Dense-ATOMIC: Towards Densely-connected ATOMIC with High Knowledge Coverage and Massive Multi-hop Paths

ATOMIC is a large-scale commonsense knowledge graph (CSKG) containing everyday if-then knowledge triplets, i.e., {head event, relation, tail event}. The one-hop annotation manner made ATOMIC a set of independent bipartite graphs, which ignored the numerous links between events in different bipartite graphs and consequently caused shortages in knowledge coverage and multi-hop paths. In this work, we aim to construct Dense-ATOMIC with high knowledge coverage and massive multi-hop paths. The events in ATOMIC are normalized to a consistent pattern at first. We then propose a CSKG completion method called Rel-CSKGC to predict the relation given the head event and the tail event of a triplet, and train a CSKG completion model based on existing triplets in ATOMIC. We finally utilize the model to complete the missing links in ATOMIC and accordingly construct Dense-ATOMIC. Both automatic and human evaluation on an annotated subgraph of ATOMIC demonstrate the advantage of Rel-CSKGC over strong baselines. We further conduct extensive evaluations on Dense-ATOMIC in terms of statistics, human evaluation, and simple downstream tasks, all proving Dense-ATOMIC's advantages in Knowledge Coverage and Multi-hop Paths. Both the source code of Rel-CSKGC and Dense-ATOMIC are publicly available on https://github.com/NUSTM/Dense-ATOMIC.Comment: Accepted by ACL 2023 Main Conferenc

Blind men and elephants: What do citation summaries tell us about a research article?

The old Asian legend about the blind men and the elephant comes to mind when looking at how different authors of scientific papers describe a piece of related prior work. It turns out that different citations to the same paper often focus on different aspects of that paper and that neither provides a full description of its full set of contributions. In this article, we will describe our investigation of this phenomenon. We studied citation summaries in the context of research papers in the biomedical domain. A citation summary is the set of citing sentences for a given article and can be used as a surrogate for the actual article in a variety of scenarios. It contains information that was deemed by peers to be important. Our study shows that citation summaries overlap to some extent with the abstracts of the papers and that they also differ from them in that they focus on different aspects of these papers than do the abstracts. In addition to this, co-cited articles (which are pairs of articles cited by another article) tend to be similar. We show results based on a lexical similarity metric called cohesion to justify our claims.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/57540/1/20707_ftp.pd

Development and evaluation of 4WSS electric-driven chassis for high-clearance sprayer

IntroductionThe high clearance sprayer with conventional steering mechanisms, as an intelligent spraying machine, is frequently stuck or broken in muddy fields due to the excessive torque load.MethodsA Four-Wheel Self-Steering (4WSS) electric-driven chassis with a smaller turning radius and better passability is developed to handle complex agricultural terrains. The 4WSS chassis is mainly composed of two custom-designed steering bridges and four in-wheel drive motors. It can achieve steering and driving forward simultaneously through coordinate differential speed control of drive motors, saving a set of dedicated servo steering systems and requiring less torque during steering compared to conventional structures. A kinematic model depicting the speed relationships between four wheels is established via geometric analysis, and a Speed Distribution Controller (SDC) is designed to accomplish locomotion objectives.ResultsExperimental results demonstrate the effectiveness of the new prototype 4WSS chassis system in tracking speed and steering angle. Compared to conventional agricultural chassis, the 4WSS chassis has a smaller turning radius of 2,877 mm. DiscussionThe 4WSS chassis exhibits superior performance in typical field conditions, including muddy terrain, deep gullies, and ridges

Detection of co-eluted peptides using database search methods

<p>Abstract</p> <p>Background</p> <p>Current experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible. The increase in throughput however also raises concerns on the accuracy of identification or quantification. Most experimental procedures select in a given MS scan only a few relatively most intense parent ions, each to be fragmented (MS²) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost.</p> <p>Results</p> <p>We have computationally investigated the possibility of enhancing the information retrieval during a given LC/MS experiment by selecting the two or three most intense parent ions for simultaneous fragmentation. A set of spectra is created via superimposing a number of MS²spectra, each can be identified by all search methods tested with high confidence, to mimick the spectra of co-eluted peptides. The generated convoluted spectra were used to evaluate the capability of several database search methods – SEQUEST, Mascot, X!Tandem, OMSSA, and RAId_DbS – in identifying true peptides from superimposed spectra of co-eluted peptides. We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides.</p> <p>Open peer review</p> <p>Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.</p

Analysis of miRNAs and their target genes associated with lipid metabolism in duck liver

Citation: He, J. et al. Analysis of miRNAs and their target genes associated with lipid metabolism in duck liver. Sci. Rep. 6, 27418; doi: 10.1038/srep27418 (2016).Fat character is an important index in duck culture that linked to local flavor, feed cost and fat intake for costumers. Since the regulation networks in duck lipid metabolism had not been reported very clearly, we aimed to explore the potential miRNA-mRNA pairs and their regulatory roles in duck lipid metabolism. Here, Cherry-Valley ducks were selected and treated with/without 5% oil added in feed for 2 weeks, and then fat content determination was performed on. The data showed that the fat contents and the fatty acid ratios of C17:1 and C18:2 were up-regulated in livers of oil-added ducks, while the C12:0 ratio was down-regulated. Then 21 differential miRNAs, including 10 novel miRNAs, were obtain from the livers by sequencing, and 73 target genes involved in lipid metabolic processes of these miRNAs were found, which constituted 316 miRNA-mRNA pairs. Two miRNA-mRNA pairs including one novel miRNA and one known miRNA, N-miR-16020-FASN and gga-miR-144-ELOVL6, were selected to validate the miRNA-mRNA negative relation. And the results showed that N-mir-16020 and gga-miR-144 could respectively bind the 3?-UTRs of FASN and ELOVL6 to control their expressions. This study provides new sights and useful information for future research on regulation network in duck lipid metabolism

Integrated Pockels Laser

The development of integrated semiconductor lasers has miniaturized traditional bulky laser systems, enabling a wide range of photonic applications. A progression from pure III-V based lasers to III-V/external cavity structures has harnessed low-loss waveguides in different material systems, leading to significant improvements in laser coherence and stability. Despite these successes, however, key functions remain absent. In this work, we address a critical missing function by integrating the Pockels effect into a semiconductor laser. Using a hybrid integrated III-V/Lithium Niobate structure, we demonstrate several essential capabilities that have not existed in previous integrated lasers. These include a record-high frequency modulation speed of 2 exahertz/s (2.0$\times$10$^{18}$ Hz/s) and fast switching at 50 MHz, both of which are made possible by integration of the electro-optic effect. Moreover, the device co-lases at infrared and visible frequencies via the second-harmonic frequency conversion process, the first such integrated multi-color laser. Combined with its narrow linewidth and wide tunability, this new type of integrated laser holds promise for many applications including LiDAR, microwave photonics, atomic physics, and AR/VR

Inside-out Ca2+ signalling prompted by STIM1 conformational switch

Store-operated Ca(2+) entry mediated by STIM1 and ORAI1 constitutes one of the major Ca(2+) entry routes in mammalian cells. The molecular choreography of STIM1–ORAI1 coupling is initiated by endoplasmic reticulum (ER) Ca(2+) store depletion with subsequent oligomerization of the STIM1 ER-luminal domain, followed by its redistribution towards the plasma membrane to gate ORAI1 channels. The mechanistic underpinnings of this inside-out Ca(2+) signalling were largely undefined. By taking advantage of a unique gain-of-function mutation within the STIM1 transmembrane domain (STIM1-TM), here we show that local rearrangement, rather than alteration in the oligomeric state of STIM1-TM, prompts conformational changes in the cytosolic juxtamembrane coiled-coil region. Importantly, we further identify critical residues within the cytoplasmic domain of STIM1 (STIM1-CT) that entail autoinhibition. On the basis of these findings, we propose a model in which STIM1-TM reorganization switches STIM1-CT into an extended conformation, thereby projecting the ORAI-activating domain to gate ORAI1 channels

A SPectroscopic Survey of Biased Halos in the Reionization Era (ASPIRE): JWST Reveals a Filamentary Structure around a z = 6.61 Quasar

© 2023. The Author(s). Published by the American Astronomical Society. This is an open access article distributed under the Creative Commons Attribution License, to view a copy of the license, see: https://creativecommons.org/licenses/by/4.0/We present the first results from the JWST program A SPectroscopic survey of biased halos In the Reionization Era (ASPIRE). This program represents an imaging and spectroscopic survey of 25 reionization-era quasars and their environments by utilizing the unprecedented capabilities of NIRCam Wide Field Slitless Spectroscopy (WFSS) mode. ASPIRE will deliver the largest ( ∼280arcmin2 ) galaxy redshift survey at 3–4 μm among JWST Cycle 1 programs and provide extensive legacy values for studying the formation of the earliest supermassive black holes, the assembly of galaxies, early metal enrichment, and cosmic reionization. In this first ASPIRE paper, we report the discovery of a filamentary structure traced by the luminous quasar J0305–3150 and 10 [O iii] emitters at z = 6.6. This structure has a 3D galaxy overdensity of δ gal = 12.6 over 637 cMpc3, one of the most overdense structures known in the early universe, and could eventually evolve into a massive galaxy cluster. Together with existing VLT/MUSE and ALMA observations of this field, our JWST observations reveal that J0305–3150 traces a complex environment where both UV-bright and dusty galaxies are present and indicate that the early evolution of galaxies around the quasar is not simultaneous. In addition, we discovered 31 [O iii] emitters in this field at other redshifts, 5.3 < z < 6.7, with half of them situated at z ∼ 5.4 and 6.2. This indicates that star-forming galaxies, such as [O iii] emitters, are generally clustered at high redshifts. These discoveries demonstrate the unparalleled redshift survey capabilities of NIRCam WFSS and the potential of the full ASPIRE survey data set.Peer reviewe

A SPectroscopic Survey of Biased Halos in the Reionization Era (ASPIRE): A First Look at the Rest-frame Optical Spectra of z > 6.5 Quasars Using JWST

© 2023. The Author(s). Published by the American Astronomical Society. This is an open access article distributed under the Creative Commons Attribution License, to view a copy of the license, see: https://creativecommons.org/licenses/by/4.0/Studies of rest-frame optical emission in quasars at z > 6 have historically been limited by the wavelengths accessible by ground-based telescopes. The James Webb Space Telescope (JWST) now offers the opportunity to probe this emission deep into the reionization epoch. We report the observations of eight quasars at z > 6.5 using the JWST/NIRCam Wide Field Slitless Spectroscopy as a part of the “A SPectroscopic survey of biased halos In the Reionization Era (ASPIRE)” program. Our JWST spectra cover the quasars’ emission between rest frame ∼4100 and 5100 Å. The profiles of these quasars’ broad Hβ emission lines span a full width at half maximum from 3000 to 6000 km s−1. The Hβ-based virial black hole (BH) masses, ranging from 0.6 to 2.1 billion solar masses, are generally consistent with their Mg ii-based BH masses. The new measurements based on the more reliable Hβ tracer thus confirm the existence of a billion solar-mass BHs in the reionization epoch. In the observed [O iii] λ λ 4960,5008 doublets of these luminous quasars, broad components are more common than narrow core components (≤ 1200 km s−1), and only one quasar shows stronger narrow components than broad. Two quasars exhibit significantly broad and blueshifted [O iii] emission, thought to trace galactic-scale outflows, with median velocities of −610 and −1430 km s−1 relative to the [C ii] 158 μm line. All eight quasars show strong optical Fe ii emission and follow the eigenvector 1 relations defined by low-redshift quasars. The entire ASPIRE program will eventually cover 25 quasars and provide a statistical sample for the studies of the BHs and quasar spectral properties.Peer reviewe