Subnanometer-resolution structures of the grass carp reovirus core and virion.

Grass carp reovirus (GCRV) is a member of the Aquareovirus genus of the family Reoviridae, a large family of double-stranded RNA (dsRNA) viruses infecting plants, insects, fishes and mammals. We report the first subnanometer-resolution three-dimensional structures of both GCRV core and virion by cryoelectron microscopy. These structures have allowed the delineation of interactions among the over 1000 molecules in this enormous macromolecular machine and a detailed comparison with other dsRNA viruses at the secondary-structure level. The GCRV core structure shows that the inner proteins have strong structural similarities with those of orthoreoviruses even at the level of secondary-structure elements, indicating that the structures involved in viral dsRNA interaction and transcription are highly conserved. In contrast, the level of similarity in structures decreases in the proteins situated in the outer layers of the virion. The proteins involved in host recognition and attachment exhibit the least similarities to other members of Reoviridae. Furthermore, in GCRV, the RNA-translocating turrets are in an open state and lack a counterpart for the sigma1 protein situated on top of the close turrets observed in mammalian orthoreovirus. Interestingly, the distribution and the organization of GCRV core proteins resemble those of the cytoplasmic polyhedrosis virus, a cypovirus and the structurally simplest member of the Reoviridae family. Our results suggest that GCRV occupies a unique structure niche between the simpler cypoviruses and the considerably more complex mammalian orthoreovirus, thus providing an important model for understanding the structural and functional conservation and diversity of this enormous family of dsRNA viruses

Unsupervised Explanation Generation via Correct Instantiations

While large pre-trained language models (PLM) have shown their great skills at solving discriminative tasks, a significant gap remains when compared with humans for explanation-related tasks. Among them, explaining the reason why a statement is wrong (e.g., against commonsense) is incredibly challenging. The major difficulty is finding the conflict point, where the statement contradicts our real world. This paper proposes Neon, a two-phrase, unsupervised explanation generation framework. Neon first generates corrected instantiations of the statement (phase I), then uses them to prompt large PLMs to find the conflict point and complete the explanation (phase II). We conduct extensive experiments on two standard explanation benchmarks, i.e., ComVE and e-SNLI. According to both automatic and human evaluations, Neon outperforms baselines, even for those with human-annotated instantiations. In addition to explaining a negative prediction, we further demonstrate that Neon remains effective when generalizing to different scenarios.Comment: Accepted to AAAI-2

AgentBoard: An Analytical Evaluation Board of Multi-turn LLM Agents

Evaluating large language models (LLMs) as general-purpose agents is essential for understanding their capabilities and facilitating their integration into practical applications. However, the evaluation process presents substantial challenges. A primary obstacle is the benchmarking of agent performance across diverse scenarios within a unified framework, especially in maintaining partially-observable environments and ensuring multi-round interactions. Moreover, current evaluation frameworks mostly focus on the final success rate, revealing few insights during the process and failing to provide a deep understanding of the model abilities. To address these challenges, we introduce AgentBoard, a pioneering comprehensive benchmark and accompanied open-source evaluation framework tailored to analytical evaluation of LLM agents. AgentBoard offers a fine-grained progress rate metric that captures incremental advancements as well as a comprehensive evaluation toolkit that features easy assessment of agents for multi-faceted analysis through interactive visualization. This not only sheds light on the capabilities and limitations of LLM agents but also propels the interpretability of their performance to the forefront. Ultimately, AgentBoard serves as a significant step towards demystifying agent behaviors and accelerating the development of stronger LLM agents.Comment: Preprin

Antenna arrangement and energy-transfer pathways of PSI-LHCI from the moss Physcomitrella patens

Plants harvest light energy utilized for photosynthesis by light-harvesting complex I and II (LHCI and LHCII) surrounding photosystem I and II (PSI and PSII), respectively. During the evolution of green plants, moss is at an evolutionarily intermediate position from aquatic photosynthetic organisms to land plants, being the first photosynthetic organisms that landed. Here, we report the structure of the PSI-LHCI supercomplex from the moss Physcomitrella patens (Pp) at 3.23 angstrom resolution solved by cryo-electron microscopy. Our structure revealed that four Lhca subunits are associated with the PSI core in an order of Lhca1-Lhca5-Lhca2-Lhca3. This number is much decreased from 8 to 10, the number of subunits in most green algal PSI-LHCI, but the same as those of land plants. Although Pp PSI-LHCI has a similar structure as PSI-LHCI of land plants, it has Lhca5, instead of Lhca4, in the second position of Lhca, and several differences were found in the arrangement of chlorophylls among green algal, moss, and land plant PSI-LHCI. One chlorophyll, PsaF-Chl 305, which is found in the moss PSI-LHCI, is located at the gap region between the two middle Lhca subunits and the PSI core, and therefore may make the excitation energy transfer from LHCI to the core more efficient than that of land plants. On the other hand, energy-transfer paths at the two side Lhca subunits are relatively conserved. These results provide a structural basis for unravelling the mechanisms of light-energy harvesting and transfer in the moss PSI-LHCI, as well as important clues on the changes of PSI-LHCI after landing

Lemur: Harmonizing Natural Language and Code for Language Agents

We introduce Lemur and Lemur-Chat, openly accessible language models optimized for both natural language and coding capabilities to serve as the backbone of versatile language agents. The evolution from language chat models to functional language agents demands that models not only master human interaction, reasoning, and planning but also ensure grounding in the relevant environments. This calls for a harmonious blend of language and coding capabilities in the models. Lemur and Lemur-Chat are proposed to address this necessity, demonstrating balanced proficiencies in both domains, unlike existing open-source models that tend to specialize in either. Through meticulous pre-training using a code-intensive corpus and instruction fine-tuning on text and code data, our models achieve state-of-the-art averaged performance across diverse text and coding benchmarks among open-source models. Comprehensive experiments demonstrate Lemur's superiority over existing open-source models and its proficiency across various agent tasks involving human communication, tool usage, and interaction under fully- and partially- observable environments. The harmonization between natural and programming languages enables Lemur-Chat to significantly narrow the gap with proprietary models on agent abilities, providing key insights into developing advanced open-source agents adept at reasoning, planning, and operating seamlessly across environments. https://github.com/OpenLemur/Lemu

Assembly and Capsid Expansion Mechanism of Bacteriophage P22 Revealed by High-Resolution Cryo-EM Structures

The formation of many double-stranded DNA viruses, such as herpesviruses and bacteriophages, begins with the scaffolding-protein-mediated assembly of the procapsid. Subsequently, the procapsid undergoes extensive structural rearrangement and expansion to become the mature capsid. Bacteriophage P22 is an established model system used to study virus maturation. Here, we report the cryo-electron microscopy structures of procapsid, empty procapsid, empty mature capsid, and mature capsid of phage P22 at resolutions of 2.6 Å, 3.9 Å, 2.8 Å, and 3.0 Å, respectively. The structure of the procapsid allowed us to build an accurate model of the coat protein gp5 and the C-terminal region of the scaffolding protein gp8. In addition, interactions among the gp5 subunits responsible for procapsid assembly and stabilization were identified. Two C-terminal α-helices of gp8 were observed to interact with the coat protein in the procapsid. The amino acid interactions between gp5 and gp8 in the procapsid were consistent with the results of previous biochemical studies involving mutant proteins. Our structures reveal hydrogen bonds and salt bridges between the gp5 subunits in the procapsid and the conformational changes of the gp5 domains involved in the closure of the local sixfold opening and a thinner capsid shell during capsid maturation

Assembly and Capsid Expansion Mechanism of Bacteriophage P22 Revealed by High-Resolution Cryo-EM Structures

The formation of many double-stranded DNA viruses, such as herpesviruses and bacteriophages, begins with the scaffolding-protein-mediated assembly of the procapsid. Subsequently, the procapsid undergoes extensive structural rearrangement and expansion to become the mature capsid. Bacteriophage P22 is an established model system used to study virus maturation. Here, we report the cryo-electron microscopy structures of procapsid, empty procapsid, empty mature capsid, and mature capsid of phage P22 at resolutions of 2.6 Å, 3.9 Å, 2.8 Å, and 3.0 Å, respectively. The structure of the procapsid allowed us to build an accurate model of the coat protein gp5 and the C-terminal region of the scaffolding protein gp8. In addition, interactions among the gp5 subunits responsible for procapsid assembly and stabilization were identified. Two C-terminal α-helices of gp8 were observed to interact with the coat protein in the procapsid. The amino acid interactions between gp5 and gp8 in the procapsid were consistent with the results of previous biochemical studies involving mutant proteins. Our structures reveal hydrogen bonds and salt bridges between the gp5 subunits in the procapsid and the conformational changes of the gp5 domains involved in the closure of the local sixfold opening and a thinner capsid shell during capsid maturation

Dataset for the submission in Estuarine, Coastal and Shelf Science YECSS-D-23-00597

<p>The data are saved as matlab data file.</p><p>1) ssc_fit.mat is used for producing figure 2.</p><p>2) Reynolds_shear_stress.mat is used for producing figures 3, 5, 8 and 9.</p><p>3) hydrodynamics.mat is used for producing figure 4.</p><p>4) shear_stress_&_ssc.mat is uesd for producing figures 5 and 9.</p><p>5) SSF.mat is used for producing figures 6.</p><p>6) breaking_wave_criteria.mat is used for producing figure 7.</p><p> </p&gt

Structure determination of a human virus by the combination of cryo-EM and X-ray crystallography

Virus 3D atomic structures provide insight into our understanding of viral life cycles and the development of antiviral drugs. X-ray crystallography and cryo-EM have been used to determine the atomic structure of viruses. However, limited availability of biological samples, biosafety issues due to virus infection, and sometimes inherent characteristics of viruses, pose difficulties on combining both methods in determining viral structures. These have made solving the high resolution structure of some medically important viruses very challenging. Here, we describe our recently employed protocols for determining the high-resolution structure of the virus-like particle of hepatitis E virus (HEV), a pathogen of viral hepatitis in human. These protocols include utilizing recombinant baculovirus system to generate sufficient amount of virus particles, single-particle cryo-EM to get an intermediate resolution structure as a phasing model, and X-ray crystallography for final atomic structure determination. Our protocols have solved the hepatitis E virus structure to the resolution of 3.5 Å. The combined methodology is generally applicable to other human infectious viruses

A Capsid Structure of Ralstonia solanacearum podoviridae GP4 with a Triangulation Number T = 9

GP4, a new Ralstonia solanacearum phage, is a short-tailed phage. Few structures of Ralstonia solanacearum phages have been resolved to near-atomic resolution until now. Here, we present a 3.7 Å resolution structure of the GP4 head by cryo-electron microscopy (cryo-EM). The GP4 head contains 540 copies of major capsid protein (MCP) gp2 and 540 copies of cement protein (CP) gp1 arranged in an icosahedral shell with a triangulation number T = 9. The structures of gp2 and gp1 show a canonical HK97-like fold and an Ig-like fold, respectively. The trimeric CPs stick on the surface of the head along the quasi-threefold axis of the icosahedron generating a sandwiched three-layer electrostatic complementary potential, thereby enhancing the head stability. The assembly pattern of the GP4 head provides a platform for the further exploration of the interaction between Ralstonia solanacearum and corresponding phages