Lack of IFN-γ Receptor Signaling Inhibits Graft-versus-Host Disease by Potentiating Regulatory T Cell Expansion and Conversion.

IFN-γ is a pleiotropic cytokine that plays a controversial role in regulatory T cell (Treg) activity. In this study, we sought to understand how IFN-γ receptor (IFN-γR) signaling affects donor Tregs following allogeneic hematopoietic cell transplant (allo-HCT), a potentially curative therapy for leukemia. We show that IFN-γR signaling inhibits Treg expansion and conversion of conventional T cells (Tcons) to peripheral Tregs in both mice and humans. Mice receiving IFN-γR-deficient allo-HCT showed markedly reduced graft-versus-host disease (GVHD) and graft-versus-leukemia (GVL) effects, a trend associated with increased frequencies of Tregs, compared with recipients of wild-type allo-HCT. In mice receiving Treg-depleted allo-HCT, IFN-γR deficiency-induced peripheral Treg conversion was effective in preventing persistent GVHD while minimally affecting GVL effects. Thus, impairing IFN-γR signaling in Tcons may offer a promising strategy for achieving GVL effects without refractory GVHD. Similarly, in a human PBMC-induced xenogeneic GVHD model, significant inhibition of GVHD and an increase in donor Tregs were observed in mice cotransferred with human CD4 T cells that were deleted of IFN-γR1 by CRISPR/Cas9 technology, providing proof-of-concept support for using IFN-γR-deficient T cells in clinical allo-HCT.

Global Burden of Stroke Attributable to Low Physical Activity/High Body Mass Index Among People Aged 55 Years and Older.

BACKGROUND: This study aimed to quantify the global stroke burden attributable to low physical activity and high body mass index in adults aged ≥55 years using data from the Global Burden of Disease 2019 study. METHODS: We extracted data on stroke mortality, disability-adjusted life years, and risk factor exposure from the Global Burden of Disease 2019 study for people aged ≥55 years. We calculated the population-attributable fraction and absolute number of stroke cases and disability-adjusted life years attributable to low physical activity and high body mass index by location, age group, sex, and year. RESULTS: Globally, body mass index and physical inactivity-attributable stroke burden have declined modestly since 1990, but with diverging escalatory regional trajectories. Population growth and aging drive this rising burden. CONCLUSIONS: Multidimensional, context-specific strategies focused on modifiable lifestyle risks are imperative to address the modest declines and escalatory regional trajectories in body mass index and physical inactivity-attributable stroke burden.

Predicting miRNA-disease associations using an ensemble learning framework with resampling method.

MOTIVATION: Accumulating evidences have indicated that microRNA (miRNA) plays a crucial role in the pathogenesis and progression of various complex diseases. Inferring disease-associated miRNAs is significant to explore the etiology, diagnosis and treatment of human diseases. As the biological experiments are time-consuming and labor-intensive, developing effective computational methods has become indispensable to identify associations between miRNAs and diseases. RESULTS: We present an Ensemble learning framework with Resampling method for MiRNA-Disease Association (ERMDA) prediction to discover potential disease-related miRNAs. Firstly, the resampling strategy is proposed for building multiple different balanced training subsets to address the challenge of sample imbalance within the database. Then, ERMDA extracts miRNA and disease feature representations by integrating miRNA-miRNA similarities, disease-disease similarities and experimentally verified miRNA-disease association information. Next, the feature selection approach is applied to reduce the redundant information and increase the diversity among these subsets. Lastly, ERMDA constructs an individual learner on each subset to yield primitive outcomes, and the soft voting method is introduced for making the final decision based on the prediction results of individual learners. A series of experimental results demonstrates that ERMDA outperforms other state-of-the-art methods on both balanced and unbalanced testing sets. Besides, case studies conducted on the three human diseases further confirm the ERMDA's prediction capability for identifying potential disease-related miRNAs. In conclusion, these experimental results demonstrate that our method can serve as an effective and reliable tool for researchers to explore the regulatory role of miRNAs in complex diseases.

GraphCDA: a hybrid graph representation learning framework based on GCN and GAT for predicting disease-associated circRNAs.

MOTIVATION: CircularRNA (circRNA) is a class of noncoding RNA with high conservation and stability, which is considered as an important disease biomarker and drug target. Accumulating pieces of evidence have indicated that circRNA plays a crucial role in the pathogenesis and progression of many complex diseases. As the biological experiments are time-consuming and labor-intensive, developing an accurate computational prediction method has become indispensable to identify disease-related circRNAs. RESULTS: We presented a hybrid graph representation learning framework, named GraphCDA, for predicting the potential circRNA-disease associations. Firstly, the circRNA-circRNA similarity network and disease-disease similarity network were constructed to characterize the relationships of circRNAs and diseases, respectively. Secondly, a hybrid graph embedding model combining Graph Convolutional Networks and Graph Attention Networks was introduced to learn the feature representations of circRNAs and diseases simultaneously. Finally, the learned representations were concatenated and employed to build the prediction model for identifying the circRNA-disease associations. A series of experimental results demonstrated that GraphCDA outperformed other state-of-the-art methods on several public databases. Moreover, GraphCDA could achieve good performance when only using a small number of known circRNA-disease associations as the training set. Besides, case studies conducted on several human diseases further confirmed the prediction capability of GraphCDA for predicting potential disease-related circRNAs. In conclusion, extensive experimental results indicated that GraphCDA could serve as a reliable tool for exploring the regulatory role of circRNAs in complex diseases.

miPEPPred-FRL: A Novel Method for Predicting Plant MiRNA-Encoded Peptides Using Adaptive Feature Representation Learning.

MicroRNAs (miRNAs) are an essential type of small molecule RNAs that play significant regulatory roles in organisms. Recent studies have demonstrated that small open reading frames (sORFs) harbored in primary miRNAs (pri-miRNAs) can encode small peptides, known as miPEPs. Plant miPEPs can increase the abundance and activity of cognate miRNAs by promoting the transcription of their corresponding pri-miRNAs, thereby modulating plant traits. Biological experiments are the most effective way to accurately identify miPEPs; however, they are time-consuming and expensive. Hence, an efficient computational method for the identification of miPEPs on a large scale is highly desirable. Up to now, there have been no specialized computational tools for identifying miPEPs. In this work, a novel predictor named miPEPPred-FRL based on an adaptive feature representation learning framework that consists of the feature transformation module and the cascade architecture has been proposed. The feature transformation module integrating a newly designed feature selection method and classifier selection rule is developed to convert sequence-based features into primary class and probabilistic features, which are then fed into the improved cascade architecture to obtain more stable and discriminative augmented features. Finally, the augmented features are utilized to construct the final predictor. Cross-validation experiments illustrate that the novel feature selection method and classifier selection rule contribute to boosting the feature representation ability of the framework. Furthermore, the high accuracy of miPEPPred-FRL on independent testing data suggests that it is a trustworthy and valuable tool for the identification of miPEPs.

TAGAP activates Th17 cell differentiation by promoting RhoA and NLRP3 to accelerate rheumatoid arthritis development.

Rheumatoid arthritis (RA) is a chronic autoimmune disorder that can give rise to joint swelling and inflammation, potentially affecting the entire body, closely linked to the state of T cells. The T-cell activation Rho GTPase activating protein (TAGAP) is associated with many autoimmune diseases including RA and is directly linked to the differentiation of Th17 cells. The present study intends to investigate the influence of TAGAP on the RA progression and its mechanism to empower new treatments for RA. A collagen-induced-arthritis (CIA) rat model was constructed, as well as the extraction of CD4+ T cells. RT-qPCR, H&E staining and safranin O/fast green staining revealed that TAGAP interference reduced TAGAP production in the ankle joint of CIA rats, and joint inflammation and swelling were alleviated, which reveals that TAGAP interference reduces synovial inflammation and cartilage erosion in the rat ankle joint. Expression of inflammatory factors (TNF-α, IL-1ß, and IL-17) revealed that TAGAP interference suppressed the inflammatory response. Expression of pro-inflammatory cytokines, matrix-degrading enzymes, and anti-inflammatory cytokines at the mRNA level was detected by RT-qPCR and revealed that TAGAP interference contributed to the remission of RA. Mechanistically, TAGAP interference caused a significant decrease in the levels of RhoA and NLRP3. Assessment of Th17/Treg levels by flow cytometry revealed that TAGAP promotes Th17 cells differentiation and inhibits Treg cells differentiation in vitro and in vivo. In conclusion, TAGAP interference may decrease the differentiation of Th17 cells by suppressing the expression of RhoA and NLRP3 to slow down the RA progression.

Bioaccumulation of novel brominated flame retardants in crucian carp (Carassius auratus): Implications for electronic waste recycling area monitoring.

Bioaccumulation factor (BAF) of pollutants is an important parameter for evaluating their bioaccumulation potential and an important indicator for evaluating their environmental risks. However, little study exits on the BAF of novel brominated flame retardants (NBFRs). The present study determined 17 NBFRs in 24 water samples in dissolved phase and 93 crucian carp samples collected from an electronic waste recycling site in northern China, in order to examine their contamination, distribution and bioaccumulation. The results showed that the targeted NBFRs were widely detectable in the dissolved phase and crucian carps. In dissolved phase, allyl 2,4,6-tribromophenyl ether (ATE) had the highest detectable rate (100%) and concentration (mean: 1.3 ± 0.62 ng/L), but in crucian carp, hexachlorocyclopentenyl-dibromocyclooctane (HCDBCO) was the one with the highest detectable rate (89%) and concentration (mean: 16 ± 9.2 ng/g wet weight (ww)) among all 17 NBFRs. The discharge and water solubility of NBFRs determined their concentration in the dissolved phase, while the concentration of NBFRs in crucian carp was the results of their discharge and food exposure. The estimated BAFs exceeded 5000 L/kg for petabromoethylbenzene (PBEB), pentabromotoluene (PBT), HCDBCO, pentabromobenzyl acrylate (PBBA), 1,2,3,4,5-pentabromobenzene (PBBZ), 2,3-dibromopropyl-2,4,6-tribromophenyl ether (DPTE), hexabromobenzene (HBBZ), and α-1,2,5,6-tetrabromocyclooctane (α-TBCO), suggesting that these compounds were above the hazard standard of bioaccumulation. Although the BAFs of 2,3,5,6-tetrabromo-p-xylene (p-TBX), 1,2-bis(2,4,6-tribromophenoxy)-ethane (BTBPE), α-/ß-tetrabromoethylcyclohexane (α-/ß-TBECH) and ATE were less than 5000, the potential of bioaccumulation cannot be ignored. The log BAF of tested NBFRs showed a pattern of first increasing and then decreasing with the increase of log KOW, the water solubility of NBFRs, the exposure to fish, the uptake and depuration of fish were the key factor to this pattern. To our knowledge, the BAF values of the most of NBFRs calculated in this study were not reported in the published work previously.

Fast and Low-Overhead Time Synchronization for Industrial Wireless Sensor Networks with Mesh-Star Architecture.

Low-overhead, robust, and fast-convergent time synchronization is important for resource-constrained large-scale industrial wireless sensor networks (IWSNs). The consensus-based time synchronization method with strong robustness has been paid more attention in wireless sensor networks. However, high communication overhead and slow convergence speed are inherent drawbacks for consensus time synchronization due to inefficient frequent iterations. In this paper, a novel time synchronization algorithm for IWSNs with a mesh-star architecture is proposed, namely, fast and low-overhead time synchronization (FLTS). The proposed FLTS divides the synchronization phase into two layers: mesh layer and star layer. A few resourceful routing nodes in the upper mesh layer undertake the low-efficiency average iteration, and the massive low-power sensing nodes in the star layer synchronize with the mesh layer in a passive monitoring manner. Therefore, a faster convergence and lower communication overhead time synchronization is achieved. The theoretical analysis and simulation results demonstrate the efficiency of the proposed algorithm in comparison with the state-of-the-art algorithms, i.e., ATS, GTSP, and CCTS.

Improvement of human myeloid and natural killer cell development in humanized mice via hydrodynamic injection of transposon plasmids containing multiple human cytokine genes.

Humanized mice reconstituted with a functional human immune system (HIS) are instrumental in studying human immunity and immune disorders in vivo. The poor or lack of cross-reactivity between mouse cytokines and human cells limits the development and/or function of human immune cell subsets including human myeloid, natural killer and B cells. Here we explored the potential to achieve long-term production of human cytokines in immunodeficient mice using a transposon-plasmid-based hydrodynamic injection approach. We constructed a transposon-plasmid carrying five human cytokine coding sequences (named PB-5F), and observed that four of the cytokines (granulocyte-macrophage colony-stimulating factor, interleukin (IL)-15, IL-6 and IL-3) were detectable in sera and three (granulocyte-macrophage colony-stimulating factor, IL-15 and IL-6) showed long-term production in immunodeficient mice that received a single hydrodynamic injection of PB-5F plus the transposase plasmid (Super PB). Furthermore, a single injection of PB-5F/Super PB markedly enhanced the reconstitution of human myeloid cells and natural killer cells, and promoted human B-cell maturation in HIS mice. Taken together, our data revealed that hydrodynamic injection of the PB-5F/Super PB vectors may serve as a convenient and efficacious means to promote human immune function in HIS mice.

Clinical characteristics and risk factors of lower extremity amputation in patients with diabetic foot.

Objectives: To investigate the risk factors of lower limb amputation, and help physicians better understand the clinical characteristics of patients with diabetic foot, and make treatment strategies for these patients correctly. Methods: In this study, the inpatients with diabetic foot treated in our hospital form January 2013 to February 2021 were reviewed retrospectively. The patients were divided into amputation and conservative treatment groups. The variables of the patients, consisting of age, gender, smoking history, alcohol use, diabetes and ulcer duration, ulcer size, Wagner classification, ankle brachial index, previous amputation history, laboratory data, and medical comorbidities including hypertension, coronary artery disease, peripheral arterial disease, chronic renal insufficiency, retinopathy, and sequelae of cerebral infarction were selected for analysis to determine the risk factors of lower limb amputation. Results: In this study, a total of 856 patients with diabetic foot were enrolled, in which 487 patients received amputation surgeries, and the amputation rate was 56.9%. There were significant differences between the two groups in gender (p=0.014), smoking history (p=0.011), ulcer duration (p=0.023), ulcer size (p=0.000), Wagner classification (p=0.000), ABI (p=0.031), peripheral arterial disease (p=0.000), HDL-C (p=0.013), osteomyelitis (p=0.000), and fibrinogen (p=0.001). A stepwise multiple logistic regression analysis revealed that male gender (p=0.003), larger ulcer size (p=0.001), higher Wagner classification grades (p=0.002), higher rate of peripheral arterial disease (p=0.02) and osteomyelitis (p=0.0001), and increased fibrinogen level (p=0.004) were independent risk factors of lower limb amputation in patients with diabetic foot. Conclusion: The diabetic foot patients with male sex, larger ulcer size, higher grade of Wagner classification, peripheral arterial disease or higher fibrinogen level may face higher risk of lower limb amputation.

Thalidomide with blockade of co-stimulatory molecules prolongs the survival of alloantigen-primed mice with cardiac allografts.

BACKGROUND: Miscellaneous memory cell populations that exist before organ transplantation are crucial barriers to transplantation. In the present study, we used a skin-primed heart transplantation model in mouse to evaluate the abilities of Thalidomide (TD), alone or in combination with co-stimulatory blockade, using monoclonal antibodies (mAbs) against memory T cells and alloantibodies to prolong the second cardiac survival. RESULTS: In the skin-primed heart transplantation model, TD combined with mAbs significantly prolonged the second cardiac survival, accompanied by inhibition of memory CD8+ T cells. This combined treatment enhanced the CD4+Foxp3+ regulatory T cells ratio in the spleen, restrained the infiltration of lymphocytes into the allograft, and suppressed the allo-response of spleen T cells in the recipient. The levels of allo-antibodies also decreased in the recipient serum. In addition, we detected low levels of the constitutions of the lytic machinery of cytotoxic cells, which cause allograft damage. CONCLUSIONS: Our study indicated a potential synergistic action of TD in combination with with mAbs to suppress the function of memory T cells and increase the survival of second allografts in alloantigen-primed mice.

A long-acting isomer of Ac-SDKP attenuates pulmonary fibrosis through SRPK1-mediated PI3K/AKT and Smad2 pathway inhibition.

Idiopathic pulmonary fibrosis (IPF) is a progressive, life-threatening lung disease with a poor prognosis. N-acetyl-seryl-aspartyl-lysyl-proline (Ac-SDKP) is a critical negative regulator of fibrosis development. However, it's extremely short half-life greatly limits its applications. Previously, we reported an Ac-SDKP analog peptide in which Asp and Lys residues were replaced with D-amino acids (Ac-SDD KD P). Ac-SDD KD P exhibits better resistance to angiotensin-1-converting enzyme (ACE)-mediated degradation and a longer half-life than Ac-SDKP in rat and human sera. The objective of this study was to explore the potential application of Ac-SDD KD P for the treatment of IPF and to clarify the underlying mechanisms. We found that Ac-SDD KD P exerted similar antifibrotic effects as Ac-SDKP on human fetal lung fibroblast-1 (HFL-1) proliferation, α-smooth muscle actin (α-SMA), collagen I and collagen III expression, and Smad-2 phosphorylation in vitro. In vivo, Ac-SDD KD P exhibited significantly greater protective effects against bleomycin-induced pulmonary fibrosis than Ac-SDKP in mice. α-SMA, CD45, collagen I and collagen III expression, and Smad-2 phosphorylation were significantly decreased in the lungs of Ac-SDD KD P-treated but not Ac-SDKP-treated mice. Furthermore, a pull-down experiment was used to screen for molecules that interact with Ac-SDKP. Co-immunoprecipitation (Co-IP) and computer-based molecular docking experiments demonstrated an interaction between Ac-SDKP or Ac-SDD KD P (Ac-SDKP/Ac-SDD KD P) and serine/arginine-rich protein-specific kinase 1 (SRPK1) that caused inhibition SRPK1-mediated phosphatidylinositol-3 kinase/ serine/threonine kinase (PIK3/AKT) signaling pathway activation and Smad2 phosphorylation and thereby attenuated lung fibrosis. Our data suggest that long-acting Ac-SDD KD P may potentially be an effective drug for the treatment of pulmonary fibrosis. The interacting molecule and antifibrotic mechanism of Ac-SDKP/Ac-SDD KD P were also identified, providing an experimental and theoretical foundation for the clinical application of the drug.

Upregulation of lincRNA-p21 in thoracic aortic aneurysms is involved in the regulation of proliferation and apoptosis of vascular smooth muscle cells by activating TGF-ß1 signaling pathway.

OBJECTIVE: Long intergenic noncoding RNA-p21 (lincRNA-p21) has been proved in the pathogenesis of aortic aneurysms, while its functionality in thoracic aortic aneurysms (TAA) and the mechanism of function remains unclear. Therefore our study aimed to investigate the role of lincRNA-p21 in TAA. METHODS: Aortic media specimens and blood samples were collected from both patients with TAA and healthy controls. Expression of lincRNA-p21 in those tissues was detected by reverse-transcription quantitative polymerase chain reaction (qRT-PCR). Diagnostic values of lincRNA-p21 in aortic media and blood for TAA were evaluated by receiver operating characteristic curve analysis. LincRNA-p21 overexpression human vascular smooth muscle cells (VSMCs) were prepared and the effects of lincRNA-p21 overexpression on cell proliferation and apoptosis were explored by cell counting kit-8 assay and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay, respectively. Expression of lincRNA-p21 and transforming growth factor ß1 (TGF-ß1) in VSMCs with different treatment was detected by qRT-PCR and Western blot analysis, respectively. RESULTS: Expression of lincRNA-p21 in aortic media tissues and blood was significantly upregulated in TAA patients than in healthy controls. Expression of lincRNA-p21 in aortic media and blood can be used to effectively distinguish TAA patients form healthy controls. LincRNA-p21 overexpression inhibited proliferation and promoted apoptosis of VSMCs, while TGF-ß1 inhibitor reduced those effects. LincRNA-p21 overexpression upregulated TGF-ß1 expression, while TGF-ß1 activator showed no significant effects on lincRNA-p21 expression in VSMC. CONCLUSION: LincRNA-p21 participates in TAA by regulating the proliferation and apoptosis of VSMCs through the activation of TGF-ß1 signaling pathway.

Human Norovirus NS3 Has RNA Helicase and Chaperoning Activities.

RNA-remodeling proteins, including RNA helicases and chaperones, act to remodel RNA structures and/or protein-RNA interactions and are required for all processes involving RNAs. Although many viruses encode RNA helicases and chaperones, their in vitro activities and their roles in infected cells largely remain elusive. Noroviruses are a diverse group of positive-strand RNA viruses in the family Caliciviridae and constitute a significant and potentially fatal threat to human health. Here, we report that the protein NS3 encoded by human norovirus has both ATP-dependent RNA helicase activity that unwinds RNA helices and ATP-independent RNA-chaperoning activity that can remodel structured RNAs and facilitate strand annealing. Moreover, NS3 can facilitate viral RNA synthesis in vitro by norovirus polymerase. NS3 may therefore play an important role in norovirus RNA replication. Lastly, we demonstrate that the RNA-remodeling activity of NS3 is inhibited by guanidine hydrochloride, an FDA-approved compound, and, more importantly, that it reduces the replication of the norovirus replicon in cultured human cells. Altogether, these findings are the first to demonstrate the presence of RNA-remodeling activities encoded by Caliciviridae and highlight the functional significance of NS3 in the noroviral life cycle.IMPORTANCE Noroviruses are a diverse group of positive-strand RNA viruses, which annually cause hundreds of millions of human infections and over 200,000 deaths worldwide. For RNA viruses, cellular or virus-encoded RNA helicases and/or chaperones have long been considered to play pivotal roles in viral life cycles. However, neither RNA helicase nor chaperoning activity has been demonstrated to be associated with any norovirus-encoded proteins, and it is also unknown whether norovirus replication requires the participation of any viral or cellular RNA helicases/chaperones. We found that a norovirus protein, NS3, not only has ATP-dependent helicase activity, but also acts as an ATP-independent RNA chaperone. Also, NS3 can facilitate in vitro viral RNA synthesis, suggesting the important role of NS3 in norovirus replication. Moreover, NS3 activities can be inhibited by an FDA-approved compound, which also suppresses norovirus replicon replication in human cells, raising the possibility that NS3 could be a target for antinoroviral drug development.

d-amino acid modification protects N-Acetyl-seryl-aspartyl-lysyl-proline from physiological hydroxylation and increases its antifibrotic effects on hepatic fibrosis.

N-Acetyl-seryl-aspartyl-lysyl-proline (Ac-SDKP) is a critical negative regulator of fibrosis development in the liver. However, its extremely short half-life in vivo greatly compromises its potential applications. Here, we report an Ac-SDKP analog peptide with d-amino acid replacement (Ac-SDD KD P). The stability of Ac-SDD KD P and its prevention of liver fibrosis were investigated in vitro and in vivo. The stabilities of Ac-SDKP and Ac-SDD KD P exposed to angiotensin-1-converting enzyme (ACE) and their half-lives in rats and human sera were determined by high-performance liquid chromatography. The inhibitory effects of Ac-SDKP and Ac-SDD KD P on the proliferation and activation of hepatic stellate cells (HSC-T6) were evaluated using the Cell Counting Kit-8, Western blotting, reverse transcription quantitative polymerase chain reaction, and immunofluorescence assays. Finally, the protective effects of Ac-SDKP and Ac-SDD KD P on carbon tetrachloride (CCl4 )-induced liver fibrosis in rats were compared. d-Amino acid replacement significantly enhanced the stability of the peptide to ACE and prolonged the half-life of Ac-SDKP in rats and human sera. The Ac-SDKP-mediated inhibition of HSC-T6 cell proliferation was well preserved, and Ac-SDD KD P exerted inhibitory effects comparable to Ac-SDKP on α-smooth muscle actin (α-SMA), collagen I and III expression, and phosphorylated-Smad-2 expression. After intraperitoneal (i.p.) administration, Ac-SDD KD P exhibited significantly greater protection than Ac-SDKP against CCl4 -induced liver fibrosis in rats. The serum alanine aminotransferase, aspartate aminotransferase, albumin, and total protein levels of the Ac-SDD KD P-treated rats were significantly lower than those of the Ac-SDKP-treated rats. α-SMA, CD45, and collagen I and III expression, as well as Smad-2 phosphorylation were significantly attenuated in the livers of the Ac-SDD KD P-treated rats compared to those of the Ac-SDKP-treated rats. Furthermore, we showed that the Ac-SDD KD P concentration in the rat liver increased to a physiological level of 60 min after i.p. administration, although i.p. administration of Ac-SDKP failed to enhance the peptide concentration in the rat liver. Our findings indicate that d-amino acid replacement is a simple and effective method to enhance the stability of Ac-SDKP. Ac-SDD KD P represents potential application of Ac-SDKP in fibrosis treatment and provides a new potential treatment strategy for liver fibrosis. © 2019 IUBMB Life, 71(9):1302-1312, 2019.

Failure mode transformation of ZnO nanowires under uniaxial compression: from phase transition to buckling.

The failure modes of ZnO nanowires (NWs) with hexagonal cross section subjected to a uniaxial load are systematically investigated by using molecular dynamics (MD) simulations and two theoretical models considering the surface effect. Our results show that two different failure modes of the phase transition and buckling are triggered when the NWs are under uniaxial compression along the [0001] direction, in which the transformation between the two modes is related to the slenderness ratios of the NWs. Such slenderness-ratio-dependent mode transformation is mainly attributed to the competition between the critical stresses of phase transition and buckling. The Euler and Timoshenko models considering surface effect are further proposed to derive the critical slenderness for such mode transformation. The obtained analytical threshold values agree well with those of present MD simulations. Our results should be of great help for shedding some light on the design and application of functional devices based on ZnO NWs.

First-principles thermodynamics and experimental study of interface oxidation in Ni/Ni3Al structures.

Anti-oxidation is one of the significant properties of nickel-based superalloys useful for their potential applications in industry. However, previous research mainly focused on single-phase compounds of NiAl or Ni3Al. In the present study, first-principles density functional theory coupled with thermodynamics analysis are employed to investigate the atomistic oxidation behaviours of the Ni/Ni3Al composites systematically. An oxidation experiment with a DD6 alloy is conducted as well to further confirm the theoretical prediction. Initial surface formation energy analysis shows that the systems composed of Ni(111) and Ni3Al(100)/(111) surfaces are more stable and therefore are selected for further investigation. Thermodynamics calculations indicate that the Ni3Al phase is oxidized first, accompanied by Al-segregation on the top surfaces. This is followed by subsequent oxidation of the Ni phase. Surface oxidation diagrams with respect to the surface formation energies show that oxygen adsorption could enhance Al-segregation to the surface and Ni3Al(111) surfaces tend to be oxidized completely with slightly lower oxygen coverage. Oxidation at the interface is also investigated and the results show that oxygen atoms bind with the upper layers of the Ni3Al phase from the point of view of binding energy. The experimental results provide a reasonable explanation for the selective oxidation of Al atoms at the atomic-scale so as to form a dense anti-oxidation membrane. The present work could serve as a beneficial reference for subsequent investigations of oxidation or adsorption processes of two-phase composites.

Correlation Between Smoking and Passive Smoking with Multiple Sclerosis and the Underlying Molecular Mechanisms.

Multiple sclerosis (MS) is a chronic immune-mediated disease of the spinal cord and brain. Many studies have shown that smoking and passive smoking are key environmental risk factors for MS. Here, we provide an overview of the human leukocyte antigen (HLA) gene studies on smoking and MS risk, and we discuss recent studies on between epigenetics and smoking-induced MS. In addition, in this review we also summarize current research advances in biological pathways and smoking-induced MS. This review provides an overview of studies on the association between smoking, passive smoking, and MS susceptibility, and the underlying molecular mechanism.

Opposite effects of Drosophila C3PO on gene silencing mediated by esi-2.1 and miRNA-bantam.

Translin/TRAX complex, also named as C3PO, is evolutionarily conserved and participates in diverse cellular processes in different organisms from yeast to human. C3PO plays a critical role in the activation of RNA-induced silencing complexes by promoting the unwinding and degradation of passenger strand of exogenous siRNAs (exo-siRNAs) in Drosophila and human. Moreover, human C3PO (hC3PO) has been found to broadly repress miRNAs by degrading miRNA precursors. However, the effect of Drosophila melanogaster C3PO (dmC3PO) on endogenous siRNA (endo-siRNA) and miRNA pathways remains unknown. Here, we found that the loss of dmC3PO promoted the accumulation of the passenger strand of esi-2.1 (hp-CG4068B), and resulted in the de-repression of the DNA-damage-response gene mutagensensitive 308 (mus308), which is an endogenous slicer target of esi-2.1 in Drosophila. Moreover, we also found that depletion of dmC3PO increased the accumulation of miR-bantam. Taken together, our findings indicated that dmC3PO not only involves in siRNA pathway triggered by dsRNA, but also regulates the abundance of certain endogenous small RNAs in Drosophila.

pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization.

MS-based de novo peptide sequencing has been improved remarkably with significant development of mass-spectrometry and computational approaches but still lacks quality-control methods. Here we proposed a novel algorithm pSite to evaluate the confidence of each amino acid rather than the full-length peptides obtained by de novo peptide sequencing. A semi-supervised learning approach was used to discriminate correct amino acids from random one; then, an expectation-maximization algorithm was used to adaptively control the false amino-acid rate (FAR). On three test data sets, pSite recalled 86% more amino acids on average than PEAKS at the FAR of 5%. pSite also performed superiorly on the modification site localization problem, which is essentially a special case of amino acid confidence evaluation. On three phosphopeptide data sets, at the false localization rate of 1%, the average recall of pSite was 91% while those of Ascore and phosphoRS were 64 and 63%, respectively. pSite covered 98% of Ascore and phosphoRS results and contributed 21% more phosphorylation sites. Further analyses show that the use of distinct fragmentation features in high-resolution MS/MS spectra, such as neutral loss ions, played an important role in improving the precision of pSite. In summary, the effective and universal model together with the extensive use of spectral information makes pSite an excellent quality control tool for both de novo peptide sequencing and modification site localization.