 2020pni to a sample of other shock-photoionization events. We find no evidence of correlations among the physical parameters of the explosions and the characteristics of the CSM surrounding the progenitors of these events. This favors the idea that the mass loss experienced by massive stars during their final years could be governed by stochastic phenomena and that, at the same time, the physical mechanisms responsible for this mass loss must be common to a variety of different progenitors.« less
    Free, publicly-accessible full text available February 1, 2023
  5. Two-dimensional van der Waals (vdWs) materials have gathered a lot of attention recently. However, the majority of these materials have Curie temperatures that are well below room temperature, making it challenging to incorporate them into device applications. In this work, we synthesized a room-temperature vdW magnetic crystal Fe5GeTe2 with a Curie temperature T$_c = 332$ K, and studied its magnetic properties by vibrating sample magnetometry (VSM) and broadband ferromagnetic resonance (FMR) spectroscopy. The experiments were performed with external magnetic fields applied along the c-axis (H$\parallel$c) and the ab-plane (H$\parallel$ab), with temperatures ranging from 300 to 10 K. We have found a sizable Landé g-factor difference between the H$\parallel$c and H$\parallel$ab cases. In both cases, the Landé g-factor values deviated from g = 2. This indicates contribution of orbital angular momentum to the magnetic moment. The FMR measurements reveal that Fe5GeTe2 has a damping constant comparable to Permalloy. With reducing temperature, the linewidth was broadened. Together with the VSM data, our measurements indicate that Fe5GeTe2 transitions from ferromagnetic to ferrimagnetic at lower temperatures. Our experiments highlight key information regarding the magnetic state and spin scattering processes in Fe5GeTe2, which promote the understanding of magnetism in Fe5GeTe2, leading to implementations of Fe5GeTe2more »based room-temperature spintronic devices.« less
  6. Abstract Objective The Unified Medical Language System (UMLS) integrates various source terminologies to support interoperability between biomedical information systems. In this article, we introduce a novel transformation-based auditing method that leverages the UMLS knowledge to systematically identify missing hierarchical IS-A relations in the source terminologies. Materials and Methods Given a concept name in the UMLS, we first identify its base and secondary noun chunks. For each identified noun chunk, we generate replacement candidates that are more general than the noun chunk. Then, we replace the noun chunks with their replacement candidates to generate new potential concept names that may serve as supertypes of the original concept. If a newly generated name is an existing concept name in the same source terminology with the original concept, then a potentially missing IS-A relation between the original and the new concept is identified. Results Applying our transformation-based method to English-language concept names in the UMLS (2019AB release), a total of 39 359 potentially missing IS-A relations were detected in 13 source terminologies. Domain experts evaluated a random sample of 200 potentially missing IS-A relations identified in the SNOMED CT (U.S. edition) and 100 in Gene Ontology. A total of 173 of 200 and 63more »of 100 potentially missing IS-A relations were confirmed by domain experts, indicating that our method achieved a precision of 86.5% and 63% for the SNOMED CT and Gene Ontology, respectively. Conclusions Our results showed that our transformation-based method is effective in identifying missing IS-A relations in the UMLS source terminologies.« less
  7. Background: We investigated the association between reproductive risk factors and breast cancer subtype in Black women. On the basis of the previous literature, we hypothesized that the relative prevalence of specific breast cancer subtypes might differ according to reproductive factors. Methods: We conducted a pooled analysis of 2,188 (591 premenopausal, 1,597 postmenopausal) Black women with a primary diagnosis of breast cancer from four studies in the southeastern United States. Breast cancers were classified by clinical subtype. Case-only polytomous logistic regression models were used to estimate ORs and 95% confidence intervals (CI) for HER2+ and triple-negative breast cancer (TNBC) status in relation to estrogen receptor–positive (ER+)/HER2− status (referent) for reproductive risk factors. Results: Relative to women who had ER+/HER2− tumors, women who were age 19–24 years at first birth (OR, 1.78; 95% CI, 1.22–2.59) were more likely to have TNBC. Parous women were less likely to be diagnosed with HER2+ breast cancer and more likely to be diagnosed with TNBC relative to ER+/HER2− breast cancer. Postmenopausal parous women who breastfed were less likely to have TNBC [OR, 0.65 (95% CI, 0.43–0.99)]. Conclusions: This large pooled study of Black women with breast cancer revealed etiologic heterogeneity among breast cancer subtypes. Impact: Blackmore »parous women who do not breastfeed are more likely to be diagnosed with TNBC, which has a worse prognosis, than with ER+/HER2− breast cancer.« less
  8. Free, publicly-accessible full text available January 13, 2023