East China Normal University

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

Oxygen is fundamental to life. Not only is it essential for the survival of individual animals, but it regulates global cycles of major nutrients and carbon. The oxygen content of the open ocean and coastal waters has been declining for at least the past half-century, largely because of human activities that have increased global temperatures and nutrients discharged to coastal waters. These changes have accelerated consumption of oxygen by microbial respiration, reduced solubility of oxygen in water, and reduced the rate of oxygen resupply from the atmosphere to the ocean interior, with a wide range of biological and ecological consequences. Further research is needed to understand and predict long-term, global- and regional-scale oxygen changes and their effects on marine and estuarine fisheries and ecosystems.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) and molecular mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods for binding free energy prediction since they are more accurate than most scoring functions of molecular docking and less computationally demanding than alchemical free energy methods. MM/PBSA and MM/GBSA have been widely used in biomolecular studies such as protein folding, protein-ligand binding, protein-protein interaction, etc. In this review, methods to adjust the polar solvation energy and to improve the performance of MM/PBSA and MM/GBSA calculations are reviewed and discussed. The latest applications of MM/GBSA and MM/PBSA in drug design are also presented. This review intends to provide readers with guidance for practically applying MM/PBSA and MM/GBSA in drug design and related research fields.

The impact of the development of sulfur therapeutics is instrumental to the evolution of the pharmaceutical industry. Sulfur-derived functional groups can be found in a broad range of pharmaceuticals and natural products. For centuries, sulfur continues to maintain its status as the dominating heteroatom integrated into a set of 362 sulfur-containing FDA approved drugs (besides oxygen or nitrogen) through the present. Sulfonamides, thioethers, sulfones and Penicillin are the most common scaffolds in sulfur containing drugs, which are well studied both on synthesis and application during the past decades. In this review, these four moieties in pharmaceuticals and recent advances in the synthesis of the corresponding core scaffolds are presented.

Abstract Tailored to the specific tumour microenvironment, which involves acidity and the overproduction of hydrogen peroxide, advanced nanotechnology has been introduced to generate the hydroxyl radical ( . OH) primarily for tumour chemodynamic therapy (CDT) through the Fenton and Fenton‐like reactions. Numerous studies have investigated the enhancement of CDT efficiency, primarily the increase in the amount of . OH generated. Notably, various strategies based on the Fenton reaction have been employed to enhance . OH generation, including nanomaterials selection, modulation of the reaction environment, and external energy fields stimulation, which are discussed systematically in this Minireview. Furthermore, the potential challenges and the methods used to facilitate CDT effectiveness are also presented to support this cutting‐edge research area.

Significance Exceedingly high levels of fine particulate matter (PM) occur frequently in China, but the mechanism of severe haze formation remains unclear. From atmospheric measurements in two Chinese megacities and laboratory experiments, we show that the oxidation of SO 2 by NO 2 occurs efficiently in aqueous media under two polluted conditions: first, during the formation of the 1952 London Fog via in-cloud oxidation; and second, on fine PM with NH 3 neutralization during severe haze in China. We suggest that effective haze mitigation is achievable by intervening in the sulfate formation process with NH 3 and NO 2 emission control measures. Hence, our results explain the outstanding sulfur problem during the historic London Fog formation and elucidate the chemical mechanism of severe haze in China.

The kesterite-structured semiconductors Cu2ZnSnS4 and Cu2ZnSnSe4 are drawing considerable attention recently as the active layers in earth-abundant low-cost thin-film solar cells. The additional number of elements in these quaternary compounds, relative to binary and ternary semiconductors, results in increased flexibility in the material properties. Conversely, a large variety of intrinsic lattice defects can also be formed, which have important influence on their optical and electrical properties, and hence their photovoltaic performance. Experimental identification of these defects is currently limited due to poor sample quality. Here recent theoretical research on defect formation and ionization in kesterite materials is reviewed based on new systematic calculations, and compared with the better studied chalcopyrite materials CuGaSe2 and CuInSe2 . Four features are revealed and highlighted: (i) the strong phase-competition between the kesterites and the coexisting secondary compounds; (ii) the intrinsic p-type conductivity determined by the high population of acceptor CuZn antisites and Cu vacancies, and their dependence on the Cu/(Zn+Sn) and Zn/Sn ratio; (iii) the role of charge-compensated defect clusters such as [2CuZn +SnZn ], [VCu +ZnCu ] and [ZnSn +2ZnCu ] and their contribution to non-stoichiometry; (iv) the electron-trapping effect of the abundant [2CuZn +SnZn ] clusters, especially in Cu2ZnSnS4. The calculated properties explain the experimental observation that Cu poor and Zn rich conditions (Cu/(Zn+Sn) ≈ 0.8 and Zn/Sn ≈ 1.2) result in the highest solar cell efficiency, as well as suggesting an efficiency limitation in Cu2ZnSn(S,Se)4 cells when the S composition is high.

. We further tested MN15 for 10 transition-metal coordination energies, the entire S66x8 database of noncovalent interactions, 21 transition-metal reaction barrier heights, 69 electronic excitation energies of organic molecules, 31 semiconductor band gaps, seven transition-metal dimer bond lengths, and 193 bond lengths of 47 organic molecules. The MN15 functional not only performs very well for our training set, which has 481 pieces of data, but also performs very well for our test set, which has 823 data that are not in our training set. The test set includes both ground-state properties and molecular excitation energies. For the latter MN15 achieves simultaneous accuracy for both valence and Rydberg electronic excitations when used with linear-response time-dependent density functional theory, with an MUE of less than 0.3 eV for both types of excitations.

Abstract. Water masses can become undersaturated with oxygen when natural processes alone or in combination with anthropogenic processes produce enough organic carbon that is aerobically decomposed faster than the rate of oxygen re-aeration. The dominant natural processes usually involved are photosynthetic carbon production and microbial respiration. The re-supply rate is indirectly related to its isolation from the surface layer. Hypoxic water masses (<2 mg L−1, or approximately 30% saturation) can form, therefore, under "natural" conditions, and are more likely to occur in marine systems when the water residence time is extended, water exchange and ventilation are minimal, stratification occurs, and where carbon production and export to the bottom layer are relatively high. Hypoxia has occurred through geological time and naturally occurs in oxygen minimum zones, deep basins, eastern boundary upwelling systems, and fjords. Hypoxia development and continuation in many areas of the world's coastal ocean is accelerated by human activities, especially where nutrient loading increased in the Anthropocene. This higher loading set in motion a cascading set of events related to eutrophication. The formation of hypoxic areas has been exacerbated by any combination of interactions that increase primary production and accumulation of organic carbon leading to increased respiratory demand for oxygen below a seasonal or permanent pycnocline. Nutrient loading is likely to increase further as population growth and resource intensification rises, especially with increased dependency on crops using fertilizers, burning of fossil fuels, urbanization, and waste water generation. It is likely that the occurrence and persistence of hypoxia will be even more widespread and have more impacts than presently observed. Global climate change will further complicate the causative factors in both natural and human-caused hypoxia. The likelihood of strengthened stratification alone, from increased surface water temperature as the global climate warms, is sufficient to worsen hypoxia where it currently exists and facilitate its formation in additional waters. Increased precipitation that increases freshwater discharge and flux of nutrients will result in increased primary production in the receiving waters up to a point. The interplay of increased nutrients and stratification where they occur will aggravate and accelerate hypoxia. Changes in wind fields may expand oxygen minimum zones onto more continental shelf areas. On the other hand, not all regions will experience increased precipitation, some oceanic water temperatures may decrease as currents shift, and frequency and severity of tropical storms may increase and temporarily disrupt hypoxia more often. The consequences of global warming and climate change are effectively uncontrollable at least in the near term. On the other hand, the consequences of eutrophication-induced hypoxia can be reversed if long-term, broad-scale, and persistent efforts to reduce substantial nutrient loads are developed and implemented. In the face of globally expanding hypoxia, there is a need for water and resource managers to act now to reduce nutrient loads to maintain, at least, the current status.

International challenges have become the de facto standard for comparative assessment of image analysis algorithms. Although segmentation is the most widely investigated medical image processing task, the various challenges have been organized to focus only on specific clinical tasks. We organized the Medical Segmentation Decathlon (MSD)-a biomedical image analysis challenge, in which algorithms compete in a multitude of both tasks and modalities to investigate the hypothesis 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. MSD results confirmed this hypothesis, moreover, MSD winner continued generalizing well to a wide range of other clinical problems for the next two years. Three main conclusions can be drawn from this study: (1) state-of-the-art image segmentation algorithms 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 scientists that are not versed in AI model training.

Nanoformulations that can respond to the specific tumor microenvironment (TME), such as a weakly acidic pH, low oxygen, and high glutathione (GSH), show promise for killing cancer cells with minimal invasiveness and high specificity. In this study, we demonstrate self-assembled copper–amino acid mercaptide nanoparticles (Cu-Cys NPs) for in situ glutathione-activated and H2O2-reinforced chemodynamic therapy for drug-resistant breast cancer. After endocytosis into tumor cells, the Cu-Cys NPs could first react with local GSH, induce GSH depletion, and reduce Cu2+ to Cu+. Subsequently, the generated Cu+ would react with local H2O2 to generate toxic hydroxyl radicals (·OH) via a Fenton-like reaction, which has a fast reaction rate in the weakly acidic TME, that are responsible for tumor-cell apoptosis. Due to the high GSH and H2O2 concentration in tumor cells, which sequentially triggers the redox reactions, Cu-Cys NPs exhibited relatively high cytotoxicity to cancer cells, whereas normal cells were left alive. The in vivo results also proved that Cu-Cys NPs efficiently inhibited drug-resistant breast cancer without causing obvious systemic toxicity. As a novel copper mercaptide nanoformulation responsive to the TME, these Cu-Cys NPs may have great potential in chemodynamic cancer therapy.

Allenes are the simplest class of cumulenes, with two contiguous C=C bonds, and show unique physical and chemical properties. These features make allenes particularly attractive in modern organic chemistry. In this Review, attention is paid to the advances made in catalytic asymmetric synthesis and natural product syntheses based on well-established reactions of allenes, such as propargylation, addition, cycloaddition, cycloisomerization, cyclization, etc., with or without catalysts. Their versatile reactivity, substituent-loading ability, axial to center chirality transfer, and controllable selectivity allow access to target molecules by unique and efficient approaches. The main topics in this Review are presented with selected examples from 2003 to 2011.

Central sensitization, increased sensitivity in spinal cord dorsal horn neurons after injuries, plays an essential role in the induction and maintenance of chronic pain. However, synaptic mechanisms underlying central sensitization are incompletely known. Growing evidence suggests that proinflammatory cytokines (PICs), such as interleukin-1beta (IL-1beta), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNFalpha), are induced in the spinal cord under various injury conditions and contribute to pain hypersensitivity. Using patch-clamp recordings in lamina II neurons of isolated spinal cord slices, we compared the effects of IL-1beta, IL-6, and TNFalpha on excitatory and inhibitory synaptic transmission. Whereas TNFalpha enhanced the frequency of spontaneous EPSCs (sEPSCs), IL-6 reduced the frequency of spontaneous IPSCs (sIPSCs). Notably, IL-1beta both enhanced the frequency and amplitude of sEPSCs and reduced the frequency and amplitude of sIPSCs. Consistently, TNFalpha and IL-1beta enhanced AMPA- or NMDA-induced currents, and IL-1beta and IL-6 suppressed GABA- and glycine-induced currents. Furthermore, all the PICs increased cAMP response element-binding protein (CREB) phosphorylation in superficial dorsal horn neurons and produced heat hyperalgesia after spinal injection. Surprisingly, soluble IL-6 receptor (sIL-6R) produced initial decrease of sEPSCs, followed by increase of sEPSCs and CREB phosphorylation. Spinal injection of sIL-6R also induced heat hyperalgesia that was potentiated by coadministration with IL-6. Together, our data have demonstrated that PICs induce central sensitization and hyperalgesia via distinct and overlapping synaptic mechanisms in superficial dorsal horn neurons either by increasing excitatory synaptic transmission or by decreasing inhibitory synaptic transmission. PICs may further induce long-term synaptic plasticity through CREB-mediated gene transcription. Blockade of PIC signaling could be an effective way to suppress central sensitization and alleviate chronic pain.

Microplastics have been found in seas all over the world. We hypothesize that sea salts might contain microplastics, because they are directly supplied by seawater. To test our hypothesis, we collected 15 brands of sea salts, lake salts, and rock/well salts from supermarkets throughout China. The microplastics content was 550-681 particles/kg in sea salts, 43-364 particles/kg in lake salts, and 7-204 particles/kg in rock/well salts. In sea salts, fragments and fibers were the prevalent types of particles compared with pellets and sheets. Microplastics measuring less than 200 μm represented the majority of the particles, accounting for 55% of the total microplastics, and the most common microplastics were polyethylene terephthalate, followed by polyethylene and cellophane in sea salts. The abundance of microplastics in sea salts was significantly higher than that in lake salts and rock/well salts. This result indicates that sea products, such as sea salts, are contaminated by microplastics. To the best of our knowledge, this is the first report on microplastic pollution in abiotic sea products.

Medical image segmentation is crucial for healthcare, yet convolution-based methods like U-Net face limitations in modeling long-range dependencies. To address this, Transformers designed for sequence-to-sequence predictions have been integrated into medical image segmentation. However, a comprehensive understanding of Transformers' self-attention in U-Net components is lacking. TransUNet, first introduced in 2021, is widely recognized as one of the first models to integrate Transformer into medical image analysis. In this study, we present the versatile framework of TransUNet that encapsulates Transformers' self-attention into two key modules: (1) a Transformer encoder tokenizing image patches from a convolution neural network (CNN) feature map, facilitating global context extraction, and (2) a Transformer decoder refining candidate regions through cross-attention between proposals and U-Net features. These modules can be flexibly inserted into the U-Net backbone, resulting in three configurations: Encoder-only, Decoder-only, and Encoder+Decoder. TransUNet provides a library encompassing both 2D and 3D implementations, enabling users to easily tailor the chosen architecture. Our findings highlight the encoder's efficacy in modeling interactions among multiple abdominal organs and the decoder's strength in handling small targets like tumors. It excels in diverse medical applications, such as multi-organ segmentation, pancreatic tumor segmentation, and hepatic vessel segmentation. Notably, our TransUNet achieves a significant average Dice improvement of 1.06% and 4.30% for multi-organ segmentation and pancreatic tumor segmentation, respectively, when compared to the highly competitive nn-UNet, and surpasses the top-1 solution in the BrasTS2021 challenge. 2D/3D Code and models are available at https://github.com/Beckschen/TransUNet and https://github.com/Beckschen/TransUNet-3D, respectively.

Levels of microplastics (MPs) in China are completely unknown. This study characterizes suspended MPs quantitatively and qualitatively for the Yangtze Estuary and East China Sea. MPs were extracted via a floatation method. MPs were counted and categorized according to shape and size under a stereomicroscope. The MP densities were 4137.3±2461.5 and 0.167±0.138 n/m(3), respectively, in the estuarine and the sea samples. Plastic abundances varied significantly in the estuary. Higher densities in three sea trawls confirmed that rivers were the important sources of MP to the marine environment. Plastic particles (>5mm) were observed with a maximum size of 12.46 mm, but MPs (0.5-5 mm) constituted more than 90% by number of items. The most frequent geometries were fibres, followed by granules and films. Plastic spherules occurred sparsely. Transparent and coloured plastics comprised the majority of the particles. This study provides clues in understanding the fate and potential sources of MPs.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTADDITION / CORRECTIONThis article has been corrected. View the notice.Lamellarins and Related Pyrrole-Derived Alkaloids from Marine OrganismsHui Fan, Jiangnan Peng, Mark T. Hamann, and Jin-Feng HuView Author Information Department of Natural Products for Chemical Genetic Research, Key Laboratory of Brain Functional Genomics, Ministry of Education & Shanghai Key Laboratory of Brain Functional Genomics (MOE & SBFG), East China Normal University, Shanghai, 200062, China and Department of Pharmacognosy and National Center for Natural Products Research (NCNPR), School of Pharmacy, The University of Mississippi, Oxford, Mississippi 38677 Cite this: Chem. Rev. 2008, 108, 1, 264–287Publication Date (Web):December 21, 2007Publication History Received4 May 2007Published online21 December 2007Published inissue 1 January 2008https://pubs.acs.org/doi/10.1021/cr078199mhttps://doi.org/10.1021/cr078199mresearch-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views6786Altmetric-Citations930LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Cells,Chemical synthesis,Inhibition,Organic compounds,Organic synthesis Get e-Alerts

The ubiquity of microplastics in aquatic and terrestrial environments and related ecological impacts have gained global attention. Microplastics have been detected in table salt, drinking water, and air, posing inevitable human exposure risk. However, rigorous analytical methods for detection and characterization of microplastics remain scarce. Knowledge about the potential adverse effects on human health via dietary and respiratory exposures is also limited. To address these issues, we reviewed 46 publications concerning abundances, potential sources, and analytical methods of microplastics in table salt, drinking water, and air. We also summarized probable translocation and accumulation pathways of microplastics within human body. Human body burdens of microplastics through table salt, drinking water, and inhalation were estimated to be (0–7.3)×104, (0–4.7)×103, and (0–3.0)×107 items per person per year, respectively. The intake of microplastics via inhalation, especially via indoor air, was much higher than those via other exposure routes. Moreover, microplastics in the air impose threats to both respiratory and digestive systems through breathing and ingestion. Given the lifetime inevitable exposure to microplastics, we urgently call for a better understanding of the potential hazards of microplastics to human health.

Single-cell RNA sequencing (scRNA-seq) technologies allow the dissection of gene expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A number of scRNA-seq protocols have been developed, and these methods possess their unique features with distinct advantages and disadvantages. Due to technical limitations and biological factors, scRNA-seq data are noisier and more complex than bulk RNA-seq data. The high variability of scRNA-seq data raises computational challenges in data analysis. Although an increasing number of bioinformatics methods are proposed for analyzing and interpreting scRNA-seq data, novel algorithms are required to ensure the accuracy and reproducibility of results. In this review, we provide an overview of currently available single-cell isolation protocols and scRNA-seq technologies, and discuss the methods for diverse scRNA-seq data analyses including quality control, read mapping, gene expression quantification, batch effect correction, normalization, imputation, dimensionality reduction, feature selection, cell clustering, trajectory inference, differential expression calling, alternative splicing, allelic expression, and gene regulatory network reconstruction. Further, we outline the prospective development and applications of scRNA-seq technologies.