210 research outputs found
CoGANPPIS: Coevolution-enhanced Global Attention Neural Network for Protein-Protein Interaction Site Prediction
Protein-protein interactions are essential in biochemical processes. Accurate
prediction of the protein-protein interaction sites (PPIs) deepens our
understanding of biological mechanism and is crucial for new drug design.
However, conventional experimental methods for PPIs prediction are costly and
time-consuming so that many computational approaches, especially ML-based
methods, have been developed recently. Although these approaches have achieved
gratifying results, there are still two limitations: (1) Most models have
excavated some useful input features, but failed to take coevolutionary
features into account, which could provide clues for inter-residue
relationships; (2) The attention-based models only allocate attention weights
for neighboring residues, instead of doing it globally, neglecting that some
residues being far away from the target residues might also matter.
We propose a coevolution-enhanced global attention neural network, a
sequence-based deep learning model for PPIs prediction, called CoGANPPIS. It
utilizes three layers in parallel for feature extraction: (1) Local-level
representation aggregation layer, which aggregates the neighboring residues'
features; (2) Global-level representation learning layer, which employs a novel
coevolution-enhanced global attention mechanism to allocate attention weights
to all the residues on the same protein sequences; (3) Coevolutionary
information learning layer, which applies CNN & pooling to coevolutionary
information to obtain the coevolutionary profile representation. Then, the
three outputs are concatenated and passed into several fully connected layers
for the final prediction. Application on two benchmark datasets demonstrated a
state-of-the-art performance of our model. The source code is publicly
available at https://github.com/Slam1423/CoGANPPIS_source_code
MAP: Multimodal Uncertainty-Aware Vision-Language Pre-training Model
Multimodal semantic understanding often has to deal with uncertainty, which
means the obtained messages tend to refer to multiple targets. Such uncertainty
is problematic for our interpretation, including inter- and intra-modal
uncertainty. Little effort has studied the modeling of this uncertainty,
particularly in pre-training on unlabeled datasets and fine-tuning in
task-specific downstream datasets. In this paper, we project the
representations of all modalities as probabilistic distributions via a
Probability Distribution Encoder (PDE) by utilizing sequence-level
interactions. Compared to the existing deterministic methods, such uncertainty
modeling can convey richer multimodal semantic information and more complex
relationships. Furthermore, we integrate uncertainty modeling with popular
pre-training frameworks and propose suitable pre-training tasks:
Distribution-based Vision-Language Contrastive learning (D-VLC),
Distribution-based Masked Language Modeling (D-MLM), and Distribution-based
Image-Text Matching (D-ITM). The fine-tuned models are applied to challenging
downstream tasks, including image-text retrieval, visual question answering,
visual reasoning, and visual entailment, and achieve state-of-the-art results.Comment: CVPR 2023 accep
Viable but nonculturable bacteria and their resuscitation: implications for cultivating uncultured marine microorganisms
Culturing has been the cornerstone of microbiology since Robert Koch first successfully cultured bacteria in the late nineteenth century. However, even today, the majority of microorganisms in the marine environment remain uncultivated. There are various explanations for the inability to culture bacteria in the laboratory, including lack of essential nutrients, osmotic support or incubation conditions, low growth rate, development of micro-colonies, and the presence of senescent or viable but nonculturable (VBNC) cells. In the marine environment, many bacteria have been associated with dormancy, as typified by the VBNC state. VBNC refers to a state where bacteria are metabolically active, but are no longer culturable on routine growth media. It is apparently a unique survival strategy that has been adopted by many microorganisms in response to harsh environmental conditions and the bacterial cells in the VBNC state may regain culturability under favorable conditions. The resuscitation of VBNC cells may well be an important way to cultivate the otherwise uncultured microorganisms in marine environments. Many resuscitation stimuli that promote the restoration of culturability have so far been identified; these include sodium pyruvate, quorum sensing autoinducers, resuscitation-promoting factors Rpfs and YeaZ, and catalase. In this review, we focus on the issues associated with bacterial culturability, the diversity of bacteria entering the VBNC state, mechanisms of induction into the VBNC state, resuscitation factors of VBNC cells and implications of VBNC resuscitation stimuli for cultivating these otherwise uncultured microorganisms. Bringing important microorganisms into culture is still important in the era of high-throughput sequencing as their ecological functions in the marine environment can often only be known through isolation and cultivation
Silver nanoparticles promote osteogenic differentiation of human urine-derived stem cells at noncytotoxic concentrations
The influence of H2O or/and O2 introduction during the low-temperature gas-phase sulfation of organic COS + CS2 on the conversion and deposition of sulfur-containing species in the sulfated CeO2-OS catalyst for NH3-SCR
Herein, the typical components of blast furnace gas, including H O and O , were introduced to improve the NH -SCR activity of the sulfated CeO -OS catalyst during the gas-phase sulfation of organic COS + CS at 50 °C. The characterization results demonstrate that the introduction of O or H O during gas-phase sulfation enhances the conversion of organic COS + CS on a cubic fluorite CeO surface and reduces the formation of sulfur and sulfates in the catalyst, but decreases the BET surface area and pore volume of the sulfated CeO -OS catalyst. However, the introduction of O or H O during the gas-phase sulfation increases the molar ratios of Ce /(Ce + Ce ) and O /(O + O + O ) on the sulfated CeO -OS catalyst surface, thus promoting the formation of surface oxygen vacancies and chemisorbed oxygen, and these properties of the catalyst are further enhanced by the co-existence of O and H O. Furthermore, the reduction of sulfates formed under the action of O or H O decreases the weak acid sites of the sulfated CeO -OS catalyst, but the few and highly dispersive sulfates present stronger reducibility, and the proportion of medium-strong acid sites of the catalyst increases. These factors help to improve the NH -SCR activity of the sulfated CeO -OS catalyst. Thus, there exists a synergistic effect of H O and O introduction during gas-phase sulfation on the physical-chemical properties and catalytic performance of the sulfated CeO -OS catalyst by organic COS + CS at 50 °C
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