Consensus Fold Recognition by Predicted Model Quality

Protein structure prediction has been a fundamental challenge in the biological field. In this post-genomic era, the need for automated protein structure prediction has never been more evident and researchers are now focusing on developing computational techniques to predict three-dimensional structures with high throughput. Consensus-based protein structure prediction methods are state-of-the-art in automatic protein structure prediction. A consensus-based server combines the outputs of several individual servers and tends to generate better predictions than any individual server. Consensus-based methods have proved to be successful in recent CASP (Critical Assessment of Structure Prediction). In this thesis, a Support Vector Machine (SVM) regression-based consensus method is proposed for protein fold recognition, a key component for high throughput protein structure prediction and protein function annotation. The SVM first extracts the features of a structural model by comparing the model to the other models produced by all the individual servers. Then, the SVM predicts the quality of each model. The experimental results from several LiveBench data sets confirm that our proposed consensus method, SVM regression, consistently performs better than any individual server. Based on this method, we developed a meta server, the Alignment by Consensus Estimation (ACE)

Undermined climate policies : a study on the impact of regulatory and financial discrimination across heterogeneous firms in China

Firms in China within the same industry but with different ownership and size have very different production functions and can face very different emission regulations and financial conditions. This fact has largely been ignored in most of the existing literature on climate change. Using a newly augmented Chinese input–output table in which information about firm size and ownership are explicitly reported, this paper employs a dynamic computable general equilibrium (CGE) model to analyze the impact of alternative climate policy designs with respect to regulation and financial conditions on heterogeneous firms. The simulation results indicate that with a business-as-usual regulatory structure, the effectiveness and economic efficiency of climate policies is significantly undermined. Expanding regulation to cover additional firms has a first-order effect of improving efficiency. However, over-investment in energy technologies in certain firms may decrease the overall efficiency of investments and dampen long-term economic growth by competing with other fixed-capital investments for financial resources. Therefore, a market-oriented arrangement for sharing emission reduction burden and a mechanism for allocating green investment is crucial for China to achieve a more ambitious emission target in the long run

Flow-Guided Diffusion for Video Inpainting

Video inpainting has been challenged by complex scenarios like large movements and low-light conditions. Current methods, including emerging diffusion models, face limitations in quality and efficiency. This paper introduces the Flow-Guided Diffusion model for Video Inpainting (FGDVI), a novel approach that significantly enhances temporal consistency and inpainting quality via reusing an off-the-shelf image generation diffusion model. We employ optical flow for precise one-step latent propagation and introduces a model-agnostic flow-guided latent interpolation technique. This technique expedites denoising, seamlessly integrating with any Video Diffusion Model (VDM) without additional training. Our FGDVI demonstrates a remarkable 10% improvement in flow warping error E_warp over existing state-of-the-art methods. Our comprehensive experiments validate superior performance of FGDVI, offering a promising direction for advanced video inpainting. The code and detailed results will be publicly available in https://github.com/NevSNev/FGDVI

Chemoenzymatic synthesis of N-acetyl analogues of 9-O-acetylated b-series gangliosides

The stable N-acetyl analogues of biologically important 9-O-acetylated b-series gangliosides including 9NAc-GD3, 9NAc-GD2, 9NAc-GD1b, and 9NAc-GT1b were chemoenzymatically synthesized from a GM3 sphingosine. Two chemoenzymatic methods using either 6-azido-6-deoxy-N-acetylmannosamine (ManNAc6N3) as a chemoenzymatic synthon or 6-acetamido-6-deoxy-N-acetylmannosamine (ManNAc6NAc) as an enzymatic precursor for 9-acetamido-9-deoxy-N-acetylneuraminic acid (Neu5Ac9NAc) were developed and compared for the synthesis of 9NAc-GD3. The latter method was found to be more efficient and was used to produce the desired 9-N-acetylated glycosylsphingosines. Furthermore, glycosylsphingosine acylation reaction conditions were improved to obtain target 9-N-acetylated gangliosides in a faster reaction with an easier purification process compared to the previous acylation conditions

The Mitochondrial Genomes of the Early Land Plants Treubia lacunosa and Anomodon rugelii: Dynamic and Conservative Evolution

Early land plant mitochondrial genomes captured important changes of mitochondrial genome evolution when plants colonized land. The chondromes of seed plants show several derived characteristics, e.g., large genome size variation, rapid intra-genomic rearrangement, abundant introns, and highly variable levels of RNA editing. On the other hand, the chondromes of charophytic algae are still largely ancestral in these aspects, resembling those of early eukaryotes. When the transition happened has been a long-standing question in studies of mitochondrial genome evolution. Here we report complete mitochondrial genome sequences from an early-diverging liverwort, Treubia lacunosa, and a late-evolving moss, Anomodon rugelii. The two genomes, 151,983 and 104,239 base pairs in size respectively, contain standard sets of protein coding genes for respiration and protein synthesis, as well as nearly full sets of rRNA and tRNA genes found in the chondromes of the liverworts Marchantia polymorpha and Pleurozia purpurea and the moss Physcomitrella patens. The gene orders of these two chondromes are identical to those of the other liverworts and moss. Their intron contents, with all cis-spliced group I or group II introns, are also similar to those in the previously sequenced liverwort and moss chondromes. These five chondromes plus the two from the hornworts Phaeoceros laevis and Megaceros aenigmaticus for the first time allowed comprehensive comparative analyses of structure and organization of mitochondrial genomes both within and across the three major lineages of bryophytes. These analyses led to the conclusion that the mitochondrial genome experienced dynamic evolution in genome size, gene content, intron acquisition, gene order, and RNA editing during the origins of land plants and their major clades. However, evolution of this organellar genome has remained rather conservative since the origin and initial radiation of early land plants, except within vascular plants

Tidal wind mapping from observations of a meteor radar chain in December 2011

This article proposes a technique to map the tidal winds in the mesosphere and lower thermosphere (MLT) region from the observations of a four-station meteor radar chain located at middle- and low-latitudes along the 120 degrees E meridian in the Northern Hemisphere. A 1month dataset of the horizontal winds in the altitude range of 80-100km is observed during December 2011. We first decompose the tidal winds into mean, diurnal, semidiurnal, and terdiurnal components for each station. It is found that the diurnal/semidiurnal components dominate at the low-latitude/midlatitude stations. Their amplitudes increase at lower altitudes and then decrease at higher altitudes after reaching a peak in the MLT region. Hough functions of the classical tidal theory are then used to fit the latitudinal distribution of each decomposed component. The diurnal component is found to be dominated by the first symmetric (1, 1) mode. Yet for the semidiurnal and terdiurnal components, the corresponding dominant modes are the second symmetric modes (2, 4) and (3, 5), and considerable contributions are also from the first antisymmetric modes (2, 3), (3, 4) and second antisymmetric modes (2, 5), (3, 6). Based on the decomposed results, we further map the horizontal winds in the domains of latitude, altitude and local time. The mapped horizontal winds successfully reproduce the local time versus altitudinal distributions of the original observations at the four stations. Thus, we conclude that the meteor radar chain is useful to monitor and study the regional characteristics of the tidal winds in the MLT region

CLIP-KD: An Empirical Study of Distilling CLIP Models

CLIP has become a promising language-supervised visual pre-training framework and achieves excellent performance over a wide range of tasks. This paper aims to distill small CLIP models supervised by a large teacher CLIP model. We propose several distillation strategies, including relation, feature, gradient and contrastive paradigm, to examine the impact on CLIP distillation. We show that the simplest feature mimicry with MSE loss performs best. Moreover, interactive contrastive learning and relation-based distillation are also critical in performance improvement. We apply the unified method to distill several student networks trained on 15 million (image, text) pairs. Distillation improves the student CLIP models consistently over zero-shot ImageNet classification and cross-modal retrieval benchmarks. We hope our empirical study will become an important baseline for future CLIP distillation research. The code is available at \url{https://github.com/winycg/CLIP-KD}

Multiphysics Investigation on Coolant Thermohydraulic Conditions and Fuel Rod Behavior During a Loss-of-Coolant Accident

This article simulates the multiphysics coolant thermohydraulic conditions and fuel performance of a pressurized water reactor (PWR) during a loss-of-coolant accident (LOCA). In the coolant channel of a PWR, the coolant undergoes a series of different boiling regimes along the axial direction. At the inlet of the coolant channel, heat exchange between the cladding wall and coolant is based on single-phase forced convection. As the coolant flow distance increases, the boiling regime gradually converts to nucleate boiling. When a LOCA occurs, on the one hand, the coolant flux and coolant pressure decrease sharply; on the other hand, the heat flux at the cladding wall decreases relatively slowly. They both contribute to a swift increase in coolant temperature. As a consequence, a boiling crisis may occur as critical heat flux (CHF) decreases. In this article, the void fraction along the length of coolant channel in a reactor and mechanical performance of Zr cladding enwrapping UO2 fuel are investigated by establishing a fully coupled multiphysics model based on the CAMPUS code. Physical models of coolant boiling regimes are implemented into the CAMPUS code by adopting different heat transfer models and void fraction models. Physical properties of the coolant are implemented into the CAMPUS code using curve-fitting results. All physical models and parameters related to solid heat transfer are implemented into the CAMPUS code with a 2D axisymmetric geometry. The modeling results help enhance our understanding of void fraction along the length of the coolant channel and mechanical performance of Zr cladding enwrapping UO2 fuel under different coolant pressure and mass flux conditions during a LOCA