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Chronic limb-threatening ischemia (CLTI), representing the end-stage of peripheral arterial disease (PAD), is associated with a one-year limb amputation rate of ∼15-20% and significant mortality. A key characteristic of CLTI is the failure of the innate regenerative capacity of skeletal muscle, though the underlying mechanisms remain unclear. Here, single-cell transcriptome analysis of ischemic and non-ischemic muscle from the same CLTI patients demonstrated that ischemic-damaged tissue is enriched with pro-inflammatory macrophages. Comparable results were also observed in a murine CLTI model. Importantly, integrated analyses of both human and murine data revealed premature differentiation of muscle satellite cells (MuSCs) in damaged tissue and indications of defects in intercellular signaling communication between MuSCs and their inflammatory niche. Collectively, our research provides the first single-cell transcriptome atlases of skeletal muscle from CLTI patients and murine models, emphasizing the crucial role of macrophages and inflammation in regulating muscle regeneration in CLTI through interactions with MuSCs.

P-Nitrophenol (4-NP) is a high toxicity material and has harmful effects on the environment. Thus, the analysis of 4-NP is an important topic at present. In this work, the fabrication of a novel electrochemical sensor based on coal-liquefaction-residue (CLR)-derived porous carbon (PC) materials. CLR-based porous carbon material was prepared by the high-temperature carbonization method and the morphology and structure of the materials were characterized by scanning electron microscopy and other characterization methods. Subsequently, the electrochemical properties of the modified electrodes were studied by cyclic voltammetry (CV) and differential pulse voltammetry (DPV) measurements. The results showed that under optimal conditions, the sensor had a good electrochemical performance for environmental pollutant 4-NP. In particular, the linear range of the sensor was 10–200 μmol·L-1 and the detection limit was 1.169 μmol·L−1 on the basis of the signal-to-noise ratio S/N = 3. The electrode showed excellent stability, reproducibility and repetitiveness and the sensor also had good selectivity. In addition, the newly constructed sensor exhibited adsorption-controlled kinetics and the recovery rate of 4-NP in actual water samples could reach 90.06~95.17%, indicating that the sensor had good practical application prospects.

Transposable elements (TEs) are parasitic DNA sequences accounting for over half of the human genome. Tight control of the repression and activation states of TEs is critical for genome integrity, development, immunity, and diseases, including cancer. However, precisely how this regulation is achieved remains unclear. To address this question, we develop a targeted proteomic proximity labeling approach to capture TE-associated proteins in human embryonic stem cells (hESCs). We find that the RNA N6-methyladenosine(m6A)-reader, YTHDC2, occupies genomic loci of the primate-specific TE, LTR7/HERV-H, specifically through its interaction with m6A-modified HERV-H RNAs. Unexpectedly, YTHDC2 recruits the DNA 5-methylcytosine(5mC)-demethylase, TET1, to remove 5mC from LTR7/HERV-H and prevent epigenetic silencing. Functionally, the YTHDC2/LTR7-axis inhibits neural differentiation of hESCs. Our results reveal both an underappreciated crosstalk between RNA m6A and DNA 5mC, the most abundant regulatory modifications of RNA and DNA in eukaryotes, and the fact that in hESCs this interplay controls TE activity and cell fate.

Although major advances in genomics have initiated an exciting new era of research, a lack of information regarding cis-regulatory elements has limited the genetic improvement or manipulation of pigs as a meat source and biomedical model. Here, we systematically characterize cis-regulatory elements and their functions in 12 diverse tissues from four pig breeds by adopting similar strategies as the ENCODE and Roadmap Epigenomics projects, which include RNA-seq, ATAC-seq, and ChIP-seq. In total, we generate 199 datasets and identify more than 220,000 cis-regulatory elements in the pig genome. Surprisingly, we find higher conservation of cis-regulatory elements between human and pig genomes than those between human and mouse genomes. Furthermore, the differences of topologically associating domains between the pig and human genomes are associated with morphological evolution of the head and face. Beyond generating a major new benchmark resource for pig epigenetics, our study provides basic comparative epigenetic data relevant to using pigs as models in human biomedical research., To date, little is known about the regulatory landscape of the pig genome. Here, the authors characterize cis-regulatory elements in the pig genome using RNA-seq, ChIP-Seq and ATAC-seq, finding a higher degree of usage conservation between pig and human than mouse and human.

Introduction: Skeletal muscle regeneration in the ischemic limb is a complex complex process dependent on coordinated intercellular communication involving an array of cell types. These interactions are not well understood, and the development of novel regenerative therapies for peripheral arterial disease will require new insight into the cellular heterogeneity and intercellular signaling that occurs in the ischemic limb. Macrophages play a role in orchestrating critical events in muscle regeneration; hence we sought to characterize their transcriptional signature and identify candidate signaling pathways in the context of limb ischemia. Methods: We applied single-cell RNA sequencing (scRNA-seq) to skeletal muscle obtained from regenerative (C57BL/6) and non-regenerative (BALB/c) mouse limbs at multiple time points following ligation of the femoral artery. We used CellChat, a computation tool, to predict signaling pathway activity between macrophages and muscle satellite cells (MuSC) based on our single-cell data. Results: We identified 12 distinct macrophage populations in the regenerative and non-regenerative limb, including strain-specific macrophage clusters associated with the response to ischemia. Regenerative macrophages displayed a proliferative phenotype, while non-regenerative macrophages exhibited a persistent pro-inflammatory phenotype. Additionally, we identified several candidate signaling interactions between specific macrophage clusters and MuSCs. Notable potential interactions included enhanced FN1 to SDC4 and THBS1 to SDC4 signaling between regenerative macrophage and MuSCs, as well as OPN to CD44 signaling between non-regenerative macrophages and MuSCs. Conclusions: Our study maps the dynamic macrophage response in the ischemic limb at single-cell resolution. This provides a valuable resource to investigate macrophage-mediated mechanisms of skeletal muscle regeneration in response to limb ischemia.

Obesity-induced chronic liver inflammation is a hallmark of nonalcoholic steatohepatitis (NASH)-an aggressive form of nonalcoholic fatty liver disease. However, it remains unclear how such a low-grade, yet persistent, inflammation is sustained in the liver. Here, we show that the macrophage phagocytic receptor TREM2, induced by hepatocyte-derived sphingosine-1-phosphate, was required for efferocytosis of lipid-laden apoptotic hepatocytes and thereby maintained liver immune homeostasis. However, prolonged hypernutrition led to the production of proinflammatory cytokines TNF and IL-1β in the liver to induce TREM2 shedding through ADAM17-dependent proteolytic cleavage. Loss of TREM2 resulted in aberrant accumulation of dying hepatocytes, thereby further augmenting proinflammatory cytokine production. This ultimately precipitated a vicious cycle that licensed chronic inflammation to drive simple steatosis transition to NASH. Therefore, impaired macrophage efferocytosis is a previously unrecognized key pathogenic event that enables chronic liver inflammation in obesity. Blocking TREM2 cleavage to restore efferocytosis may represent an effective strategy to treat NASH.

Objective. We aimed to determine the efficacy of different idiopathic macular hole treatment methods to improve recovery time and patient outcomes using Frequency Domain Optical Coherence Tomography (SD-OCT) and Optical Coherence Tomography Angiography (OCTA). Methods. This retrospective study included patients with idiopathic macular hole who were admitted to our hospital between 1st January 2019 and 31st October 2021. The control group was treated with internal limiting membrane tamponade, and the study group was treated with clamshell therapy. Treatment conditions (internal limiting membrane treatment duration and hole closure rate), best corrected visual acuity (BCVA) before and after surgery, OCTA measurements, and SD-OCT were assessed. The retinal nerve fiber layer (RNFL), retinal ganglion cell layer (GCL), and retinal pigment epithelium (RPE) thicknesses were also analyzed. Results. The treatment time and hole closure rate of the internal limiting membrane in the study group were higher than those in the control group. The curative effect of the study group was better than that of the control group. The postoperative DCP blood vessel density in both groups was higher than that before operation, and the study group was higher than the control group. The FAZ area and circumference were lower than those before surgery, and the study group was lower than the control group. At 3 months after operation, the thickness of DIOA, nasal temporal RNFL, and GCL were decreased in both groups, and the observed values in the study group were lower than those in the control group. At 3-month follow-up, there was no significant difference in RPE thickness between the two groups. Conclusion. Flip and cover therapy is the most effective treatment. SD-OCT and OCTA provide an objective basis for clinical intervention by comparing the effects of different procedures on the retinal condition of patients.

Although large-scale and accurate identification of cis-regulatory elements on pig protein-coding and long non-coding genes has been reported, similar study on pig miRNAs is still lacking. Here, we systematically characterized the cis-regulatory elements of pig miRNAs in muscle and fat by adopting miRNAomes, ChIP-seq, ATAC-seq, RNA-seq and Hi-C data. In total, the cis-regulatory elements of 257 (85.95%) expressed miRNAs including 226 known and 31 novel miRNAs were identified. Especially, the miRNAs associated with super-enhancers, active promoters, and "A" compartment were significantly higher than those associated by typical enhancers, prompters without H3K27ac, and "B" compartment, respectively. The tissue specific transcription factors were the primary determination of core miRNA expression pattern in muscle and fat. Moreover, the miRNA promoters are more evolutionarily conserved than miRNA enhancers, like other type genes. Our study adds additional important information to existing pig epigenetic data and provides essential resource for future in-depth investigation of pig epigenetics.

miRNAs reportedly participate in various biological processes, such as skeletal muscle proliferation and differentiation. However, the regulation of differentially expressed (DE) miRNAs and their function in myogenesis remain unclear. Herein, miRNA expression profiles and regulation during C2C12 differentiation were analyzed in relation to chromatin states by RNA-seq, ATAC-seq, and ChIP-seq. We identified 19 known and nine novel differentially expressed miRNAs at days 0, 1, 2, and 4. The expression of the differentially expressed miRNAs was related to the chromatin states of the 113 surrounding open chromatin regions defined by ATAC-seq peaks. Of these open chromatin regions, 44.25% were colocalized with MyoD/MyoG binding sites. The remainder of the above open chromatin regions were enriched with motifs of the myoblast-expressed AP-1 family, Ctcf, and Bach2 transcription factors (TFs). Additionally, the target genes of the above differentially expressed miRNAs were enriched primarily in muscle growth and development pathways, especially the Hippo signaling pathway. Moreover, via combining a loss-of-function assay with Q-PCR, western blotting, and immunofluorescence, we confirmed that the Hippo signaling pathway was responsible for C2C12 myoblast differentiation. Thus, our results showed that these differentially expressed miRNAs were regulated by chromatin states and affected muscle differentiation through the Hippo signaling pathway. Our findings provide new insights into the function of these differentially expressed miRNAs and the regulation of their expression during myoblast differentiation.

Objective This study aims to clarify the mechanisms underlying transcriptional regulation and regulatory roles of lncRNAs in skeletal muscle cell differentiation. Methods We analysed the expression patterns of lncRNAs via time‐course RNA‐seq. Then, we further combined the ATAC‐seq and ChIP‐seq to investigate the governing mechanisms of transcriptional regulation of differentially expressed (DE) lncRNAs. Weighted correlation network analysis and GO analysis were conducted to identify the transcription factor (TF)‐lncRNA pairs related to skeletal muscle cell differentiation. Results We identified 385 DE lncRNAs during C2C12 differentiation, the transcription of which is determined by chromatin states around their transcriptional start sites. The TF‐lncRNA correlation network showed substantially concordant changes in DE lncRNAs between C2C12 differentiation and satellite cell rapid growth stages. Moreover, the up‐regulated lncRNAs showed a significant decrease following the differentiation capacity of satellite cells, which gradually declines during skeletal muscle development. Notably, inhibition of the lncRNA Atcayos and Trp53cor1 led to the delayed differentiation of satellite cells. Those lncRNAs were significantly up‐regulated during the rapid growth stage of satellite cells (4‐6 weeks) and down‐regulated with reduced differentiation capacity (8‐12 weeks). It confirms that these lncRNAs are positively associated with myogenic differentiation of satellite cells during skeletal muscle development. Conclusions This study extends the understanding of mechanisms governing transcriptional regulation of lncRNAs and provides a foundation for exploring their functions in skeletal muscle cell differentiation., Schematic of TF (MyoD, MyoG, Mef2c and Heyl) and lncRNA (Atcayos and Trp53cor1) regulatory interactions in differentiating C2C12 and ageing satellite cells.

Embryonic and neonatal skeletal muscles grow via the proliferation and fusion of myogenic cells, whereas adult skeletal muscle adapts largely by remodelling pre-existing myofibers and optimizing metabolic balance. It has been reported that miRNAs played key roles during skeletal muscle development through targeting different genes at post-transcriptional level. In this study, we show that a single miRNA (miR-208b) can modulate both the myogenesis and homoeostasis of skeletal muscle by distinct targets. As results, miR-208b accelerates the proliferation and inhibits the differentiation of myogenic cells by targeting the E-protein family member transcription factor 12 (TCF12). Also, miR-208b can stimulate fast-to-slow fibre conversion and oxidative metabolism programme through targeting folliculin interacting protein 1 (FNIP1) but not TCF12 gene. Further, miR-208b could active the AMPK/PGC-1a signalling and mitochondrial biogenesis through targeting FNIP1. Thus, miR-208b could mediate skeletal muscle development and homoeostasis through specifically targeting of TCF12 and FNIP1.

In order to calculate the spectral radiation characteristics of OH(A2∑) molecules more accurately, an improved collision-radiation (C-R) model is proposed to determine the excited states OH(A) number density. The six-components air model (CO, CO2, H2, H2O, N2, and O2) instead of the two-components air model (N2 and O2) are used as other plume products in the excitation/de-excitation radiation reaction, and the rate of the four reactions are modified to improve the accuracy and applicability of the number density. Effects of temperature and other plume products on the number density of excited states are analyzed in the experiment, and the spectral radiation characteristics of OH(A) can be obtained by using this improved C-R model. Results of these calculations are then compared with other series of experimental data of exhaust plume and shock layer, the results show that both the original model and the improved model can be used to calculate the radiation characteristics in shock layer, however, due to the great error, the original model not apply to calculation of the OH(A) number density in exhaust plume, and the result of the improved model is in good agreement with the Atlas experimental data. As the vibrational-rotational level distribution number density has a close relationship with radiative spectral characteristics, a more focused OH(A) particle number density model will be more helpful to the hypersonic target detection and recognition.

The liver plays a key role in metabolism and affects pig production. However, the functional annotation of noncoding regions of the pig liver remains poorly understood. We revealed the landscape of cis-regulatory elements and their functional characterization in pig liver. We identified 102,373 cis-regulatory elements in the pig liver, including enhancers, promoters, super-enhancers, and broad H3K4me3 domains, and highlighted 26 core transcription regulatory factors in the pig liver as well. We found similarity of cis-regulatory elements among those of pigs, humans, and cattle. Despite the low proportion of functionally conserved enhancers (~30%) between pig and human liver tissue, ~78% of the pig liver enhancer orthologues sequence could play an enhancer role in other human tissues. Additionally, we observed that the ratio of consistent super-enhancer-associated genes was significantly higher than the ratio of functionally conserved super-enhancers. Approximately 54% of the core regulation factors driven by super-enhancers were consistent across the liver from these three species. Our pig liver annotation and functional characterization studies provide a system and resource for noncoding annotation for future gene regulatory studies in pigs. Furthermore, our study also showed the high level functional conservation of cis-regulatory elements in mammals; it also improved our understanding of regulation function of mammal cis-regulatory elements.

The liver plays a key role in metabolism and affects pig production. However, the functional annotation of noncoding regions of the pig liver remains poorly understood. We revealed the landscape of cis-regulatory elements and their functional characterization in pig liver. We identified 102,373 cis-regulatory elements in the pig liver, including enhancers, promoters, super-enhancers, and broad H3K4me3 domains, and highlighted 26 core transcription regulatory factors in the pig liver as well. We found similarity of cis-regulatory elements among those of pigs, humans, and cattle. Despite the low proportion of functionally conserved enhancers (~30%) between pig and human liver tissue, ~78% of the pig liver enhancer orthologues sequence could play an enhancer role in other human tissues. Additionally, we observed that the ratio of consistent super-enhancer-associated genes was significantly higher than the ratio of functionally conserved super-enhancers. Approximately 54% of the core regulation factors driven by super-enhancers were consistent across the liver from these three species. Our pig liver annotation and functional characterization studies provide a system and resource for noncoding annotation for future gene regulatory studies in pigs. Furthermore, our study also showed the high level functional conservation of cis-regulatory elements in mammals; it also improved our understanding of regulation function of mammal cis-regulatory elements.

O presente estudo pretende estudar a censura cultural no Estado Novo português e na Grande Revolução Cultural da China, através da análise das censuras culturais e das suas consequências. O estudo é constituído por quatro capítulos: a contextualização histórica do Estado Novo e da Revolução Cultural, as censuras culturais salazaristas, as censuras culturais maoístas e uma visão presente. De modo a estudar esta área, o estudo tem como objetivo destacar a censura cultural desses dois períodos, descrevendo o seu objetivo, método, caráter, leis, consequências e significados, para mostrar os factos históricos de ambos os países e pensar na liberdade criativa na atualidade. The present dissertation aims to study cultural censorships in the New State, Portugal and in the Chinese Cultural Revolution, by analyzing cultural censorships and their respective consequences in both two countries. Our study consists of four chapters: the historical contextualization of the New State and the Chinese Cultural Revolution, the Salazarism cultural censorships, the Maoist cultural censorship and a present vision. By studying this area, the study aims to highlight the cultural censorship of these two periods, describing its purpose, method, character, laws, consequences and meanings to show the historical facts of both countries and to think about creative freedom in the present time. Mestrado em Português Língua Estrangeira/Língua Segunda

Alumina particles experience phase transition as an undercooling process along the plume, during which the liquid alumina clusters transform into multiphase, and then into α phase. The phase transformation model was built by an improved diffusion limited aggregation (DLA) algorithm with monomers of stratified structure. The effects of phase transformation on the ultraviolet optical characteristics of alumina clusters were studied using the superposition T-matrix method (STMM). We found that the alumina clusters in phase transition had completely different optical properties compared with the fixed phase ones. Forward scattering, absorption efficiency and asymmetry parameter gradually decreased, whereas backward scattering, scattering efficiency, and single-scattering albedo gradually increased during the phase transformation process. Besides, multiphase alumina clusters were compared with the other two equivalent models, including the sphere model approximated by equivalent volume sphere (EVS) and the equivalent surface sphere (ESS) approaches and single-phase cluster model approximated by Maxwell-Garnett (MG) and Bruggeman (BR) approaches. Generally speaking, the optical properties of the single-phase cluster approximated by MG and BR approaches were relatively close to those of the real multiphase alumina cluster. Whereas the spheres approximated by EVS and ESS had great deviations, especially when the number of monomers in the cluster was 20, the relative error of scattering efficiency calculated by ESS was up to 52%. Therefore, approximate approaches for multiphase clusters should be chosen cautiously. Our results give further the understanding of the optical properties of alumina clusters. As the phase states are usually closely related to the plume radiation and burning process, these kinds of researches will be helpful to aircraft detection, identification, and other related fields.

Feed efficiency (FE) is one of the main factors that determine the production costs in the pig industry. In this study, RNA Sequencing (RNA-seq) was applied to identify genes and long intergenic non-coding RNAs (lincRNAs) that are differentially expressed (DE) in the adipose tissues of Yorkshire pigs with extremely high and low FE. In total, 147 annotated genes and 18 lincRNAs were identified as DE between high- and low-FE pigs. Seventeen DE lincRNAs were significantly correlated with 112 DE annotated genes at the transcriptional level. Gene ontology (GO) analysis revealed that DE genes were significantly associated with cyclic adenosine monophosphate (cAMP) metabolic process and Ca2+ binding. cAMP, a second messenger has an important role in lipolysis, and its expression is influenced by Ca2+ levels. In high-FE pigs, nine DE genes with Ca2+ binding function, were down-regulated, whereas S100G, which encodes calbindin D9K that serve as a Ca2+ bumper, was up-regulated. Furthermore, ATP2B2, ATP1A4, and VIPR2, which participate in the cAMP signaling pathway, were down-regulated in the upstream of lipolysis pathways. In high-FE pigs, the key genes involved in the lipid biosynthetic process (ELOVL7 and B4GALT6), fatty acid oxidation (ABCD2 and NR4A3), and lipid homeostasis (C1QTNF3 and ABCB4) were down-regulated. These results suggested that cAMP was involved in the regulation on FE of pigs by affecting lipid metabolism in adipose tissues.

Summary Satellite cells play a key role in the aging, generation, and damage repair of skeletal muscle. The molecular mechanism of satellite cells in these processes remains largely unknown. This study systematically investigated for the first time the characteristics of mouse satellite cells at ten different ages. Results indicated that the number and differentiation capacity of satellite cells decreased with age during skeletal muscle development. Transcriptome analysis revealed that 2,907 genes were differentially expressed at six time points at postnatal stage. WGCNA and GO analysis indicated that 1,739 of the 2,907 DEGs were mainly involved in skeletal muscle development processes. Moreover, the results of WGCNA and protein interaction analysis demonstrated that Tgfβ2, Wnt9a, and Fgfr4 were the key genes responsible for the differentiation of satellite cells. Functional analysis showed that TGFβ2 and WNT9a inhibited, whereas FGFR4 promoted the differentiation of satellite cells. Furthermore, each two of them had a regulatory relationship at the protein level. In vivo study also confirmed that TGFβ2 could regulate the regeneration of skeletal muscle, as well as the expression of WNT9a and FGFR4. Therefore, we concluded that the synergistic effects of TGFβ2, WNT9a, and FGFR4 were responsible for attenuating of the differentiation of aging satellite cells during skeletal muscle development. This study provided new insights into the molecular mechanism of satellite cell development. The target genes and signaling pathways investigated in this study would be useful for improving the muscle growth of livestock or treating muscle diseases in clinical settings.

Feed efficiency (FE) is a highly important economic trait in pig production. Investigating the molecular mechanisms of FE is essential for trait improvement. In this study, the skeletal muscle proteome of high-FE and low-FE pigs were investigated by the iTRAQ approach. A total of 1780 proteins were identified, among which 124 proteins were differentially expressed between the high- and low-FE pigs, with 74 up-regulated and 50 down-regulated in the high-FE pigs. Ten randomly selected differentially expressed proteins (DEPs) were validated by Western blotting and quantitative PCR (qPCR). Gene ontology (GO) analysis showed that all the 25 DEPs located in mitochondria were down-regulated in the high-FE pigs. Furthermore, the glucose-pyruvate-tricarboxylic acid (TCA)-oxidative phosphorylation energy metabolism signaling pathway was found to differ between high- and low-FE pigs. The key enzymes involved in the conversion of glucose to pyruvate were up-regulated in the high-FE pigs. Thus, our results suggested mitochondrial energy metabolism in the skeletal muscle tissue was negatively correlated with FE in pigs, and glucose utilization to generate ATP was more efficient in the skeletal muscle tissue of high-FE pigs. This study offered new targets and pathways for improvement of FE in pigs.

Due to static traffic assignment has poor performance in reflecting actual case and dynamic traffic assignment may incurs excessive compute cost, method of multi-time dynamic traffic assignment combining static and dynamic traffic assignment balances factors of precision and cost effectively. A method based on Dial's logit algorithm is proposed in the article to solve the dynamic stochastic user equilibrium problem in dynamic traffic assignment. Before that, a fitting function that can proximately reflect overloaded traffic condition of link is proposed and used to give corresponding model. Numerical example is given to illustrate heuristic procedure of method and to compare results with one of same example solved by other literature's algorithm. Results show that method based on Dial's algorithm is preferable to algorithm from others.

Disturbance of endoplasmic reticulum (ER) homeostasis causes ER stress and leads to activation of the unfolded protein response, which reduces the stress and promotes cell survival at the early stage of stress, or triggers cell death and apoptosis when homeostasis is not restored under prolonged ER stress. Here, we report that Cab45S, a member of the CREC family, inhibits ER stress-induced apoptosis. Depletion of Cab45S increases inositol-requiring kinase 1 (IRE1) activity, thus producing more spliced forms of X-box-binding protein 1 mRNA at the early stage of stress and leads to phosphorylation of c-Jun N-terminal kinase, which finally induces apoptosis. Furthermore, we find that Cab45S specifically interacts with 78-kDa glucose-regulated protein/immunoglobulin heavy chain binding protein (GRP78/BiP) on its nucleotide-binding domain. Cab45S enhances GRP78/BiP protein level and stabilizes the interaction of GRP78/BiP with IRE1 to inhibit ER stress-induced IRE1 activation and apoptosis. Together, Cab45S, a novel regulator of GRP78/BiP, suppresses ER stress-induced IRE1 activation and apoptosis by binding to and elevating GRP78/BiP, and has a role in the inhibition of ER stress-induced apoptosis.