A new perspective on building efficient and expressive 3D equivariant graph neural networks

Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects. Despite rapid progress in encoding 3D symmetries into Graph Neural Networks (GNNs), a comprehensive evaluation of the expressiveness of these networks through a local-to-global analysis lacks today. In this paper, we propose a local hierarchy of 3D isomorphism to evaluate the expressive power of equivariant GNNs and investigate the process of representing global geometric information from local patches. Our work leads to two crucial modules for designing expressive and efficient geometric GNNs; namely local substructure encoding (LSE) and frame transition encoding (FTE). To demonstrate the applicability of our theory, we propose LEFTNet which effectively implements these modules and achieves state-of-the-art performance on both scalar-valued and vector-valued molecular property prediction tasks. We further point out the design space for future developments of equivariant graph neural networks. Our codes are available at \url{https://github.com/yuanqidu/LeftNet}

Long-term postoperative quality of life in childhood survivors with cerebellar mutism syndrome

BackgroundTo investigate the long-term quality of life (QoL) of children with cerebellar mutism syndrome (CMS) and explore the risk factors for a low QoL.ProcedureThis cross-sectional study investigated children who underwent posterior fossa surgery using an online Pediatric Quality of Life Inventory questionnaire. CMS and non-CMS patients were included to identify QoL predictors.ResultsSixty-nine patients were included (male, 62.3%), 22 of whom had CMS. The mean follow-up time was 45.2 months. Children with CMS had a significantly lower mean QoL score (65.3 vs. 83.7, p < 0.001) and subdomain mean scores (physical; 57.8 vs. 85.3, p < 0.001; social: 69.5 vs. 85.1, p = 0.001; academic: p = 0.001) than those without CMS, except for the emotional domain (78.0 vs. 83.7, p = 0.062). Multivariable analysis revealed that CMS (coefficient = −14.748.61, p = 0.043), chemotherapy (coefficient = −7.629.82, p = 0.013), ventriculoperitoneal (VP) shunt placement (coefficient = −10.14, p = 0.024), and older age at surgery (coefficient = −1.1830, p = 0.007) were independent predictors of low total QoL scores. Physical scores were independently associated with CMS (coefficient = −27.4815.31, p = 0.005), VP shunt placement (coefficient = −12.86, p = 0.025), and radiotherapy (coefficient = −13.62, p = 0.007). Emotional score was negatively associated with age at surgery (coefficient = −1.92, p = 0.0337) and chemotherapy (coefficient = −9.11, p = 0.003). Social scores were negatively associated with male sex (coefficient = −13.68, p = 0.001) and VP shunt placement (coefficient = −1.36, p = 0.005), whereas academic scores were negatively correlated with chemotherapy (coefficient = −17.45, p < 0.001) and age at surgery (coefficient = −1.92, p = 0.002). Extent of resection (coefficient = 13.16, p = 0.021) was a good predictor of higher academic scores.ConclusionCMS results in long-term neurological and neuropsychological deficits, negatively affecting QoL, and warranting early rehabilitation

Effects of Surgery on Prognosis of Young Women With Operable Breast Cancer in Different Marital Statuses: A Population-Based Cohort Study

BackgroundThe influence of surgical approaches [including mastectomy, breast-conserving therapy (BCT) and post-mastectomy breast reconstruction (PMBR) on prognosis of young women (<40 years old) with operable breast cancer has not been determined yet, and this might vary in patients with different marital statuses. Therefore, we aimed to investigate the effect of surgery on survival outcomes for young women with operable breast cancer in different marital statuses.MethodsWe used the Surveillance, Epidemiology, and End Results (SEER) database to identify young women with operable breast cancer between 2004 and 2016, who underwent mastectomy, BCT or PMBR. We assessed overall survival (OS) and breast cancer-specific survival (BCSS) using the Kaplan–Meier method and hazard ratios using multivariate Cox proportional hazard regression.ResultsCompared to mastectomy, both of BCT and PMBR conferred better OS (BCT: HR = 0.79, 95%CI: 0.69–0.90, p <0.001; PMBR: HR = 0.70, 95%CI: 0.63–0.78, p <0.001) and BCSS (BCT: HR = 0.79, 95%CI: 0.69–0.91, p = 0.001; PMBR: HR = 0.73, 95%CI: 0.65–0.81, p <0.001), but there was no significant difference of survival between BCT and PMBR group. The survival benefit of BCT compared to mastectomy remained significant in unmarried young women (OS: HR = 0.68, 95%CI: 0.55–0.83, p <0.001; BCSS: HR = 0.69, 95%CI: 0.56–0.86, p = 0.001) but not in the married (OS: HR = 0.89, 95%CI: 0.75–1.05, p = 0.177; BCSS: HR = 0.89, 95%CI: 0.75–1.05, p = 0.161), while no matter married or not, PMBR group had better OS and BCSS than mastectomy group but not BCT group.ConclusionBoth of BCT and PMBR had improved survival compared to mastectomy for young women with operable breast cancer. The survival benefit of BCT compared to mastectomy remained significant in unmarried patients but not in married patients

Epidemiological characteristics, clinical presentations, and prognoses of pediatric brain tumors: Experiences of national center for children’s health

BackgroundWe aimed to describe the epidemiological characteristics, clinical presentations, and prognoses in a national health center for children.MethodsFrom January 2015 to December 2020, 484 patients aged 0-16 years, who were diagnosed with brain tumors and received neurosurgery treatment, were enrolled in the study. Pathology was based on the World Health Organization 2021 nervous system tumor classification, and tumor behaviors were classified according to the International Classification of Diseases for Oncology, third edition.ResultsAmong the 484 patients with brain tumors, the median age at diagnosis was 4.62 [2.19, 8.17] years (benign tumors 4.07 [1.64, 7.13] vs. malignant tumors 5.36 [2.78, 8.84], p=0.008). The overall male-to-female ratio was 1.33:1(benign 1.09:1 vs. malignant 1.62:1, p=0.029). Nausea, vomiting, and headache were the most frequent initial symptoms. The three most frequent tumor types were embryonal tumors (ET, 22.8%), circumscribed astrocytic gliomas (20.0%), and pediatric-type diffuse gliomas (11.0%). The most common tumor locations were the cerebellum and fourth ventricle (38.67%), the sellar region (22.9%) and ventricles (10.6%). Males took up a higher proportion than females in choroid plexus tumors (63.6%), ET (61.1%), ependymal tumors (68.6%), and germ cell tumors (GCTs, 78.1%). Patients were followed for 1 to 82 months. The overall 5-year survival rate was 77.5%, with survival rates of 91.0% for benign tumors and 64.6% for malignant tumors.ConclusionBrain tumors presented particularly sex-, age-, and regional-dependent epidemiological characteristics. Our results were consistent with previous reports and might reflect the real epidemiological status in China

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science

Polydopamine-Assisted Rapid One-Step Immobilization of L-Arginine in Capillary as Immobilized Chiral Ligands for Enantioseparation of Dansyl Amino Acids by Chiral Ligand Exchange Capillary Electrochromatography

Herein, a novel L-arginine (L-Arg)-modified polydopamine (PDA)-coated capillary (PDA/L-Arg@capillary) was firstly fabricated via the basic amino-acid-induced PDA co-deposition strategy and employed to constitute a new chiral ligand exchange capillary electrochromatography (CLE-CEC) method for the high-performance enantioseparation of D,L-amino acids (D,L-AAs) with L-Arg as the immobilized chiral ligand coordinating with the central metal ion Zn(II) as running buffer. Assisted by hydrothermal treatment, the robust immobilization of L-Arg on the capillary inner wall could be facilely achieved within 1 h, prominently improving the synthesis efficiency and simplifying the preparation procedure. The successful preparation of PDA/L-Arg coatings in the capillary was systematically characterized and confirmed using several methods. In comparison with bare and PDA-functionalized capillaries, the enantioseparation capability of the presented CLE-CEC system was significantly enhanced. Eight D,L-AAs were completely separated and three pairs were partially separated under the optimal conditions. The prepared PDA/L-Arg@capillary showed good repeatability and stability. The potential mechanism of the greatly enhanced enantioseparation performance obtained by PDA/L-Arg@capillary was also explored. Moreover, the proposed method was further utilized for studying the enzyme kinetics of L-glutamic dehydrogenase, exhibiting its promising prospects in enzyme assays and other related applications

Regulating the Homogeneity of Thiol-Maleimide Michael-Type Addition-Based Hydrogels Using Amino Biomolecules

Poly(ethylene glycol) (PEG)-based synthetic hydrogels based on Michael-type addition reaction have been widely used for cell culture and tissue engineering. However, recent studies showed that these types of hydrogels were not homogenous as expected since micro domains generated due to the fast reaction kinetics. Here, we demonstrated a new kind of method to prepare homogenous poly(ethylene glycol) hydrogels based on Michael-type addition using the side chain amine-contained short peptides. By introducing such a kind of short peptides, the homogeneity of crosslinking and mechanical property of the hydrogels has been also significantly enhanced. The compressive mechanical and recovery properties of the homogeneous hydrogels prepared in the presence of side chain amine-contained short peptides were more reliable than those of inhomogeneous hydrogels while the excellent biocompatibility remained unchanged. Furthermore, the reaction rate and gelation kinetics of maleimide- and thiol-terminated PEG were proved to be significantly slowed down in the presence of the side chain amine-contained short peptides, thus leading to the improved homogeneity of the hydrogels. We anticipate that this new method can be widely applied to hydrogel preparation and modification based on Michael-type addition gelation

Temperature and photoperiod changes affect cucumber sex expression by different epigenetic regulations

Abstract Background Cucumbers (Cucumis sativus) are known for their plasticity in sex expression. DNA methylation status determines gene activity but is susceptible to environmental condition changes. Thus, DNA methylation-based epigenetic regulation may at least partially account for the instability of cucumber sex expression. Do temperature and photoperiod that are the two most important environmental factors have equal effect on cucumber sex expression by similar epigenetic regulation mechanism? To answer this question, we did a two-factor experiment of temperature and photoperiod and generated methylome and transcriptome data from cucumber shoot apices. Results The seasonal change in the femaleness of a cucumber core germplasm collection was investigated over five consecutive years. As a result, 71.3% of the 359 cucumber accessions significantly decreased their femaleness in early autumn when compared with spring. High temperature and long-day photoperiod treatments, which mimic early autumn conditions, are both unfavorable for female flower formation, and temperature is the predominant factor. High temperatures and long-day treatments both predominantly resulted in hypermethylation compared to demethylation, and temperature effect was decisive. The targeted cytosines shared in high-temperature and long-day photoperiod treatment showed the same change in DNA methylation level. Moreover, differentially expressed TEs (DETs) and the predicted epiregulation sites were clustered across chromosomes, and importantly, these sites were reproducible among different treatments. Essentially, the photoperiod treatment preferentially and significantly influenced flower development processes, while temperature treatment produced stronger responses from phytohormone-pathway-related genes. Cucumber AGAMOUS was likely epicontrolled exclusively by photoperiod while CAULIFLOWER A and CsACO 3 were likely epicontrolled by both photoperiod and temperature. Conclusions Seasonal change of sex expression is a germplasm-wide phenomenon in cucumbers. High temperature and long-day photoperiod might have the same effect on the methylome via the same mechanism of gene-TE interaction but resulted in different epicontrol sites that account for different mechanisms between temperature- and photoperiod-dependent sex expression changes