CryoFormer: Continuous Reconstruction of 3D Structures from Cryo-EM Data using Transformer-based Neural Representations

High-resolution heterogeneous reconstruction of 3D structures of proteins and other biomolecules using cryo-electron microscopy (cryo-EM) is essential for understanding fundamental processes of life. However, it is still challenging to reconstruct the continuous motions of 3D structures from hundreds of thousands of noisy and randomly oriented 2D cryo-EM images. Existing methods based on coordinate-based neural networks show compelling results to model continuous conformations of 3D structures in the Fourier domain, but they suffer from a limited ability to model local flexible regions and lack interpretability. We propose a novel approach, cryoFormer, that utilizes a transformer-based network architecture for continuous heterogeneous cryo-EM reconstruction. We for the first time directly reconstruct continuous conformations of 3D structures using an implicit feature volume in the 3D spatial domain. A novel deformation transformer decoder further improves reconstruction quality and, more importantly, locates and robustly tackles flexible 3D regions caused by conformations. In experiments, our method outperforms current approaches on three public datasets (1 synthetic and 2 experimental) and a new synthetic dataset of PEDV spike protein. The code and new synthetic dataset will be released for better reproducibility of our results. Project page: https://cryoformer.github.io

Advances in the Synthesis of Halide Perovskite Single Crystals for Optoelectronic Applications

Yan J, Li H, Aldamasy MH, et al. Advances in the Synthesis of Halide Perovskite Single Crystals for Optoelectronic Applications. Chemistry of Materials. 2023;35(7):2683-2712.Perovskite materials have attracted much attention in various optoelectronics applications such as solar cells, light-emitting diodes, and photodetectors. Compared to multicrystalline films, single crystal perovskites are free of grain boundaries and exhibit lower defect density, longer carrier lifetimes, longer carrier diffusion distances, and outstanding stability, thus having the potential to show superior performances in optoelectronic devices. In addition, single crystal nanostructures are ideal model systems for studying the fundamental optoelectronic properties of newly designed functional materials. This review provides a thorough introduction to the fundamental theories behind crystal nucleation and growth. In addition, we provide an in-depth analysis of the application of classic ideas to the experimental formation of perovskite crystals including inorganic and hybrid halide perovskites with low-dimensional and three-dimensional structures. Subsequently, we correlate the crystal structure and optoelectronic properties and summarize the recent advances in the application of perovskite single crystals in various optoelectronic devices. Finally, we discuss the ongoing challenges in single crystal growth and the emerging optoelectronic applications. This review will serve as a valuable resource for future studies on the synthesis and uses of perovskite single crystals

ASSIST: Interactive Scene Nodes for Scalable and Realistic Indoor Simulation

We present ASSIST, an object-wise neural radiance field as a panoptic representation for compositional and realistic simulation. Central to our approach is a novel scene node data structure that stores the information of each object in a unified fashion, allowing online interaction in both intra- and cross-scene settings. By incorporating a differentiable neural network along with the associated bounding box and semantic features, the proposed structure guarantees user-friendly interaction on independent objects to scale up novel view simulation. Objects in the scene can be queried, added, duplicated, deleted, transformed, or swapped simply through mouse/keyboard controls or language instructions. Experiments demonstrate the efficacy of the proposed method, where scaled realistic simulation can be achieved through interactive editing and compositional rendering, with color images, depth images, and panoptic segmentation masks generated in a 3D consistent manner

Analiza niezawodności oraz optymalizacja systemów fazowych typu „k z n” o równym podziale obciążenia elementów składowych

There are many studies on k-out-of-n systems, load-sharing systems (LSS) and phased-mission systems (PMS); however, little attention has been given to load-sharing k-out-of-n systems with phased-mission requirements. This paper considers equal loadsharing k-out-of-n phased-mission systems with identical components. A method is proposed for the phased-mission reliability analysis of the studied systems based on the applicable failure path (AFP). A modified universal generating function (UGF) is used in the AFP-searching algorithm because of its efficiency. The tampered failure rate load-sharing model for the exactly k-out-of-n: F system is introduced and integrated into the method. With the TFR model, the systems with arbitrary load-dependent component failure distributions can be analyzed. According to the time and space complexity analysis, this method is particularly suitable for systems with small k-values. Two applications of the method are introduced in this paper. 1) A genetic algorithm (GA) based on the method is presented to solve the operational scheduling problem of systems with independent submissions. Two theorems are provided to solve the problem under some special conditions. 2) The method is used to select the optimal number of components to make the system reliable and robust.Istnieje wiele badań na temat systemów typu „k z n”, systemów z podziałem obciążenia (load-sharing systems, LSS) oraz systemów fazowych (tj. systemów o zadaniach okresowych) (phased-missionsystems, PMS); jak dotąd mało uwagi poświęcono jednak systemom typu „k z n” z podziałem obciążenia wymagającym realizacji różnych zadań w różnych przedziałach czasowych. Niniejszy artykuł omawia systemy fazowe typu „k z n” o równym podziale obciążenia przypadającego na identyczne elementy składowe. Zaproponowano metodę analizy niezawodności badanych systemów w poszczególnych fazach ich eksploatacji opartą na pojęciu właściwej ścieżki uszkodzeń (applicablefailurepath, AFP). W algorytmie wyszukującym AFP zastosowano zmodyfikowaną uniwersalną funkcję tworzącą (universal generating function, UGF), która cechuje się dużą wydajnością. Wprowadzono model manipulowanej intensywności uszkodzeń (tamperedfailurerate, TFR) elementów o równym podziale obciążenia dla systemu, w którym liczba uszkodzeń wynosi dokładnie k z n. Model ten włączono do proponowanej metody analizy niezawodności. Przy pomocy modelu TFR można analizować systemy o dowolnych rozkładach uszkodzeń części składowych, gdzie uszkodzenia są zależne od obciążenia. Zgodnie z analizą złożoności czasowej i przestrzennej, metoda ta jest szczególnie przydatna do modelowania układów o małych wartościach k. W pracy przedstawiono dwa zastosowania metody. 1) oparty o omawianą metodę algorytm genetyczny (GA) do rozwiązywania problemu harmonogramowania prac w systemach z niezależnymi podzadaniami. Sformułowano dwa twierdzenia pozwalające na rozwiązanie problemu w pewnych szczególnych warunkach. 2) Wybór optymalnej liczby elementów składowych pozwalającej na zachowanie niezawodności i odporności systemu

Economical energy allocation for the landward invasion of Spartina alterniflora in estuaries in the Yellow River Delta, east China

Smooth cordgrass (Spartina alterniflora) introduced to China in 1970 s for coastline stabilization threatening the habitat range of native Phragmites australis and even become more adaptive than P. australis. Thus, we used electronic universal testing machine and Van Soest method to compare the morphological and biomechanical responses of these two species to wave interference in the Yellow River Delta, east China. Our study showed that the morphological response of P. australis was more sensitive to waves with shorter individuals in wave zones but larger stem diameter and higher biomass than those in none-wave zones, while S. alterniflora did not exhibit such variations. In wave zones, S. alterniflora invaded P. australis’ habitat regardless higher stem-bending resistance of P. australis with excessive energy allocated in stem growth while decreasing reproduction and fitness. Compared with the none-wave zones, S. alterniflora allocated excessive energy in the stem to resist wind interference, and they are less fitted than P. australis. Thus, economic energy allocation to wave mechanical interference contributed to the successful invasion of S. alterniflora to landward in estuaries. S. alterniflora continued to expand landward in a semi-saline area but the community pattern may maintain the status quo for areas with low salinity and high wave interference

Clinical pharmacy undergraduate education in China: a comparative analysis based on ten universities’ training programs

Abstract Background In recent years, the scale of personnel training for clinical pharmacy professionals in China has expanded increasingly, however, the shortage of clinical pharmacists is still prominent. In 2018, the Ministry of Education of China released national standards for the teaching quality of undergraduate majors at regular colleges and universities, which has developed a core policy for undergraduate clinical pharmacy training. To explore the training methods for clinical pharmacy professionals in China and to promote the healthy and sustainable development of the clinical pharmacy education system. This study comparatively analyzed the training programs for clinical pharmacy undergraduates in China’s ten universities, discussed training programs suitable for clinical pharmacy professionals in China. Methods The clinical pharmacy education programs in these ten universities were obtained through official school websites or by interviewing relevant people, and then compared and analyzed. Results The school with the largest number of courses and the most class hours in general courses is University A1 (34 courses, 1316 class hours), and the school with the most credits is University B1 (75.5 credits). The schools with the largest number of courses and the most class hours in the basic courses are University A1 (50 courses, 1997 class hours), and the schools with the most credits are University B3 and University B1 (105.5 credits). The schools with the largest number of courses in the core courses are University C1 (23 courses), and the school with the most credits and class hours is University B2 (51 credits, 914 class hours). The school with the most class hours in practical teaching is University B6 (1406 class hours), and the schools with the longest internship time are University A1 and University B6 (52 weeks). Conclusions There was substantial variation in programs. There remains a gap between the existing educational model and clinical training in pharmacy in China and developed countries. China should explore the most appropriate method for undergraduate education in clinical pharmacy based on studying foreign excellent educational models and the experience of China

Lead isotope trends and sources in the atmosphere at the artificial wetland

With the rapid development of industry, studies on lead pollution in total suspended particulate matter (TSP) have received extensive attention. This paper analyzed the concentration and pollution sources of lead in the Cuihu Wetland in Beijing during the period of 2016–2017. The results show that the lead contents in TSP in the Cuihu Wetland were approximately equal in summer and spring, greater in winter, and greatest in autumn. The corresponding lead concentrations were 0.052, 0.053, 0.101, and 0.115 ng/m3, respectively. We compared the 206Pb/207Pb data with other materials to further understand the potential sources of atmospheric lead. The mean values of 206Pb/207Pb from spring to winter were 1.082, 1.098, 1.092, and 1.078, respectively. We found that the lead sources may be associated with coal burning, brake and tire wear, and vehicle exhaust emissions. We also calculated the enrichment factor values for the four seasons, and the values were all much greater than 10, indicating that the lead pollution is closely related to human activities