32 research outputs found
SyNDock: N Rigid Protein Docking via Learnable Group Synchronization
The regulation of various cellular processes heavily relies on the protein
complexes within a living cell, necessitating a comprehensive understanding of
their three-dimensional structures to elucidate the underlying mechanisms.
While neural docking techniques have exhibited promising outcomes in binary
protein docking, the application of advanced neural architectures to multimeric
protein docking remains uncertain. This study introduces SyNDock, an automated
framework that swiftly assembles precise multimeric complexes within seconds,
showcasing performance that can potentially surpass or be on par with recent
advanced approaches. SyNDock possesses several appealing advantages not present
in previous approaches. Firstly, SyNDock formulates multimeric protein docking
as a problem of learning global transformations to holistically depict the
placement of chain units of a complex, enabling a learning-centric solution.
Secondly, SyNDock proposes a trainable two-step SE(3) algorithm, involving
initial pairwise transformation and confidence estimation, followed by global
transformation synchronization. This enables effective learning for assembling
the complex in a globally consistent manner. Lastly, extensive experiments
conducted on our proposed benchmark dataset demonstrate that SyNDock
outperforms existing docking software in crucial performance metrics, including
accuracy and runtime. For instance, it achieves a 4.5% improvement in
performance and a remarkable millionfold acceleration in speed
Key Problems and Techniques of Geophysical Exploration in Underground Salt Cavern for Compressed Air Energy Storage
[Introduction] The world′s first 300 MW compressed air energy storage (CAES) power station is in Yingcheng City, Hubei Province, China. The station uses the existing underground salt cavern which is the best of its tight sealing and high capacity as gas storage, The parameters of the underground salt cavern, such as the underground salt cavity volume, shape, and depth, are crucial for the construction feasibility of the CAES power station. [Method] Based on the Yingcheng CAES power station project practice, this paper analyzed and summarized the many key problems and processing techniques of the high precision 3D seismic geophysical exploration methods in detecting deep salt cavity shapes. [Result] For the purpose of proving the occurrence characteristics of existing underground salt cavity, the 3D seismic geophysical exploration observation system shall be designed to meet the high resolution requirements, and the CDP gridding shall have an accuracy of at least 5 m×5 m, in order to make sure the fold number of the target area is more than 30 times. It is indispensable to improve the salt cavern 3D seismic data quality by conducting static correction and pre-stack denoising. Consistency processing technique is used and accurate velocity field is constructed according to different excitation and receiving conditions to realize precise depth homing. We find the track integral attribute, reflection strength attribute and sweetness attribute have an obvious advantage in identifying salt cavern space distribution, while edge detection attribute has a strong indication on cavity border depiction and connectivity. [Conclusion] Through research on key techniques of data processing and interpretation in geophysical exploration, the salt cavity parameters such as volume, shape, and depth are clearly detected to provide detailed and reliable data support for the salt cavern project. Research on the key problems and techniques of the 3D seismic geophysical exploration for the salt cavern can provide reference to the construction of large-scale CAES power stations of underground salt cavern type
Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing
The gastrointestinal tract, the largest human microbial reservoir, is highly dynamic. The gut microbes play essential roles in causing colorectal diseases. In the present study, we explored potential keystone taxa during the development of colorectal diseases in central China. Fecal samples of some patients were collected and were allocated to the adenoma (Group A), colorectal cancer (Group C), and hemorrhoid (Group H) groups. The 16S rRNA amplicon and shallow metagenomic sequencing (SMS) strategies were used to recover the gut microbiota. Microbial diversities obtained from 16S rRNA amplicon and SMS data were similar. Group C had the highest diversity, although no significant difference in diversity was observed among the groups. The most dominant phyla in the gut microbiota of patients with colorectal diseases were Bacteroidetes, Firmicutes, and Proteobacteria, accounting for >95% of microbes in the samples. The most abundant genera in the samples were Bacteroides, Prevotella, and Escherichia/Shigella, and further species-level and network analyses identified certain potential keystone taxa in each group. Some of the dominant species, such as Prevotella copri, Bacteroides dorei, and Bacteroides vulgatus, could be responsible for causing colorectal diseases. The SMS data recovered diverse antibiotic resistance genes of tetracycline, macrolide, and beta-lactam, which could be a result of antibiotic overuse. This study explored the gut microbiota of patients with three different types of colorectal diseases, and the microbial diversity results obtained from 16S rRNA amplicon sequencing and SMS data were found to be similar. However, the findings of this study are based on a limited sample size, which warrants further large-scale studies. The recovery of gut microbiota profiles in patients with colorectal diseases could be beneficial for future diagnosis and treatment with modulation of the gut microbiota. Moreover, SMS data can provide accurate species- and gene-level information, and it is economical. It can therefore be widely applied in future clinical metagenomic studies
Optical vortices enabled by structural vortices
The structural symmetry of solids plays an important role in defining their
linear and nonlinear optical properties. The quest for versatile,
cost-effective, large-scale, and defect-free approaches and materials platforms
for tailoring structural and optical properties on demand has been underway for
decades. We experimentally demonstrate a bottom-up self-assembly-based organic
engineered material comprised of synthesized molecules with large dipole
moments that are crystallized into a spherulite structure. The molecules align
in an azimuthal direction, resulting in a vortex polarity with spontaneously
broken symmetry leading to strong optical anisotropy and nonlinear optical
responses. These unique polarization properties of the judiciously designed
organic spherulite combined with the symmetry of structured optical beams
enable a plethora of new linear and nonlinear light-matter interactions,
including the generation of optical vortex beams with complex spin states and
on-demand topological charges at the fundamental, doubled, and tripled
frequencies. The results of this work are likely to enable numerous
applications in areas such as high-dimensional quantum information processing,
with large capacity and high security. The demonstrated spherulite crystals
facilitate stand-alone micro-scale devices that rely on the unique micro-scale
spontaneous vortex polarity that is likely to enable future applications for
high-dimensional quantum information processing, spatiotemporal optical
vortices, and a novel platform for optical manipulation and trapping
AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation
Despite the considerable progress in automatic abdominal multi-organ
segmentation from CT/MRI scans in recent years, a comprehensive evaluation of
the models' capabilities is hampered by the lack of a large-scale benchmark
from diverse clinical scenarios. Constraint by the high cost of collecting and
labeling 3D medical data, most of the deep learning models to date are driven
by datasets with a limited number of organs of interest or samples, which still
limits the power of modern deep models and makes it difficult to provide a
fully comprehensive and fair estimate of various methods. To mitigate the
limitations, we present AMOS, a large-scale, diverse, clinical dataset for
abdominal organ segmentation. AMOS provides 500 CT and 100 MRI scans collected
from multi-center, multi-vendor, multi-modality, multi-phase, multi-disease
patients, each with voxel-level annotations of 15 abdominal organs, providing
challenging examples and test-bed for studying robust segmentation algorithms
under diverse targets and scenarios. We further benchmark several
state-of-the-art medical segmentation models to evaluate the status of the
existing methods on this new challenging dataset. We have made our datasets,
benchmark servers, and baselines publicly available, and hope to inspire future
research. Information can be found at https://amos22.grand-challenge.org
The Medical Segmentation Decathlon
International challenges have become the de facto standard for comparative
assessment of image analysis algorithms given a specific task. Segmentation is
so far the most widely investigated medical image processing task, but the
various segmentation challenges have typically been organized in isolation,
such that algorithm development was driven by the need to tackle a single
specific clinical problem. We hypothesized that a method capable of performing
well on multiple tasks will generalize well to a previously unseen task and
potentially outperform a custom-designed solution. To investigate the
hypothesis, we organized the Medical Segmentation Decathlon (MSD) - a
biomedical image analysis challenge, in which algorithms compete in a multitude
of both tasks and modalities. The underlying data set was designed to explore
the axis of difficulties typically encountered when dealing with medical
images, such as small data sets, unbalanced labels, multi-site data and small
objects. The MSD challenge confirmed that algorithms with a consistent good
performance on a set of tasks preserved their good average performance on a
different set of previously unseen tasks. Moreover, by monitoring the MSD
winner for two years, we found that this algorithm continued generalizing well
to a wide range of other clinical problems, further confirming our hypothesis.
Three main conclusions can be drawn from this study: (1) state-of-the-art image
segmentation algorithms are mature, accurate, and generalize well when
retrained on unseen tasks; (2) consistent algorithmic performance across
multiple tasks is a strong surrogate of algorithmic generalizability; (3) the
training of accurate AI segmentation models is now commoditized to non AI
experts
Novel Variants of PPP2R1A in Catalytic Subunit Binding Domain and Genotype–Phenotype Analysis in Neurodevelopmentally Delayed Patients
Neurodevelopmental disorders (NDDs) are a group of high-incidence rare diseases with genetic heterogeneity. PPP2R1A, the regulatory subunit of protein phosphatase 2A, is a recently discovered gene associated with NDDs. Whole/clinical exome sequencing was performed in five patients with a family with NDDs. In vitro experiments were performed to evaluate the mutants’ expression and interactions with the complex. The genotype–phenotype correlations of reported cases as well as our patients with PPP2R1A variants were reviewed. We reported five unrelated individuals with PPP2R1A variants, including two novel missense variants and one frameshift variant. The protein expression of the Arg498Leu variant was less than that of the wild-type protein, the frameshift variant Asn282Argfs*14 was not decreased but truncated, and these two variants impaired the interactions with endogenous PPP25RD and PPP2CA. Furthermore, we found that pathogenic variants clustered in HEAT repeats V, VI and VII, and patients with the Met180Val/Thr variants had macrocephaly, severe ID and hypotonia, but no epilepsy, whereas those with Arg258 amino acid changes had microcephaly, while a few had epilepsy or feeding problems. In this study, we reported five NDD patients with PPP2R1A gene variants and expanded PPP2R1A pathogenic variant spectrum. The genotype and phenotype association findings provide reminders regarding the prognostication and evidence for genetic counseling
DDP: Diffusion Model for Dense Visual Prediction
We propose a simple, efficient, yet powerful framework for dense visual
predictions based on the conditional diffusion pipeline. Our approach follows a
"noise-to-map" generative paradigm for prediction by progressively removing
noise from a random Gaussian distribution, guided by the image. The method,
called DDP, efficiently extends the denoising diffusion process into the modern
perception pipeline. Without task-specific design and architecture
customization, DDP is easy to generalize to most dense prediction tasks, e.g.,
semantic segmentation and depth estimation. In addition, DDP shows attractive
properties such as dynamic inference and uncertainty awareness, in contrast to
previous single-step discriminative methods. We show top results on three
representative tasks with six diverse benchmarks, without tricks, DDP achieves
state-of-the-art or competitive performance on each task compared to the
specialist counterparts. For example, semantic segmentation (83.9 mIoU on
Cityscapes), BEV map segmentation (70.6 mIoU on nuScenes), and depth estimation
(0.05 REL on KITTI). We hope that our approach will serve as a solid baseline
and facilitate future researchComment: Added controlnet ex