Hangzhou 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.

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.

Recent studies have suggested that the brain's structural and functional networks (i.e., connectomics) can be constructed by various imaging technologies (e.g., EEG/MEG; structural, diffusion and functional MRI) and further characterized by graph theory. Given the huge complexity of network construction, analysis and statistics, toolboxes incorporating these functions are largely lacking. Here, we developed the GRaph thEoreTical Network Analysis (GRETNA) toolbox for imaging connectomics. The GRETNA contains several key features as follows: (i) an open-source, Matlab-based, cross-platform (Windows and UNIX OS) package with a graphical user interface (GUI); (ii) allowing topological analyses of global and local network properties with parallel computing ability, independent of imaging modality and species; (iii) providing flexible manipulations in several key steps during network construction and analysis, which include network node definition, network connectivity processing, network type selection and choice of thresholding procedure; (iv) allowing statistical comparisons of global, nodal and connectional network metrics and assessments of relationship between these network metrics and clinical or behavioral variables of interest; and (v) including functionality in image preprocessing and network construction based on resting-state functional MRI (R-fMRI) data. After applying the GRETNA to a publicly released R-fMRI dataset of 54 healthy young adults, we demonstrated that human brain functional networks exhibit efficient small-world, assortative, hierarchical and modular organizations and possess highly connected hubs and that these findings are robust against different analytical strategies. With these efforts, we anticipate that GRETNA will accelerate imaging connectomics in an easy, quick and flexible manner. GRETNA is freely available on the NITRC website.

This review focuses on classifying different types of long wavelength absorbing BODIPY dyes based on the wide range of structural modification methods that have been adopted, and on tabulating their spectral and photophysical properties. The structure-property relationships are analyzed in depth with reference to molecular modeling calculations, so that the effectiveness of the different structural modification strategies for shifting the main BODIPY spectral bands to longer wavelengths can be readily compared, along with their effects on the fluorescence quantum yield (ΦF) values. This should facilitate the future rational design of red/NIR region BODIPY dyes for a wide range of different applications.

We study the process ${e}^{+}{e}^{\ensuremath{-}}\ensuremath{\rightarrow}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}J/\ensuremath{\psi}$ at a center-of-mass energy of 4.260 GeV using a $525\text{ }\text{ }{\mathrm{pb}}^{\ensuremath{-}1}$ data sample collected with the BESIII detector operating at the Beijing Electron Positron Collider. The Born cross section is measured to be $(62.9\ifmmode\pm\else\textpm\fi{}1.9\ifmmode\pm\else\textpm\fi{}3.7)\text{ }\text{ }\mathrm{pb}$, consistent with the production of the $Y(4260)$. We observe a structure at around $3.9\text{ }\text{ }\mathrm{GeV}/{c}^{2}$ in the ${\ensuremath{\pi}}^{\ifmmode\pm\else\textpm\fi{}}J/\ensuremath{\psi}$ mass spectrum, which we refer to as the ${Z}_{c}(3900)$. If interpreted as a new particle, it is unusual in that it carries an electric charge and couples to charmonium. A fit to the ${\ensuremath{\pi}}^{\ifmmode\pm\else\textpm\fi{}}J/\ensuremath{\psi}$ invariant mass spectrum, neglecting interference, results in a mass of $(3899.0\ifmmode\pm\else\textpm\fi{}3.6\ifmmode\pm\else\textpm\fi{}4.9)\text{ }\text{ }\mathrm{MeV}/{c}^{2}$ and a width of $(46\ifmmode\pm\else\textpm\fi{}10\ifmmode\pm\else\textpm\fi{}20)\text{ }\text{ }\mathrm{MeV}$. Its production ratio is measured to be $R=(\ensuremath{\sigma}\mathbf{(}{e}^{+}{e}^{\ensuremath{-}}\ensuremath{\rightarrow}{\ensuremath{\pi}}^{\ifmmode\pm\else\textpm\fi{}}{Z}_{c}(3900{)}^{\ensuremath{\mp}}\ensuremath{\rightarrow}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}J/\ensuremath{\psi}\mathbf{)}/\ensuremath{\sigma}({e}^{+}{e}^{\ensuremath{-}}\ensuremath{\rightarrow}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}J/\ensuremath{\psi}))=(21.5\ifmmode\pm\else\textpm\fi{}3.3\ifmmode\pm\else\textpm\fi{}7.5)%$. In all measurements the first errors are statistical and the second are systematic.

Major depressive disorder (MDD) is common and disabling, but its neuropathophysiology remains unclear. Most studies of functional brain networks in MDD have had limited statistical power and data analysis approaches have varied widely. The REST-meta-MDD Project of resting-state fMRI (R-fMRI) addresses these issues. Twenty-five research groups in China established the REST-meta-MDD Consortium by contributing R-fMRI data from 1,300 patients with MDD and 1,128 normal controls (NCs). Data were preprocessed locally with a standardized protocol before aggregated group analyses. We focused on functional connectivity (FC) within the default mode network (DMN), frequently reported to be increased in MDD. Instead, we found decreased DMN FC when we compared 848 patients with MDD to 794 NCs from 17 sites after data exclusion. We found FC reduction only in recurrent MDD, not in first-episode drug-naïve MDD. Decreased DMN FC was associated with medication usage but not with MDD duration. DMN FC was also positively related to symptom severity but only in recurrent MDD. Exploratory analyses also revealed alterations in FC of visual, sensory-motor, and dorsal attention networks in MDD. We confirmed the key role of DMN in MDD but found reduced rather than increased FC within the DMN. Future studies should test whether decreased DMN FC mediates response to treatment. All R-fMRI indices of data contributed by the REST-meta-MDD consortium are being shared publicly via the R-fMRI Maps Project.

Luminescent materials with efficient solid-state emissions are important for the advancement of optoelectronics. Recently, a new class of propeller-like luminogenic molecules with aggregation-induced emission (AIE) characteristics has drawn increasing research interest. Among them, tetraphenylethene (TPE) is an archetypal luminogen with a simple molecule structure but shows a splendid AIE effect. Utilizing TPE as a building block, an effective strategy to create efficient solid-state emitters is developed. In this feature article, we review mainly our recent work on the construction of luminogenic materials from TPE and present their applications in organic light-emitting diodes. The applicability of the synthetic strategy and the utility of the resulting materials are demonstrated.

The development of mild and general methods for C-S bond formation has received significant attention because the C-S bond is indispensable in many important biological and pharmaceutical compounds. Early examples for the synthesis of C-S bonds are generally limited to the condensation reaction between a metal thiolate and an organic halide. Recent chemical approaches for C-S bond formation, based upon direct C-H bond functionalization and decarboxylative reactions, not only provide new insights into the mechanistic understanding of C-S coupling reactions but also allow the synthesis of sulfur-containing compounds from more effective synthetic routes with high atom economy. This review intends to explore recent advances in C-S bond formation via C-H functionalization and decarboxylation, and the growing opportunities they present to the construction of complex chemical scaffolds for applications encompassing natural product synthesis, synthetic methodology development, and functional materials as well as nanotechnology.

Ferroptosis is a newly discovered type of cell death triggered by intracellular phospholipid peroxidation that is morphologically, biologically and genetically distinct from other types of cell death. Ferroptosis is classified as regulated necrosis and is more immunogenic than apoptosis. To date, compelling evidence indicates that ferroptosis plays an important role in inflammation, and several antioxidants functioning as ferroptosis inhibitors have been shown to exert anti-inflammatory effects in experimental models of certain diseases. Our review provides an overview of the link between ferroptosis and inflammation; a better understanding of the mechanisms underlying ferroptosis and inflammation may hasten the development of promising therapeutic strategies involving ferroptosis inhibitors to address inflammation.

Despite evidence from experimental grasslands that plant diversity increases biomass production and soil organic carbon (SOC) storage, it remains unclear whether this is true in natural ecosystems, especially under climatic variations and human disturbances. Based on field observations from 6,098 forest, shrubland, and grassland sites across China and predictions from an integrative model combining multiple theories, we systematically examined the direct effects of climate, soils, and human impacts on SOC storage versus the indirect effects mediated by species richness (SR), aboveground net primary productivity (ANPP), and belowground biomass (BB). We found that favorable climates (high temperature and precipitation) had a consistent negative effect on SOC storage in forests and shrublands, but not in grasslands. Climate favorability, particularly high precipitation, was associated with both higher SR and higher BB, which had consistent positive effects on SOC storage, thus offsetting the direct negative effect of favorable climate on SOC. The indirect effects of climate on SOC storage depended on the relationships of SR with ANPP and BB, which were consistently positive in all biome types. In addition, human disturbance and soil pH had both direct and indirect effects on SOC storage, with the indirect effects mediated by changes in SR, ANPP, and BB. High soil pH had a consistently negative effect on SOC storage. Our findings have important implications for improving global carbon cycling models and ecosystem management: Maintaining high levels of diversity can enhance soil carbon sequestration and help sustain the benefits of plant diversity and productivity.

Ferroptosis is an iron-dependent, oxidative cell death, and is characterized by iron-dependent accumulation of reactive oxygen species (ROS) within the cell. It has been implicated in various human diseases, including cancer. Recently, ferroptosis as a non-apoptotic form of cell death induced by small molecules is emerging in specific cancer types, however, its relevance in colorectal cancer (CRC) is unexplored and remains unclear. Here, we showed that ferroptosis inducer RSL3 initiated cell death and ROS accumulation in HCT116, LoVo and HT29 CRC cells over a 24 h time course. Furthermore, we determined that ROS levels and transferrin expression were elevated in CRC cells treated with RSL3 accompanied by a decrease in the expression of glutathione peroxidase 4 (GPX4), indicating an iron-dependent cell death, ferroptosis. Overexpression GPX4 resulted in decreased cell death after RSL3 treatment. Taken together, our results suggest that the induction of ferroptosis contributed to RSL3-induced cell death in CRC cells and ferroptosis may be a pervasive and dynamic form of cell death for cancer treatment.

Identifying influential nodes in dynamical processes is crucial in understanding network structure and function. Degree, H-index and coreness are widely used metrics, but previously treated as unrelated. Here we show their relation by constructing an operator , in terms of which degree, H-index and coreness are the initial, intermediate and steady states of the sequences, respectively. We obtain a family of H-indices that can be used to measure a node's importance. We also prove that the convergence to coreness can be guaranteed even under an asynchronous updating process, allowing a decentralized local method of calculating a node's coreness in large-scale evolving networks. Numerical analyses of the susceptible-infected-removed spreading dynamics on disparate real networks suggest that the H-index is a good tradeoff that in many cases can better quantify node influence than either degree or coreness.

Chitosan nanoparticles are good drug carriers because of their good biocompatibility and biodegradability, and can be readily modified. As a new drug delivery system, they have attracted increasing attention for their wide applications in, for example, loading protein drugs, gene drugs, and anticancer chemical drugs, and via various routes of administration including oral, nasal, intravenous, and ocular. This paper reviews published research on chitosan nanoparticles, including its preparation methods, characteristics, modification, in vivo metabolic processes, and applications.

Abstract Electromagnetic absorbers have drawn increasing attention in many areas. A series of plasmonic and metamaterial structures can work as efficient narrowband absorbers due to the excitation of plasmonic or photonic resonances, providing a great potential for applications in designing selective thermal emitters, biosensing, etc. In other applications such as solar‐energy harvesting and photonic detection, the bandwidth of light absorbers is required to be quite broad. Under such a background, a variety of mechanisms of broadband/multiband absorption have been proposed, such as mixing multiple resonances together, exciting phase resonances, slowing down light by anisotropic metamaterials, employing high loss materials and so on.

The human gut microbiome is a huge microbial community that plays an irreplaceable role in human life. With the further development of research, the influence of intestinal flora on human diseases has been gradually excavated. Gut microbiota (GM) dysbiosis has adverse health effects on the human body that will lead to a variety of chronic diseases. The underlying mechanisms of GM on human diseases are incredibly complicated. This review focuses on the regulation and mechanism of GM on neurodegenerative diseases, cardiovascular diseases, metabolic diseases and gastrointestinal diseases, thus providing a potential target for the prevention and treatment of disease.

Observational studies suggest that insomnia might be associated with an increased risk of depression with inconsistent results. This study aimed at conducting a meta-analysis of prospective cohort studies to evaluate the association between insomnia and the risk of depression. Relevant cohort studies were comprehensively searched from the PubMed, Embase, Web of Science, and China National Knowledge Infrastructure databases (up to October 2014) and from the reference lists of retrieved articles. A random-effects model was used to calculate the pooled risk estimates and 95 % confidence intervals (CIs). The I 2 statistic was used to assess the heterogeneity and potential sources of heterogeneity were assessed with meta-regression. The potential publication bias was explored by using funnel plots, Egger’s test, and Duval and Tweedie trim-and-fill methods. Thirty-four cohort studies involving 172,077 participants were included in this meta-analysis with an average follow-up period of 60.4 months (ranging from 3.5 to 408). Statistical analysis suggested a positive relationship between insomnia and depression, the pooled RR was 2.27 (95 % CI: 1.89–2.71), and a high heterogeneity was observed (I 2 = 92.6 %, P < 0.001). Visual inspection of the funnel plot revealed some asymmetry. The Egger’s test identified evidence of substantial publication bias (P <0.05), but correction for this bias using trim-and-fill method did not alter the combined risk estimates. This meta-analysis indicates that insomnia is significantly associated with an increased risk of depression, which has implications for the prevention of depression in non-depressed individuals with insomnia symptoms.

Magnetite nanoparticles (Fe₃O₄) represent the most promising materials in medical applications. To favor high-drug or enzyme loading on the nanoparticles, they are incorporated into mesoporous materials to form a hybrid support with the consequent reduction of magnetization saturation. The direct synthesis of mesoporous structures appears to be of interest. To this end, magnetite nanoparticles have been synthesized using a one pot co-precipitation reaction at room temperature in the presence of different bases, such as NaOH, KOH or (C₂H₅)₄NOH. Magnetite shows characteristics of superparamagnetism at room temperature and a saturation magnetization (Ms) value depending on both the crystal size and the degree of agglomeration of individual nanoparticles. Such agglomeration appears to be responsible for the formation of mesoporous structures, which are affected by the pH, the nature of alkali, the slow or fast addition of alkaline solution and the drying modality of synthesized powders.

Mixed convection is a mechanism of heat transport in a thermodynamic system in which the motion of fluid particles is produced by gravity as well as external forces like fans, pumps, or any other devices. Such type of heat transport has a fruitful application in daily life due to reliable maintenance. In this regard, numerous researchers and analyst have focused on the importance of mixed convective flow to explore its different aspects, and frequent research articles are published in this area. In this work, mixed convective entropy optimized nanomaterial magnetohydrodynamics (MHD) flow of Ree‐Eyring fluid is discussed between two rotating disks. The effects of porosity and velocity slip are considered. Both the disks are rotating with different angular frequency and stretching rates. Modeling is performed for the energy equation subject to heat generation/absorption, dissipation, radiative heat flux, and Joule heating. Four types of irreversibilities are discussed, and total entropy rate is calculated. The obtained results are compared with past studies and found good agreement with them. The physical curiosity like skin friction and Sherwood and Nusselt numbers are numerically calculated. Series solutions are computed via homotopy method. Our obtained outcomes show that the velocity and temperature fields show contrast behavior against larger magnetic parameter. It is also noticed that the entropy rate and Bejan number have opposite behaviors against higher values of Weissenberg number. The entropy rate increases for higher Weissenberg number while Bejan number decays.

Efforts to identify meaningful functional imaging-based biomarkers are limited by the ability to reliably characterize inter-individual differences in human brain function. Although a growing number of connectomics-based measures are reported to have moderate to high test-retest reliability, the variability in data acquisition, experimental designs, and analytic methods precludes the ability to generalize results. The Consortium for Reliability and Reproducibility (CoRR) is working to address this challenge and establish test-retest reliability as a minimum standard for methods development in functional connectomics. Specifically, CoRR has aggregated 1,629 typical individuals' resting state fMRI (rfMRI) data (5,093 rfMRI scans) from 18 international sites, and is openly sharing them via the International Data-sharing Neuroimaging Initiative (INDI). To allow researchers to generate various estimates of reliability and reproducibility, a variety of data acquisition procedures and experimental designs are included. Similarly, to enable users to assess the impact of commonly encountered artifacts (for example, motion) on characterizations of inter-individual variation, datasets of varying quality are included.

Depth camera such as Microsoft Kinect, is much cheaper than conventional 3D scanning devices, and thus it can be acquired for everyday users easily. However, the depth data captured by Kinect over a certain distance is of extreme low quality. In this paper, we present a novel scanning system for capturing 3D full human body models by using multiple Kinects. To avoid the interference phenomena, we use two Kinects to capture the upper part and lower part of a human body respectively without overlapping region. A third Kinect is used to capture the middle part of the human body from the opposite direction. We propose a practical approach for registering the various body parts of different views under non-rigid deformation. First, a rough mesh template is constructed and used to deform successive frames pairwisely. Second, global alignment is performed to distribute errors in the deformation space, which can solve the loop closure problem efficiently. Misalignment caused by complex occlusion can also be handled reasonably by our global alignment algorithm. The experimental results have shown the efficiency and applicability of our system. Our system obtains impressive results in a few minutes with low price devices, thus is practically useful for generating personalized avatars for everyday users. Our system has been used for 3D human animation and virtual try on, and can further facilitate a range of home&#8211;oriented virtual reality (VR) applications.