Augmenting Knowledge Transfer across Graphs

Given a resource-rich source graph and a resource-scarce target graph, how can we effectively transfer knowledge across graphs and ensure a good generalization performance? In many high-impact domains (e.g., brain networks and molecular graphs), collecting and annotating data is prohibitively expensive and time-consuming, which makes domain adaptation an attractive option to alleviate the label scarcity issue. In light of this, the state-of-the-art methods focus on deriving domain-invariant graph representation that minimizes the domain discrepancy. However, it has recently been shown that a small domain discrepancy loss may not always guarantee a good generalization performance, especially in the presence of disparate graph structures and label distribution shifts. In this paper, we present TRANSNET, a generic learning framework for augmenting knowledge transfer across graphs. In particular, we introduce a novel notion named trinity signal that can naturally formulate various graph signals at different granularity (e.g., node attributes, edges, and subgraphs). With that, we further propose a domain unification module together with a trinity-signal mixup scheme to jointly minimize the domain discrepancy and augment the knowledge transfer across graphs. Finally, comprehensive empirical results show that TRANSNET outperforms all existing approaches on seven benchmark datasets by a significant margin

Dynamic Transfer Learning across Graphs

Transferring knowledge across graphs plays a pivotal role in many high-stake domains, ranging from transportation networks to e-commerce networks, from neuroscience to finance. To date, the vast majority of existing works assume both source and target domains are sampled from a universal and stationary distribution. However, many real-world systems are intrinsically dynamic, where the underlying domains are evolving over time. To bridge the gap, we propose to shift the problem to the dynamic setting and ask: given the label-rich source graphs and the label-scarce target graphs observed in previous T timestamps, how can we effectively characterize the evolving domain discrepancy and optimize the generalization performance of the target domain at the incoming T+1 timestamp? To answer the question, for the first time, we propose a generalization bound under the setting of dynamic transfer learning across graphs, which implies the generalization performance is dominated by domain evolution and domain discrepancy between source and target domains. Inspired by the theoretical results, we propose a novel generic framework DyTrans to improve knowledge transferability across dynamic graphs. In particular, we start with a transformer-based temporal encoding module to model temporal information of the evolving domains; then, we further design a dynamic domain unification module to efficiently learn domain-invariant representations across the source and target domains. Finally, extensive experiments on various real-world datasets demonstrate the effectiveness of DyTrans in transferring knowledge from dynamic source domains to dynamic target domains

Advances in the application of CRISPR-Cas technology in rapid detection of pathogen nucleic acid

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are widely used as gene editing tools in biology, microbiology, and other fields. CRISPR is composed of highly conserved repetitive sequences and spacer sequences in tandem. The spacer sequence has homology with foreign nucleic acids such as viruses and plasmids; Cas effector proteins have endonucleases, and become a hotspot in the field of molecular diagnosis because they recognize and cut specific DNA or RNA sequences. Researchers have developed many diagnostic platforms with high sensitivity, high specificity, and low cost by using Cas proteins (Cas9, Cas12, Cas13, Cas14, etc.) in combination with signal amplification and transformation technologies (fluorescence method, lateral flow technology, etc.), providing a new way for rapid detection of pathogen nucleic acid. This paper introduces the biological mechanism and classification of CRISPR-Cas technology, summarizes the existing rapid detection technology for pathogen nucleic acid based on the trans cleavage activity of Cas, describes its characteristics, functions, and application scenarios, and prospects the future application of this technology

Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family

Molecular recognition by intrinsically disordered proteins (IDPs) commonly involves specific localized contacts and target-induced disorder to order transitions. However, some IDPs remain disordered in the bound state, a phenomenon coined "fuzziness", often characterized by IDP polyvalency, sequence-insensitivity and a dynamic ensemble of disordered bound-state conformations. Besides the above general features, specific biophysical models for fuzzy interactions are mostly lacking. The transcriptional activation domain of the Ewing's Sarcoma oncoprotein family (EAD) is an IDP that exhibits many features of fuzziness, with multiple EAD aromatic side chains driving molecular recognition. Considering the prevalent role of cation-π interactions at various protein-protein interfaces, we hypothesized that EAD-target binding involves polycation- π contacts between a disordered EAD and basic residues on the target. Herein we evaluated the polycation-π hypothesis via functional and theoretical interrogation of EAD variants. The experimental effects of a range of EAD sequence variations, including aromatic number, aromatic density and charge perturbations, all support the cation-π model. Moreover, the activity trends observed are well captured by a coarse-grained EAD chain model and a corresponding analytical model based on interaction between EAD aromatics and surface cations of a generic globular target. EAD-target binding, in the context of pathological Ewing's Sarcoma oncoproteins, is thus seen to be driven by a balance between EAD conformational entropy and favorable EAD-target cation-π contacts. Such a highly versatile mode of molecular recognition offers a general conceptual framework for promiscuous target recognition by polyvalent IDPs. © 2013 Song et al

Genetic characterization of wild-type measles viruses isolated in China, 2006-2007

Molecular characterization of wild-type measles viruses in China during 1995-2004 demonstrated that genotype H1 was endemic and widely distributed throughout the country. H1-associated cases and outbreaks caused a resurgence of measles beginning in 2005. A total of 210,094 measles cases and 101 deaths were reported by National Notifiable Diseases Reporting System (NNDRS) and Chinese Measles Laboratory Network (LabNet) from 2006 to 2007, and the incidences of measles were 6.8/100,000 population and 7.2/100,000 population in 2006 and 2007, respectively. Five hundred and sixty-five wild-type measles viruses were isolated from 24 of 31 provinces in mainland China during 2006 and 2007, and all of the wild type virus isolates belonged to cluster 1 of genotype H1. These results indicated that H1-cluster 1 viruses were the predominant viruses circulating in China from 2006 to 2007. This study contributes to previous efforts to generate critical baseline data about circulating wild-type measles viruses in China that will allow molecular epidemiologic studies to help measure the progress made toward China's goal of measles elimination by 2012

Impacts of conversion of cropland to grassland on the C-N-P stoichiometric dynamics of soil, microorganisms, and enzymes across China: A synthesis

In response to escalating land degradation, the conversion of cropland to grassland has emerged as a crucial mitigation strategy. This conversion has a significant influence on the stoichiometry of soil, microorganisms, and enzymes, specifically in relation to carbon (C), nitrogen (N), and phosphorus (P). A meta-analysis was conducted with 371 observations from 122 articles investigating the impacts of cropland to grassland conversion on the C-N-P stoichiometric dynamics of soils, microorganisms, and enzymes across China. The findings revealed that conversion significantly increased soil C:P (9.0%), soil N:P (5.6%), microbial C:N (15.5%), and notably, microbial C:P by 57.9%. This substantial increase in microbial C:P indicates that microbial communities are highly responsive to land use conversion. Contrastingly, the enzyme C:P ratio decreased by 19.8%, suggesting microbial adaptation to changing nutrient availability. The duration of conversion was positively correlated with soil C:P and N:P ratios, implying that relative P availability may decrease as conversion progresses. However, duration was negatively correlated with microbial C:P. Environmental factors such as clay content, mean annual temperature, and mean annual precipitation were positively correlated with microbial C:N and negatively correlated with microbial N:P, while soil pH was inversely correlated with microbial C:N. These results suggest the substantial influence of cropland to grassland conversion on soil, microbial, and enzyme stoichiometry, with particularly pronounced effects on microbial communities. The observed shifts in stoichiometric ratios suggest changes in nutrient cycling and availability following conversion. While these changes are primarily attributed to the land use conversion, we acknowledge that alterations in management practices, such as reduced fertilization, likely contribute to the observed stoichiometric shifts. Our findings emphasize the importance of considering both environmental factors and management practices when implementing grassland conversion initiatives

Mini percutaneous nephrolithotomy is a noninferior modality to standard percutaneous nephrolithotomy for the management of 20-40 mm renal calculi: A Multicenter randomized controlled trial

Background: High quality of evidence comparing mini percutaneous nephrolithotomy (mPNL) with standard percutaneous nephrolithotomy (sPNL) for the treatment of larger-sized renal stones is lacking. Objective: To compare the efficacy and safety of mPNL and sPNL for the treatment of 20–40 mm renal stones. Design, setting, and participants: A parallel, open-label, and noninferior randomized controlled trial was performed at 20 Chinese centers (2016–2019). The inclusion criteria were patients 18–70 yr old, with normal renal function, and 20–40 mm renal stones. Intervention: Percutaneous nephrolithotomy PNL was performed using either 18 F or 24 F percutaneous nephrostomy tracts. Outcome measurements and statistical analysis: The primary outcome was the one-session stone-free rate (SFR). The secondary outcomes included operating time, visual analog pain scale (VAS) score, blood loss, complications as per the Clavien-Dindo grading system, and length of hospitalization. Results and limitations: The 1980 intention-to-treat patients were randomized. The mPNL group achieved a noninferior one-session SFR to the sPNL group by the one-side noninferiority test (0.5% [difference], p < 0.001). The transfusion and embolization rates were comparable; however, the sPNL group had a higher hemoglobin drop (5.2 g/l, p < 0.001). The sPNL yielded shorter operating time (–2.2 min, p = 0.008) but a higher VAS score (0.8, p < 0.001). Patients in the sPNL group also had longer hospitalization (0.6 d, p < 0.001). There was no statistically significant difference in fever or urosepsis occurrences. The study's main limitation was that only 18F or 24F tract sizes were used. Conclusions: Mini mPNL achieves noninferior SFR outcomes to sPNL, but with reduced bleeding, less postoperative pain, and shorter hospitalization. Patient summary: We evaluated the surgical outcomes of percutaneous nephrolithotomy using two different sizes of nephrostomy tracts in a large population. We found that the smaller tract might be a sensible alternative for patients with 20–40 mm renal stones. This multicenter, parallel, open-label, and noninferior randomized controlled trial showed that mini percutaneous nephrolithotomy achieved noninferior stone-free rate with advantages of reduced blood loss, less postoperative pain, and shorter hospitalization. Mini percutaneous nephrolithotomy should be considered a sensible alternative treatment of 20–40 mm renal stones.grants from high-level development funding of Guangzhou Medical Universit

Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses

Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses