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Find video protocols related to scientific articles indexed in Pubmed.
Unusual Fe(CN)63-/4- capture induced by synergic effect of electropolymeric cationic surfactant and graphene: Characterization and biosensing application.
ACS Appl Mater Interfaces
PUBLISHED: 11-20-2014
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Herein, a special microheterogeneous system for Fe(CN)63-/4- capture was constructed based on graphene (GN) and the electropolymeric cationic surfactant, an amphiphilic pyrrole derivative, (11-pyrrolyl-1-yl-undecyl) triethylammonium tetrafluoroborate (A2). The morphology of the system was characterized by scanning electron microscope. The redox properties of the entrapped Fe(CN)63-/4- were investigated by cyclic voltammetry and UV-visible spectrometry. The entrapped Fe(CN)63-/4- exhibited highly electroactive with stable and symmetrical cyclic voltammetric signal. A dramatic negative shift in the half wave potential can be obtained due to the unusual Fe(CN)63-/4- partitioning in in this microheterogeneous system based on poly(A2+GN). Finally, the entrapped Fe(CN)63-/4- was applied in the construction of the enhanced biosensors to hydrogen peroxide and sulfide.
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New Risk Factors for Adult Onset Incident Asthma: A Nested Case Control Study of Host Antioxidant Defense.
Am. J. Respir. Crit. Care Med.
PUBLISHED: 11-20-2014
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Rationale: Host antioxidant defense, consisting of enzymatic antioxidant activity and non-enzymatic antioxidant micronutrients, is implicated in asthma pathogenesis. Studies of antioxidant defense and adult incident asthma have either used measures of antioxidants estimated from questionnaires or not considered enzymatic aspects of host defense. Objective: We conducted the first study designed and powered to investigate the association of antioxidant defenses on adult incident asthma. Methods: In a nested case-control study, we followed Shanghai women (ages 40-70) without prevalent asthma at baseline, over eight years. Incident asthmatics were ascertained prospectively by gold standard testing of symptomatic women and matched to two asymptomatic controls. Measurements: Baseline urinary F2-isoprostanes, plasma concentrations of antioxidant micronutrients (tocopherols, xanthins, carotenes, and lycopene) and antioxidant enzyme activity (platelet-activating factor acetylhydrolase [PAF-AH] and superoxide dismutase) were measured from samples collected prior to disease onset. Main Results: Among 65,372 women, 150 (0.24%) developed asthma. F2-isoprostane levels prior to asthma onset were not different between cases and controls. Doubling of ?-tocopherol concentrations and PAF-AH activity was associated with 50% and 37% decreased risk of incident asthma (adjusted OR; 95% confidence interval [OR; 95%CI], ?-tocopherol OR= 0.52; 95%CI: 0.32-0.84; PAF-AH OR=0.63; 95%CI:0.42-0.93). Conclusions: In this prospective study ?-tocopherol, within normal reference ranges, and PAF-AH enzymatic activity, were associated with decreased asthma development. These modifiable risk factors may be an effective strategy to test for primary asthma prevention.
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Synthesis, in Vitro Covalent Binding Evaluation, and Metabolism of (14)C-Labeled Inhibitors of 11?-HSD1.
ACS Med Chem Lett
PUBLISHED: 11-13-2014
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In this letter, we reported the design and synthesis of three potent, selective, and orally bioavailable 11?-HSD1 inhibitors labeled with (14)C: AMG 456 (1), AM-6949 (2), and AM-7715 (3). We evaluated the covalent protein binding of the labeled inhibitors in human liver microsomes in vitro and assessed their potential bioactivation risk in humans. We then studied the in vitro mechanism of 2 in human hepatocytes and the formation of reactive intermediates. Our study results suggest that 1 and 3 have low potential for metabolic bioactivation in humans, while 2 has relatively high risk.
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[Dipylidium caninum infection in an infant: one case report].
Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi
PUBLISHED: 10-28-2014
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This paper reports the diagnosis and therapy of one case of Dipylidium caninum infection in an infant.
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Abdominal and general adiposity and level of asthma control in adults with uncontrolled asthma.
Ann Am Thorac Soc
PUBLISHED: 10-25-2014
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Abdominal adiposity may be an important risk factor for uncontrolled asthma in adults, controlling for general obesity. Whether the relationship, if present, is explained by other factors (e.g., asthma onset age, sex, and/or coexisting conditions) is unclear.
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[Indirect determination of rare earth elements in Chinese herbal medicines by hydride generation-atomic fluorescence spectrometry].
Guang Pu Xue Yu Guang Pu Fen Xi
PUBLISHED: 10-02-2014
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Based on their similarity in chemical properties, rare earth elements were able to form stable coordinated compounds with arsenazo III which were extractable into butanol in the presence of diphenylguanidine. The butanol was removed under reduced pressure distillation; the residue was dissolved with diluted hydrochloric acid. As was released with the assistance of KMnO4 and determined by hydrogen generation-atomic fluorescence spectrometry in terms of rare earth elements. When cesium sulfate worked as standard solution, extraction conditions, KMnO4 amount, distillation temperature, arsenazo III amount, interfering ions, etc were optimized. The accuracy and precision of the method were validated using national standard certified materials, showing a good agreement. Under optimum condition, the linear relationship located in 0.2-25 microg x mL(-1) and detection limit was 0.44 microg x mL(-1). After the herbal samples were digested with nitric acid and hydrogen peroxide, the rare earth elements were determined by this method, showing satisfactory results with relative standard deviation of 1.3%-2.5%, and recoveries of 94.4%-106.0%. The method showed the merits of convenience and rapidness, simple instrumentation and high accuracy. With the rare earths enriched into organic phase, the separation of analytes from matrix was accomplished, which eliminated the interference. With the residue dissolved by diluted hydrochloric acid after the solvent was removed, aqueous sample introduction eliminated the impact of organic phase on the tubing connected to pneumatic pump.
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Selection of human p75NTR tag SNPs and its biological significance for clinical association studies.
Biomed Mater Eng
PUBLISHED: 09-18-2014
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To select tag single nucleotide polymorphisms (SNPs) within and around human p75 neurotrophin receptor (p75NTR) gene in Chinese Han population, the sequence involving p75NTR gene as well as the upstream and downstream of the gene was identified according to the data from National Center for Biotechnology Information (NCBI) GenBank database, and the SNP genotype data involving 63 SNPs in the regions were obtained from Chinese Han Beijing (CHB) population of HapMap database. Then, Haploview (version 4.2) was used to calculate linkage disequilibrium (LD) statistics for the selected 32 common SNPs with a minor allele frequence (MAF) more than 0.05. Haplotype blocks were constructed throughout the p75NTR gene according to the upper and the lower 95% confidence bound of D' value, and the tag SNPs were selected based on the r2 and LOD values between SNPs as well as the results of bioinformatics analysis. The results indicated that five haplotype blocks were constructed within and around p75NTR gene and 12 tag SNPs including rs2537710, rs603769, rs614455, rs2537706, rs534561, rs2072445, rs2072446, rs7219709, rs734194, rs741071, rs741073 and rs2671641 were selected to represent the other 51 SNPs in p75NTR gene. Therefore, the 12 selected SNPs may act as tag SNPs for the entire p75NTR gene in Chinese Han population, which will provide an effective way to select tag SNPs in a whole gene, and its biological significance is to further guide the clinical association studies between the candidate gene and disease susceptibility.
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[Roles of microglia and immune receptors in Alzheimer's disease].
Yao Xue Xue Bao
PUBLISHED: 09-13-2014
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Alzheimer's disease (AD) is a most common neurodegenerative disease. The mechanisms underlying AD, especially late-onset AD, remain elusive. In the past few years, results from genome-wide association studies (GWAS) and systems approaches indicated that innate immune responses mediated by microglia played critical roles in AD. Functional analysis on animal models also showed that immune receptors or proteins expressed in microglia mediated Abeta-induced inflammation, or Abeta phagocytosis by microglia. Microglia plays double sword roles in AD. More work is warranted to elucidate the exact roles of microglia in AD, which will facilitate our better understanding of the mechanisms underlying AD.
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The relationship between the plant-encoded RNA-dependent RNA polymerase 1 and alternative oxidase in tomato basal defense against Tobacco mosaic virus.
Planta
PUBLISHED: 09-05-2014
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Salicylic acid (SA) plays a critical role in plant defense against pathogen attack. The SA-induced viral defense in plants is distinct from the pathways mediating bacterial and fungal defense, which is pathogenesis-related protein-independent but involves an RNA-dependent RNA polymerase 1 (RDR1)-mediated RNA silencing mechanism and/or an alternative oxidase (AOX)-associated defense pathway. However, the relationship between these two viral defense-related pathways remains unclear. In this study, Tobacco mosaic virus (TMV) inoculation onto Solanum lycopersicum (tomato) leaves induced a rapid induction of the SlAOX1a transcript level as well as the total and CN-resistant respiration at 0.5 dpi, followed by an increase in SlRDR1 gene expression at 1 dpi in the upper uninoculated leaves. Silencing SlRDR1 using virus-induced gene silencing system significantly reduced SlRDR1 expression and tomato defense against TMV but had no evident effect on SlAOX1a transcription. Conversely, silencing SlAOX1a not only effectively reduced the AOX1a transcript level, but also blocked the TMV-induced SlRDR1 expression and decreased the basal defense against TMV. Furthermore, the application of an exogenous AOX activator on empty vector-silenced control plants greatly induced the accumulation of SlRDR1 and SlAOX1a transcript and reduced TMV viral RNA accumulation, but failed to have such effects on SlRDR1-silenced plants. Moreover, RDR1-overexpressed transgenic Nicotiana benthamiana plants enhanced defense against TMV than the empty vector-transformed plants, but these effects were not affected by the exogenous AOX activator or inhibitor. These results indicate that RDR1 is involved in the AOX-mediated defense pathway against TMV infection and plays a crucial role in enhancing RNA silencing to limit virus systemic spread.
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Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine.
J Mol Model
PUBLISHED: 09-01-2014
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A common problem with non-nucleoside reverse transcriptase inhibitors (NNRTIs) of HIV-1 is the emergence of mutations in the HIV-1 RT, in particular Lys103???Asn (K103N) and Tyr181???Cys (Y181C), which lead to resistance to this entire class of inhibitors. In this study, we theoretically designed two new non-nucleoside HIV-1 RT inhibitors, Mnev-1 and Mnev-2, derived from nevirapine, in order to reduce the resistance caused by those HIV-1 RT mutations. The binding modes of Mnev-1 and Mnev-2 with the wild-type HIV-1 RT and its mutants (K103N and Y181C) were suggested by molecular docking followed by 20-ns molecular dynamics (MD) simulations in explicit water of those binding complexes (HIV-1 RTs with the new inhibitors). A molecular mechanics/generalized Born surface area (MM/GBSA) calculation was carried out for multiple snapshots extracted from the MD trajectory to estimate the binding free energy. The results of the calculations show that each of the new inhibitors forms a stable hydrogen bond with His235 during the MD simulations, leading to tighter binding of the new inhibitors with their targets. In addition, the repulsive interaction with Cys181 in the Y181C-nevirapine complex is not present in the novel inhibitors. The binding affinities predicted using the MM/GBSA calculations indicate that the new inhibitors could be effective at bypassing the drug resistance of these HIV-1 RT mutants.
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Nonpeptidic GLP-1 receptor agonist WB4-24 blocks inflammatory nociception by stimulating ?-endorphin release from spinal microglia.
Br. J. Pharmacol.
PUBLISHED: 09-01-2014
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We recently reported that the glucagon-like peptide-1 receptor (GLP-1R) peptidic agonists exenatide and GLP-1 produced anti-hypersensitive effects in neuropathic, cancer and diabetic pain. In this study, we investigated the anti-allodynic and anti-hyperalgesic effects of the nonpeptidic agonist WB4-24 in inflammatory nociception and possible involvements of microglial ?-endorphin and pro-inflammatory cytokines.
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RNA-binding protein HuR promotes growth of small intestinal mucosa by activating the Wnt signaling pathway.
Mol. Biol. Cell
PUBLISHED: 08-27-2014
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Inhibition of growth of the intestinal epithelium, a rapidly self-renewing tissue, is commonly found in various critical disorders. The RNA-binding protein HuR is highly expressed in the gut mucosa and modulates the stability and translation of target mRNAs, but its exact biological function in the intestinal epithelium remains unclear. Here, we investigated the role of HuR in intestinal homeostasis using a genetic model and further defined its target mRNAs. Targeted deletion of HuR in intestinal epithelial cells caused significant mucosal atrophy in the small intestine, as indicated by decreased cell proliferation within the crypts and subsequent shrinkages of crypts and villi. In addition, the HuR-deficient intestinal epithelium also displayed decreased regenerative potential of crypt progenitors after exposure to irradiation. HuR deficiency decreased expression of the Wnt coreceptor LDL receptor-related protein 6 (LRP6) in the mucosal tissues. At the molecular level, HuR was found to bind the Lrp6 mRNA via its 3'-untranslated region and enhanced LRP6 expression by stabilizing Lrp6 mRNA and stimulating its translation. These results indicate that HuR is essential for normal mucosal growth in the small intestine by altering Wnt signals through up-regulation of LRP6 expression and highlight a novel role of HuR deficiency in the pathogenesis of intestinal mucosal atrophy under pathological conditions.
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In vitro and in vivo evaluation of a nanoparticulate bioceramic paste for dental pulp repair.
Acta Biomater
PUBLISHED: 08-23-2014
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Bioactive materials play an important role in facilitating dental pulp repair when living dental pulp is exposed after injuries. Mineral trioxide aggregate is the currently recommended material of choice for pulp repair procedures though has several disadvantages, especially the inconvenience of handling. Little information is yet available about the early events and molecular mechanisms involved in bioceramic-mediated dental pulp repair. We aimed to characterize and determine the apatite-forming ability of the novel ready-to-use nanoparticulate bioceramic iRoot BP Plus, and investigate its effects on the in vitro recruitment of human dental pulp stem cells (DPSCs), as well as its capacity to induce dentin bridge formation in an in vivo model of pulp repair. It was found that iRoot BP Plus was nanosized and had excellent apatite-forming ability in vitro. Treatment with iRoot BP Plus extracts promoted the adhesion, migration and attachment of DPSCs, and optimized focal adhesion formation (Vinculin, p-Paxillin and p-Focal adhesion kinase) and stress fibre assembly. Consistent with the in vitro results, we observed the formation of a homogeneous dentin bridge and the expression of odontogenic (dentin sialoprotein, dentin matrix protein 1) and focal adhesion molecules (Vinculin, p-Paxillin) at the injury site of pulp repair model by iRoot BP Plus. Our findings provide valuable insights into the mechanism of bioceramic-mediated dental pulp repair, and the novel revolutionary ready-to-use nanoparticulate bioceramic paste shows promising therapeutic potential in dental pulp repair application.
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[Early screening of developmental dysplasia of the hip among hospitalized children].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 08-23-2014
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To summarize retrospectively developmental dysplasia of the hip (DDH) screening of children within 36 months.
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MiR-218 regulates cisplatin chemosensitivity in breast cancer by targeting BRCA1.
Tumour Biol.
PUBLISHED: 08-12-2014
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Cisplatin resistance presents a major challenge in the successful treatment of breast cancer, and its mechanism has not been documented well. In this study, to determine the relationship between chemotherapy resistance and microRNA (miRNA) expression during the development of cisplatin resistance in breast cancer, we used microRNA microarrays analysis successfully identified 19 miRNAs that were either overexpressed or underexpressed (8 upregulated and 11 downregulated) in the MCF-7 cell line and its cisplatin-resistant variant MCF-7/DDP. Among them, the miR-218 was most downregulated in cisplatin-resistant cell lines and identified that breast cancer 1 (BRCA1) was the cellular targets of miR-218. In vivo assay also demonstrated that restoring miR-218 expression in MCF-7/DDP cell line could sensitize cells against cisplatin, thereby increasing cisplatin-mediated tumor cell apoptosis and reducing DNA repair. Kaplan-Meier survival analysis indicated that patients with breast cancer display high levels of miR-218 and low levels of BRCA1 expression; these patients may gain the greatest benefits in terms of increased survival when treated with cisplatin. All of these results indicated that miR-218 has a significant function in the development of cisplatin resistance in breast cancer. Restoring miR-218 expression may constitute a novel therapeutic approach by which to increase cisplatin sensitivity in breast cancer.
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Dietary pattern and asthma: a systematic review and meta-analysis.
J Asthma Allergy
PUBLISHED: 08-12-2014
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The literature on the relationship between diet and asthma has largely focused on individual nutrients, with conflicting results. People consume a combination of foods from various groups that form a dietary pattern. Studying the role of dietary patterns in asthma is an emerging area of research. The purpose of this study was to systematically review dietary patterns and asthma outcomes in adults and children, to review maternal diet and child asthma, and to conduct a meta-analysis on the association between asthma prevalence and dietary patterns in adults.
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miR-29b Modulates Intestinal Epithelium Homeostasis by Repressing Menin Translation.
Biochem. J.
PUBLISHED: 08-08-2014
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Menin regulates distinct cellular functions by regulating gene transcription through its interaction with partner transcription factors, but the exact mechanisms that control Menin levels remain largely unknown. Here we report that Men1 mRNA, encoding Menin, is a novel target of microRNA-29b (miR-29b) and that miR-29b/Men1 mRNA association regulates Menin expression posttranscriptionally in rat intestinal epithelial cells (IECs). Overexpression of a miR-29b precursor lowered modestly the levels of Men1 mRNA, but reduced robustly the de novo synthesis of Menin; conversely, antagonization of miR-29b enhanced Menin protein synthesis and steady-state levels. The repressive effect of miR-29b on Menin expression was mediated through a single binding site in the coding region of Men1 mRNA, since point mutation of this site prevented miR-29b-induced repression of Menin translation. Increasing cellular polyamines due to overexpression of ornithine decarboxylase (ODC) enhanced Menin translation by reducing miR-29b, whereas polyamine depletion by inhibiting ODC increased miR-29b, thus suppressing Menin expression. Moreover, an increase in Menin abundance in miR-29b-silenced population of IECs led to increased sensitivity to apoptosis, which was prevented by silencing Menin. These findings indicate that miR-29b represses translation of Men1 mRNA, in turn affecting intestinal epithelial homeostasis by altering IEC apoptosis.
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Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Phys Chem Chem Phys
PUBLISHED: 07-24-2014
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In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.
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Micropillar arrays as a high-throughput screening platform for therapeutics in multiple sclerosis.
Nat. Med.
PUBLISHED: 07-06-2014
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Functional screening for compounds that promote remyelination represents a major hurdle in the development of rational therapeutics for multiple sclerosis. Screening for remyelination is problematic, as myelination requires the presence of axons. Standard methods do not resolve cell-autonomous effects and are not suited for high-throughput formats. Here we describe a binary indicant for myelination using micropillar arrays (BIMA). Engineered with conical dimensions, micropillars permit resolution of the extent and length of membrane wrapping from a single two-dimensional image. Confocal imaging acquired from the base to the tip of the pillars allows for detection of concentric wrapping observed as 'rings' of myelin. The platform is formatted in 96-well plates, amenable to semiautomated random acquisition and automated detection and quantification. Upon screening 1,000 bioactive molecules, we identified a cluster of antimuscarinic compounds that enhance oligodendrocyte differentiation and remyelination. Our findings demonstrate a new high-throughput screening platform for potential regenerative therapeutics in multiple sclerosis.
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Sensitive electrochemical detection of NADH and ethanol at low potential based on pyrocatechol violet electrodeposited on single walled carbon nanotubes-modified pencil graphite electrode.
Talanta
PUBLISHED: 07-03-2014
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In this work, the electrodeposition of pyrocatechol violet (PCV) was initially investigated by the electrochemical surface plasmon resonance (ESPR) technique. Subsequently, PCV was used as redox-mediator and was electrodeposited on the surface of pencil graphite electrode (PGE) modified with single-wall carbon nanotubes (SWCNTs). Owing to the remarkable synergistic effect of SWCNTs and PCV, PGE/SWCNTs/PCV exhibited excellent electrocatalytic activity towards dihydronicotinamide adenine dinucleotide (NADH) oxidation at low potential (0.2V vs. SCE) with fast amperometric response (<10s), broad linear range (1.3-280 ?M), good sensitivity (146.2 ?A mM(-1)cm(-2)) and low detection limit (1.3 ?M) at signal-to-noise ratio of 3. Thus, this PGE/SWCNTs/PCV could be further used to fabricate a sensitive and economic ethanol biosensor using alcohol dehydrogenase (ADH) via a glutaraldehyde/BSA cross-linking procedure.
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Expression of the mouse MHC class Ib H2-T11 gene product, a paralog of H2-T23 (Qa-1) with shared peptide-binding specificity.
J. Immunol.
PUBLISHED: 06-23-2014
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The mouse MHC class Ib gene H2-T11 is 95% identical at the DNA level to H2-T23, which encodes Qa-1, one of the most studied MHC class Ib molecules. H2-T11 mRNA was observed to be expressed widely in tissues of C57BL/6 mice, with the highest levels in thymus. To circumvent the availability of a specific mAb, cells were transduced with cDNA encoding T11 with a substituted ?3 domain. Hybrid T11D3 protein was expressed at high levels similar to control T23D3 molecules on the surface of both TAP(+) and TAP(-) cells. Soluble T11D3 was generated by folding in vitro with Qa-1 determinant modifier, the dominant peptide presented by Qa-1. The circular dichroism spectrum of this protein was similar to that of other MHC class I molecules, and it was observed to bind labeled Qa-1 determinant modifier peptide with rapid kinetics. By contrast to the Qa-1 control, T11 tetramers did not react with cells expressing CD94/NKG2A, supporting the conclusion that T11 cannot replace Qa-1 as a ligand for NK cell inhibitory receptors. T11 also failed to substitute for Qa-1 in the presentation of insulin to a Qa-1-restricted T cell hybridoma. Despite divergent function, T11 was observed to share peptide-loading specificity with Qa-1. Direct analysis by tandem mass spectrometry of peptides eluted from T11D3 and T23D3 isolated from Hela cells demonstrated a diversity of peptides with a clear motif that was shared between the two molecules. Thus, T11 is a paralog of T23 encoding an MHC class Ib molecule that shares peptide-binding specificity with Qa-1 but differs in function.
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H2O2 mediates the crosstalk of brassinosteroid and abscisic acid in tomato responses to heat and oxidative stresses.
J. Exp. Bot.
PUBLISHED: 06-04-2014
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The production of H2O2 is critical for brassinosteroid (BR)- and abscisic acid (ABA)-induced stress tolerance in plants. In this study, the relationship between BR and ABA in the induction of H2O2 production and their roles in response to heat and paraquat (PQ) oxidative stresses were studied in tomato. Both BR and ABA induced increases in RBOH1 gene expression, NADPH oxidase activity, apoplastic H2O2 accumulation, and heat and PQ stress tolerance in wild-type plants. BR could only induced transient increases in these responses in the ABA biosynthetic mutant notabilis (not), whereas ABA induced strong and prolonged increases in these responses in the BR biosynthetic mutant d (^im) compared with wild-type plants. ABA levels were reduced in the BR biosynthetic mutant but could be elevated by exogenous BR. Silencing of RBOH1 compromised BR-induced apoplastic H2O2 production, ABA accumulation, and PQ stress responses; however, ABA-induced PQ stress responses were largely unchanged in the RBOH1-silenced plants. BR induces stress tolerance involving a positive feedback mechanism in which BR induces a rapid and transient H2O2 production by NADPH oxidase. The process in turn triggers increased ABA biosynthesis, leading to further increases in H2O2 production and prolonged stress tolerance. ABA induces H2O2 production in both the apoplastic and chloroplastic compartments.
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Origin of the different phytotoxicity and biotransformation of cerium and lanthanum oxide nanoparticles in cucumber.
Nanotoxicology
PUBLISHED: 06-01-2014
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Abstract To investigate how the physicochemical properties of nanoparticles (NPs) affect their biological and toxicological effects, we evaluated the phytotoxicity of CeO2 and La2O3 NPs to cucumber (Cucumis sativus) plants and tried to clarify the relation between physicochemical properties of NPs and their behaviors. CeO2 NPs had no phytotoxicity to cucumber at all tested concentrations, while La2O3 NPs showed significant inhibition on root elongation (???2?mg/L), shoot elongation (at 2000?mg/L), root biomass (???2?mg/L), and shoot biomass (???20?mg/L), as well as induced more reactive oxygen species and cell death in roots (2000?mg/L). The different distribution and speciation of Ce and La in plants were determined by synchrotron-based micro X-ray fluorescence microscopy and X-ray absorption spectroscopy. In the aerial parts, all of La was combined with phosphate or carboxylic group, while a fraction of Ce was changed to Ce(III)-carboxyl complexes, implying that La2O3 acted as its ionic form, while CeO2 displayed the behavior of particles or particle-ion mixtures. The higher dissolution of La2O3 than CeO2 NPs might be the reason for their significant difference in phytotoxicity and transporting behaviors in cucumbers. To our knowledge, this is the first detailed study of the relation between the level of dissolution of NPs and their behaviors in plant systems.
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Authentication of Polygonati Odorati Rhizoma and other two Chinese Materia Medica of the Liliaceae family by pharmacognosy technique with GC-MS analysis.
Microsc. Res. Tech.
PUBLISHED: 05-29-2014
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Yuzhu (Polygonati Odorati Rhizoma), Kangdingyuzhu (Polygonati Prattii Rhizoma), and zhugenqiyuzhu (Disporopsis Fuscopictae Rhizoma) are of the same family, but of different genera. They have all often used in Chinese Materia Medica (CMM) as Polygonati Odorati Rhizoma in China market. Three species of CMM are confused. For better application, we need to identify these plants accurately. This study use pharmacognosy technique and GC-MS analysis, three species of CMM were authenticated. In macroscopic characteristics, the fruit of Polygonati Odorati Rhizoma is blue-black, while the other two are maroon and dark purple orderly. Nodes of Polygonati Odorati Rhizoma are upward and light uplift, about 1 cm spacing, while the other are not. As for microscopic characteristics, the cortex of Polygonati Odorati Rhizoma only occupies about 1/5 of the radius of the transverse section with inconspicuous endodermis, which is much smaller than others. The type of vascular bundles of Polygonati Odorati Rhizoma is closed collateral, but the other is amphivasal. Raphides of calcium oxalate are scattered, but Raphides of the other two are like brooms and neat rows. GC-MS analysis of essential oil could provide different characteristics to distinguish three species. Twenty-three compounds were identified from essential oil of Polygonati Odorati Rhizoma and the main components were n-hexadecanoic acid (49.45%), while n-hexadecanoic acid of the other two are 23.92% and 9.45%. The content of n-hexadecanoic is strongly different. This research was aimed to establish a method by pharmacognosy and GC-MS analysis to identify three CMM and for providing scientifical data to ensure accuracy of origin of three species. Microsc. Res. Tech., 2014. © 2014 Wiley Periodicals, Inc.
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RNA-binding proteins and microRNAs in gastrointestinal epithelial homeostasis and diseases.
Curr Opin Pharmacol
PUBLISHED: 05-29-2014
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The epithelium of gastrointestinal (GI) mucosa is a rapidly self-renewing tissue in the body, and its homeostasis is preserved through strict regulation of cell proliferation and apoptosis. Epithelial cells originate from a small number of pluripotent stem cells, which divide to either renew themselves or become committed crypt cells. RNA-binding proteins (RBPs) and microRNAs (miRNAs) regulate gene expression at the posttranscriptional level and are recently shown to modulate GI mucosal growth and repair after injury. Here we highlight the roles of RBPs HuR, CUG-binding protein 1, AU-binding factor 1, and several GI epithelial-specific miRNAs in gut mucosal homeostasis and diseases and also further analyze the mechanisms through which RBPs and miRNAs modulate the stability and translation of target mRNAs.
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Fragment quantum mechanical calculation of proteins and its applications.
Acc. Chem. Res.
PUBLISHED: 05-22-2014
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Conspectus The desire to study molecular systems that are much larger than what the current state-of-the-art ab initio or density functional theory methods could handle has naturally led to the development of novel approximate methods, including semiempirical approaches, reduced-scaling methods, and fragmentation methods. The major computational limitation of ab initio methods is the scaling problem, because the cost of ab initio calculation scales nth power or worse with system size. In the past decade, the fragmentation approach based on chemical locality has opened a new door for developing linear-scaling quantum mechanical (QM) methods for large systems and for applications to large molecular systems such as biomolecules. The fragmentation approach is highly attractive from a computational standpoint. First, the ab initio calculation of individual fragments can be conducted almost independently, which makes it suitable for massively parallel computations. Second, the electron properties, such as density and energy, are typically combined in a linear fashion to reproduce those for the entire molecular system, which makes the overall computation scale linearly with the size of the system. In this Account, two fragmentation methods and their applications to macromolecules are described. They are the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method and the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. The EE-GMFCC method is developed from the MFCC approach, which was initially used to obtain accurate protein-ligand QM interaction energies. The main idea of the MFCC approach is that a pair of conjugate caps (concaps) is inserted at the location where the subsystem is divided by cutting the chemical bond. In addition, the pair of concaps is fused to form molecular species such that the overcounted effect from added concaps can be properly removed. By introducing the electrostatic embedding field in each fragment calculation and two-body interaction energy correction on top of the MFCC approach, the EE-GMFCC method is capable of accurately reproducing the QM molecular properties (such as the dipole moment, electron density, and electrostatic potential), the total energy, and the electrostatic solvation energy from full system calculations for proteins. On the other hand, the AF-QM/MM method was used for the efficient QM calculation of protein nuclear magnetic resonance (NMR) parameters, including the chemical shift, chemical shift anisotropy tensor, and spin-spin coupling constant. In the AF-QM/MM approach, each amino acid and all the residues in its vicinity are automatically assigned as the QM region through a distance cutoff for each residue-centric QM/MM calculation. Local chemical properties of the central residue can be obtained from individual QM/MM calculations. The AF-QM/MM approach precisely reproduces the NMR chemical shifts of proteins in the gas phase from full system QM calculations. Furthermore, via the incorporation of implicit and explicit solvent models, the protein NMR chemical shifts calculated by the AF-QM/MM method are in excellent agreement with experimental values. The applications of the AF-QM/MM method may also be extended to more general biological systems such as DNA/RNA and protein-ligand complexes.
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Chloroplastic thioredoxin-f and thioredoxin-m1/4 play important roles in brassinosteroids-induced changes in CO2 assimilation and cellular redox homeostasis in tomato.
J. Exp. Bot.
PUBLISHED: 05-20-2014
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Chloroplast thioredoxins (TRXs) and glutathione function as redox messengers in the regulation of photosynthesis. In this work, the roles of chloroplast TRXs in brassinosteroids (BRs)-induced changes in cellular redox homeostasis and CO2 assimilation were studied in the leaves of tomato plants. BRs-deficient d (^im) plants showed decreased transcripts of TRX-f, TRX-m2, TRX-m1/4, and TRX-x, while exogenous BRs significantly induced CO2 assimilation and the expression of TRX-f, TRX-m2, TRX-m1/4, and TRX-x. Virus-induced gene silencing (VIGS) of the chloroplast TRX-f, TRX-m2, TRX-m1/4, and TRX-y genes individually increased membrane lipid peroxidation and accumulation of 2-Cys peroxiredoxin dimers, and decreased the activities of the ascorbate-glutathione cycle enzymes and the ratio of reduced glutathione to oxidized glutathione (GSH/GSSG) in the leaves. Furthermore, partial silencing of TRX-f, TRX-m2, TRX-m1/4, and TRX-y resulted in decreased expression of genes involved in the Benson-Calvin cycle and decreased activity of the associated enzymes. Importantly, the BRs-induced increase in CO2 assimilation and the increased expression and activities of antioxidant- and photosynthesis-related genes and enzymes were compromised in the partially TRX-f- and TRX-m1/4-silenced plants. All of these results suggest that TRX-f and TRX-m1/4 are involved in the BRs-induced changes in CO2 assimilation and cellular redox homeostasis in tomato.
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Effect of strong electric field on the conformational integrity of insulin.
J Phys Chem A
PUBLISHED: 05-12-2014
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A series of molecular dynamics (MD) simulations up to 1 ?s for bovine insulin monomer in different external electric fields were carried out to study the effect of external electric field on conformational integrity of insulin. Our results show that the secondary structure of insulin is kept intact under the external electric field strength below 0.15 V/nm, but disruption of secondary structure is observed at 0.25 V/nm or higher electric field strength. Although the starting time of secondary structure disruption of insulin is not clearly correlated with the strength of the external electric field ranging between 0.15 and 0.60 V/nm, long time MD simulations demonstrate that the cumulative effect of exposure time under the electric field is a major cause for the damage of insulin's secondary structure. In addition, the strength of the external electric field has a significant impact on the lifetime of hydrogen bonds when it is higher than 0.60 V/nm. The fast evolution of some hydrogen bonds of bovine insulin in the presence of the 1.0 V/nm electric field shows that different microwaves could either speed up protein folding or destroy the secondary structure of globular proteins deponding on the intensity of the external electric field.
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N-acetylcysteine reduces oxidative stress, nuclear factor??B activity and cardiomyocyte apoptosis in heart failure.
Mol Med Rep
PUBLISHED: 04-29-2014
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The roles of oxidative stress on nuclear factor (NF)??B activity and cardiomyocyte apoptosis during heart failure were examined using the antioxidant N?acetylcysteine (NAC). Heart failure was established in Japanese white rabbits with intravenous injections of doxorubicin, with ten rabbits serving as a control group. Of the rabbits with heart failure, 12 were not treated (HF group) and 13 received NAC (NAC group). Cardiac function was assessed using echocardiography and hemodynamic analysis. Myocardial cell apoptosis, apoptosis?related protein expression, NF??Bp65 expression and activity, total anti?oxidative capacity (tAOC), 8?iso?prostaglandin F2? (8?iso?PGF2?) expression and glutathione (GSH) expression levels were determined. In the HF group, reduced tAOC, GSH levels and Bcl?2/Bax ratios as well as increased 8?iso?PGF2? levels and apoptosis were observed (all P<0.05), which were effects that were attenuated by the treatment with NAC. NF??Bp65 and iNOS levels were significantly higher and the P?I?B?? levels were significantly lower in the HF group; expression of all three proteins returned to pre?HF levels following treatment with NAC. Myocardial cell apoptosis was positively correlated with left ventricular end-diastolic pressure (LVEDP), NF??Bp65 expression and 8?iso?PGF2? levels, but negatively correlated with the maximal and minimal rates of increase in left ventricular pressure (+dp/dtmax and ?dp/dtmin, respectively) and the Bcl?2/Bax ratio (all P<0.001). The 8?iso?PGF2? levels were positively correlated with LVEDP and negatively correlated with +dp/dtmax and ?dp/dtmin (all P<0.001). The present study demonstrated that NAC increased the antioxidant capacity, decreased the NF??B activation and reduced myocardial cell apoptosis in an in vivo heart failure model.
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Ab initio molecular crystal structures, spectra, and phase diagrams.
Acc. Chem. Res.
PUBLISHED: 04-22-2014
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Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling illustrations of their unprecedented power in addressing some of the outstanding problems of solid-state chemistry, high-pressure chemistry, or geochemistry. They are the structure and spectra of ice Ih, in particular, the origin of two peaks in the hydrogen-bond-stretching region of its inelastic neutron scattering spectra, a solid-solid phase transition from CO2-I to elusive, metastable CO2-III, pressure tuning of Fermi resonance in solid CO2, and the structure and spectra of solid formic acid, all at the level of second-order Møller-Plesset perturbation theory or higher.
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Decreased P-glycoprotein is associated with the inhibitory effects of static magnetic fields and cisplatin on K562 cells.
Bioelectromagnetics
PUBLISHED: 03-23-2014
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In this study, we explored the mechanism of the killing effects of a moderate-intensity static magnetic field (SMF) and cisplatin (DDP) on K562 cells. We analyzed the metabolic activity of cells, the extracellular DDP content, and P-glycoprotein (P-gp) expression after K562 cells were exposed continuously to a uniform 8.8?mT SMF for 8?h, with or without DDP. We found that SMF combined with DDP (10?µg/ml) significantly inhibited the metabolic activity of K562 cells (P?
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Hydrogen peroxide mediates abscisic acid-induced HSP70 accumulation and heat tolerance in grafted cucumber plants.
Plant Cell Environ.
PUBLISHED: 02-26-2014
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Root-shoot communications play important roles in plant stress responses. Here, we examined the roles of root-sourced signals in the shoot response to heat in cucumber plants. Cucumber plants grafted onto their own roots and luffa roots were exposed to aerial and root-zone heat to examine their tolerance by assessing the levels of oxidative stress, PSII photoinhibition, accumulation of abscisic acid (ABA), H2 O2 and heat shock protein (HSP) 70 using immunoblotting, chlorophyll fluorescence, immunoassay, CeCl3 staining and Western blotting, respectively. Grafting onto the luffa rootstock enhanced the shoot tolerance to the heat. This enhanced tolerance was associated with increased accumulation of ABA and apoplastic H2 O2 , RBOH transcripts and HSP70 expression and a decrease in oxidative stress in the shoots. The increases in the ABA and H2 O2 concentrations in the shoots were attributed to an increase in ABA transport from roots and an increase in ABA biosynthesis in the shoots when the root-zone and shoots were heat stressed, respectively. Inhibition of H2 O2 accumulation compromised luffa rootstock-induced HSP70 expression and heat tolerance. These results suggest that, under heat stress, ABA triggers the expression of HSP70 in an apoplastic H2 O2 -dependent manner, implicating the role of an ABA-dependent H2 O2 -driven mechanism in a systemic response involving root-shoot communication.
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The sub/supra-optimal temperature-induced inhibition of photosynthesis and oxidative damage in cucumber leaves are alleviated by grafting onto figleaf gourd/luffa rootstocks.
Physiol Plant
PUBLISHED: 02-22-2014
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Shoot-root communication is involved in plant stress responses, but its mechanism is largely unknown. To determine the role of roots in stress tolerance, cucumber (Cucumis sativus) shoots from plants with roots of their own or with figleaf gourd (Cucurbita ficifolia, a chilling-tolerant species) or luffa (Luffa cylindrica (L.) M. Roem., a heat-tolerant species) rootstocks were exposed to low (18/13°C), optimal (27/22°C) and high (36/31°C) temperatures, respectively. Grafting onto figleaf gourd and luffa rootstocks significantly alleviated chilling and heat-induced reductions, respectively, in biomass production and CO2 assimilation capacity in the shoots, while levels of lipid peroxidation and protein oxidation were decreased. Figleaf gourd and luffa rootstocks upregulated a subset of stress-responsive genes involved in signal transduction (MAPK1 and RBOH), transcriptional regulation (MYB and MYC), protein protection (HSP45.9 and HSP70), the antioxidant response (Cu/Zn-SOD, cAPX and GR), and photosynthesis (RBCL, RBCS, RCA and FBPase) at low and high growth temperatures, respectively, and this was accompanied by increased activity of the encoded enzymes and reduced glutathione redox homeostasis in the leaves. Moreover, Heat Shock Protein 70 (HSP70) expression in cucumber leaves was strongly induced by the luffa rootstock at the high growth temperature but slightly induced by the figleaf gourd rootstock at low or high growth temperatures. These results indicate that rootstocks could induce significant changes in the transcripts of stress-responsive and defense-related genes, and the ROS scavenging activity via unknown signals, especially at stressful growth temperatures, and this is one of mechanisms involved in the grafting-induced stress tolerance.
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Structure, mechanism, and enantioselectivity shifting of lipase LipK107 with a simple way.
Biochim. Biophys. Acta
PUBLISHED: 02-16-2014
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Because of the complex mechanisms of enzymatic reactions, no precise and simple method of understanding and controlling the chiral selectivity of enzymes has been developed. However, structure-based rational design is a powerful approach to engineering enzymes with desired catalytic activities. In this work, a simple, structure-based, large-scale in silico design and virtual screening strategy was developed and successfully applied to enzyme engineering. We first performed protein crystallization and X-ray diffraction to determine the structure of lipase LipK107, which is a novel family I.1 lipase displaying activity for both R and S isomers in chiral resolution reactions. The catalytic mechanism of family I.1, which includes LipK107, was ascertained first through comparisons of the sequences and structures of lipases from other families. The binding states of LipK107, including the energy and the conformation of complexes with the R and S enantiomers, have been evaluated by careful biocomputation to figure out the reason for the higher S selectivity. Based on this study, a simple strategy for manipulating the chiral selectivity by modulating a crucial distance in the enzyme-substrate complex and judging virtual mutations in silico is recommended. Then, a novel electrostatic interaction analysis protocol was used to design LipK107 mutants to validate our strategy. Both positive and negative mutations determined using this theoretical protocol have been implemented in wet experiments and were proved to produce the desired enantioselectivity, showing a 176% increase or 50% decrease in enantioselectivity as desired. Because of its accuracy and versatility, the strategy is promising for practical applications.
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Prediction of clinical pregnancy in vitrified-warmed single blastocyst transfer cycles by pre-freeze morphology.
Iran J Reprod Med
PUBLISHED: 02-15-2014
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Background: The selection of blastocyst warmed for transfer is based on pre-freeze morphology in vitrified-warmed single blastocyst transfer cycles. But, it is controversial which parameter of blastocyst morphology most closely related to the clinical outcomes. Objective: To estimate the effect of blastocoele expansion, trophectoderm (TE) morphology grade, and inner cell mass (ICM) morphology grade on clinical pregnancy in vitrified-warmed single blastocyst transfers. Materials and Methods: There were 172 vitrified-warmed single blastocyst transfer cycles during the year 2012 included in this analysis. Comparison of clinical results between pregnancy and no pregnancy group based on patient and blastocyst morphology characteristics was done. Then stepwise logistic regression analysis was used to select the best morphological predictor for clinical pregnancy. Last, comparison of patient characteristics and clinical outcomes separated by the best independent morphological predictor was done. Results: Comparison of clinical results between pregnancy and no pregnancy group and logistic regression showed the clinical pregnancy rate was affected by ICM. Comparison of patient characteristics separated by ICM grade, ICM grade A cycles got higher clinical pregnancy rate than ICM grade B cycles (54.3% vs. 35.0% respectively, p=0.037). Conclusion: Blastocyst with good ICM morphology could increase clinical pregnancy rate in vitrified-warmed single blastocyst transfer cycles.
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Comparative pulmonary toxicity of two ceria nanoparticles with the same primary size.
Int J Mol Sci
PUBLISHED: 02-12-2014
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Ceria nanoparticles (nano-ceria) have recently gained a wide range of applications, which might pose unwanted risks to both the environment and human health. The greatest potential for the environmental discharge of nano-ceria appears to be in their use as a diesel fuel additive. The present study was designed to explore the pulmonary toxicity of nano-ceria in mice after a single exposure via intratracheal instillation. Two types of nano-ceria with the same distribution of a primary size (3-5 nm), but different redox activity, were used: Ceria-p, synthesized by a precipitation route, and Ceria-h, synthesized by a hydrothermal route. Both Ceria-p and Ceria-h induced oxidative stress, inflammatory responses and cytotoxicity in mice, but their toxicological profiles were quite different. The mean size of Ceria-p agglomerates was much smaller compared to Ceria-h, thereby causing a more potent acute inflammation, due to their higher number concentration of agglomerates and higher deposition rate in the deep lung. Ceria-h had a higher reactivity to catalyzing the generation of reactive oxygen species (ROS), and caused two waves of lung injury: bronchoalveolar lavage (BAL) inflammation and cytotoxicity in the early stage and redox-activity-evoked lipid peroxidation and pro-inflammation in the latter stage. Therefore, the size distribution of ceria-containing agglomerates in the exhaust, as well as their surface chemistry are essential characteristics to assess the potential risks of using nano-ceria as a fuel additive.
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Transforming growth factor-?1 in the microenvironment of ischemia reperfusion-injured kidney enhances the chemotaxis of mesenchymal stem cells to stromal cell-derived factor-1 through upregulation of surface chemokine (C-X-C motif) receptor 4.
Mol Med Rep
PUBLISHED: 02-12-2014
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Acute renal failure is one of the most common complications observed in hospitals. Although extensive studies have been carried out to search for therapeutic treatments, no effective cure has been established. In recent years, stem cell therapy for tissue engineering and repair has become a key area of study. Bone marrow mesenchymal stem cells (MSCs) have been demonstrated to exhibit a reparative role in ischemia reperfusion-injured kidney tissue, and the stromal cell-derived factor-1 (SDF-1)/chemokine (C-X-C motif) receptor 4 (CXCR4) axis has been found to play an important role in the migration and homing of MSCs. In the present study, transforming growth factor-?1 (TGF-?1) in the homogenate of the acute ischemia reperfusion-injured renal tissue was found to markedly increase the CXCR4 surface expression of MSCs, which contributes to the migration of MSCs to SDF-1. Neutralization of TGF-?1 inhibited the migration in an antibody concentration-dependent manner, through downregulation of CXCR4 localized to the membrane. These observations suggest a potential mechanism for MSC migration to the kidney which may provide a possible therapeutic target for curing acute renal failure.
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Finite-temperature second-order many-body perturbation and Hartree-Fock theories for one-dimensional solids: an application to Peierls and charge-density-wave transitions in conjugated polymers.
J Chem Phys
PUBLISHED: 01-21-2014
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Finite-temperature extensions of ab initio Gaussian-basis-set spin-restricted Hartree-Fock (HF) and second-order many-body perturbation (MP2) theories are implemented for infinitely extended, periodic, one-dimensional solids and applied to the Peierls and charge-density-wave (CDW) transitions in polyyne and all-trans polyacetylene. The HF theory predicts insulating CDW ground states for both systems in their equidistant structures at low temperatures. In the same structures, they turn metallic at high temperatures. Starting from the "dimerized" low-temperature equilibrium structures, the systems need even higher temperatures to undergo a Peierls transition, which is accompanied by geometric as well as electronic distortions from dimerized to non-dimerized forms. The conventional finite-temperature MP2 theory shows a sign of divergence in any phase at any nonzero temperature and is useless. The renormalized finite-temperature MP2 (MP2R) theory is divergent only near metallic electronic structures, but is well behaved elsewhere. MP2R also predicts CDW and Peierls transitions occurring at two different temperatures. The effect of electron correlation is primarily to lower the Peierls transition temperature.
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Role of H2O2 dynamics in brassinosteroid-induced stomatal closure and opening in Solanum lycopersicum.
Plant Cell Environ.
PUBLISHED: 01-07-2014
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Brassinosteroids (BRs) are essential for plant growth and development; however, their roles in the regulation of stomatal opening or closure remain obscure. Here, the mechanism underlying BR-induced stomatal movements is studied. The effects of 24-epibrassinolide (EBR) on the stomatal apertures of tomato (Solanum lycopersicum) were measured by light microscopy using epidermal strips of wild type (WT), the abscisic acid (ABA)-deficient notabilis (not) mutant, and plants silenced for SlBRI1, SlRBOH1 and SlGSH1. EBR induced stomatal opening within an appropriate range of concentrations, whereas high concentrations of EBR induced stomatal closure. EBR-induced stomatal movements were closely related to dynamic changes in H(2)O(2) and redox status in guard cells. The stomata of SlRBOH1-silenced plants showed a significant loss of sensitivity to EBR. However, ABA deficiency abolished EBR-induced stomatal closure but did not affect EBR-induced stomatal opening. Silencing of SlGSH1, the critical gene involved in glutathione biosynthesis, disrupted glutathione redox homeostasis and abolished EBR-induced stomatal opening. The results suggest that transient H(2)O(2) production is essential for poising the cellular redox status of glutathione, which plays an important role in BR-induced stomatal opening. However, a prolonged increase in H(2)O(2) facilitated ABA signalling and stomatal closure.
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MGMT Leu84Phe gene polymorphism and lung cancer risk: a meta-analysis.
Tumour Biol.
PUBLISHED: 01-05-2014
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Many studies have examined the association between the MGMT Leu84Phe polymorphism gene polymorphisms and lung cancer risk in various populations, but their results have been inconsistent. To assess this relationship more precisely, a meta-analysis was performed. The PubMed and CNKI database was searched for case-control studies published up to Nov. 2013. Data were extracted and pooled odds ratios (OR) with 95% confidence intervals (CI) were calculated. Ultimately, 7 studies, comprising 3,094 lung cancer cases and 4,216 controls, were included. Overall, for (Phe/Phe+Phe/Leu) versus Leu/Leu, the pooled OR for all studies was 1.08 (95% CI?=?0.97-1.21 P?=?0.518 for heterogeneity); for Phe/Phe versus Leu/Leu and Phe versus Leu, the pooled OR was 1.10 (95% CI?=?0.99-1.21 P?=?0.445 for heterogeneity) and 1.46 (95% CI?=?1.05-2.02 P?=?0.352 for heterogeneity), respectively. In the stratified analysis by ethnicity, significantly risks were found among Caucasians not in Asians. This meta-analysis suggests that the MGMT Leu84Phe polymorphisms are associated with lung cancer risk among Caucasians not in Asians.
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In vitro characterization of human adenovirus type 55 in comparison with its parental adenoviruses, types 11 and 14.
PLoS ONE
PUBLISHED: 01-01-2014
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Human adenovirus type 55 (HAdV-B55) represents a re-emerging human pathogen, and this adenovirus has been reported to cause outbreaks of acute respiratory diseases among military trainees and in school populations around the world. HAdV-B55 has been revealed to have evolved from homologous recombination between human adenovirus type 14 (HAdV-B14) and type 11 (HAdV-B11), but it presents different clinical manifestations from parental virus HAdV-B11. In the present paper, we report the distinct biological features of HAdV-B55 in comparison with the parental viruses HAdV-B11 and HAdV-B14 in cell cultures. The results showed that HAdV-B55 replicated well in various cells, similar to HAdV-B11 and HAdV-B14, but that its processing had a slower and milder cytopathic effect in the early stages of infection. Viral fitness analysis showed that HAdV-B55 exhibited higher levels of replication in respiratory cells than did either of its parents. Cytotoxicity and apoptosis analyses in A549 cells indicated that HAdV-B55 was less cytotoxic than HAdV-B11 and HAdV-B14 were and induced milder apoptosis. Finally, thermal sensitivity analysis revealed that HAdV-B55 exhibited lower thermostability than did either HAdV-B11 or HAdV-B14, which may limit the transmission of HAdV-B55 in humans. Together, the findings described here expand current knowledge about this re-emerging recombinant HAdV, shedding light on the pathogenesis of HAdV-B55.
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Parallel mRNA and microRNA profiling of HEV71-infected human neuroblastoma cells reveal the up-regulation of miR-1246 in association with DLG3 repression.
PLoS ONE
PUBLISHED: 01-01-2014
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Human enterovirus 71 (HEV71) has emerged as the leading cause of viral encephalitis in children in most Asian countries. The roles of host miRNAs in the neurological pathogenesis of HEV71 infection remain unknown. In the present study, comprehensive miRNA expression profiling in HEV71-infected human neuroblastoma SH-SY5Y cells was performed using the Affymetrix Gene Chip microarray assay and was validated using real-time RT-PCR. Among the 69 differentially expressed miRNAs, miR-1246 was specifically induced by HEV71 infection in human neuroblastoma cells, but inhibition of miR-1246 failed to affect HEV71 replication. Parallel mRNA and microRNA profiling based on the 35 K Human Genome Array identified 182 differentially regulated genes. Target prediction of miR-1246 and network modeling revealed 14 potential target genes involved in cell death and cell signaling. Finally, a combined analysis of the results from mRNA profiling and miR-1246 target predication led to the identification of disc-large homolog 3 (DLG3), which is associated with neurological disorders, for further validation. Sequence alignment and luciferase reporter assay showed that miR-1246 directly bound with the 3'-UTR of DLG3 gene. Down-regulation of miR-1246 induced significant changes in DLG3 expression levels in HEV71-infected SHSY5Y cells. Together, these results suggested that miR-1246 might play a role in neurological pathogenesis of HEV71 by regulating DLG3 gene in infected cells. These findings provide new information on the miRNA and mRNA profiles of HEV71-infected neuroblastoma cells. The biological significance of miR-1246 and DLG3 during the course of HEV71 infection deserves further investigation.
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Effect of sperm DNA fragmentation on clinical outcome of frozen-thawed embryo transfer and on blastocyst formation.
PLoS ONE
PUBLISHED: 01-01-2014
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During the last decades, many studies have shown the possible influence of sperm DNA fragmentation on assisted reproductive technique outcomes. However, little is known about the impact of sperm DNA fragmentation on the clinical outcome of frozen-thawed embryo transfer (FET) from cycles of conventional in vitro fertilization (IVF) and intra-cytoplasmic sperm injection (ICSI). In the present study, the relationship between sperm DNA fragmentation (SDF) and FET clinical outcomes in IVF and ICSI cycles was analyzed. A total of 1082 FET cycles with cleavage stage embryos (C-FET) (855 from IVF and 227 from ICSI) and 653 frozen-thawed blastocyst transfer cycles (B-FET) (525 from IVF and 128 from ICSI) were included. There was no significant change in clinical pregnancy, biochemical pregnancy and miscarriage rates in the group with a SDF >30% compared with the group with a SDF ?30% in IVF and ICSI cycles with C-FET or B-FET. Also, there was no significant impact on the FET clinic outcome in IVF and ICSI when different values of SDF (such as 10%, 20%, 25%, 35%, and 40%) were taken as proposed threshold levels. However, the blastulation rates were significantly higher in the SDF ?30% group in ICSI cycle. Taken together, our data show that sperm DNA fragmentation measured by Sperm Chromatin Dispersion (SCD) test is not associated with clinical outcome of FET in IVF and ICSI. Nonetheless, SDF is related to the blastocyst formation in ICSI cycles.
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[Study progress of spectral color science and its prospect of application in the field of Chinese medicine].
Guang Pu Xue Yu Guang Pu Fen Xi
PUBLISHED: 12-28-2013
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The paper reviewed the research progress in the spectral color science, including the common model, color measurement instrument in recent years, application of color measurement technology in agriculture, food, industry, medicine and other fields. The possibility to achieve the color quantization of Chinese medicine was explored by color measurement technology, and analyzed its application prospect in the field of Chinese medicine, provided a model for the study on quality control for Chinese medicine non-destructive online
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Second-Order Many-Body Perturbation Theory: An Eternal Frontier.
J Phys Chem A
PUBLISHED: 12-26-2013
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Second-order many-body perturbation theory [MBPT(2)] is the lowest-ranked member of a systematic series of approximations convergent at the exact solutions of the Schrödinger equations. It has served and continues to serve as the testing ground for new approximations, algorithms, and even theories. This article introduces this basic theory from a variety of viewpoints including the Rayleigh-Schrödinger perturbation theory, the many-body Greens function theory based on the Dyson equation, and the related Feynman-Goldstone diagrams. It also explains the important properties of MBPT(2) such as size consistency, its ability to describe dispersion interactions, and divergence in metals. On this basis, this article surveys three major advances made recently by the authors to this theory. They are a finite-temperature extension of MBPT(2) and the resolution of the Kohn-Luttinger conundrum, a stochastic evaluation of the correlation and self-energies of MBPT(2) using the Monte Carlo integration of their Laplace-transformed expressions, and an extension to anharmonic vibrational zero-point energies and transition frequencies based on the Dyson equation.
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Human Enterovirus 71 Uncoating Captured at Atomic Resolution.
J. Virol.
PUBLISHED: 12-18-2013
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Human enterovirus 71 (EV71) is the major causative agent of severe hand-foot-and-mouth diseases (HFMD) in young children, and structural characterization of EV71 during its lifecycle can aid in the development of therapeutics against HFMD. Here, we present the atomic structures of the full virion and an uncoating intermediate of a clinical EV71 C4 strain to illustrate the structural changes in the full virion that lead to the formation of the uncoating intermediate prepared for RNA release. Although the VP1 N-terminal regions, observed to penetrate through the junction channel at the quasi 3-fold axis in the uncoating intermediate of coxsackievirus A16, were not observed in the EV71 uncoating intermediate, drastic conformational changes occur in this region, as has been observed in all capsid proteins. Additionally, the RNA genome interacts with the N-terminal extensions of VP1 and residues 32-36 of VP3, both of which are situated at the bottom of the junction. These observations highlight the importance of the junction for genome release. Furthermore, EV71 uncoating is associated with apparent rearrangements and expansion around the 2- and 5-fold axes without obvious changes around the 3-fold axes. Therefore, these structures enabled the identification of hot spots for capsid rearrangements, which led to the hypothesis that the protomer interface near the junction and the 2-fold axis permits the opening of large channels for the exit of polypeptides and viral RNA, which is an uncoating mechanism that is likely conserved in enteroviruses.
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An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins.
J Chem Phys
PUBLISHED: 12-11-2013
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An efficient approach that combines the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method with conductor-like polarizable continuum model (CPCM), termed EE-GMFCC-CPCM, is developed for ab initio calculation of the electrostatic solvation energy of proteins. Compared with the previous MFCC-CPCM study [Y. Mei, C. G. Ji, and J. Z. H. Zhang, J. Chem. Phys. 125, 094906 (2006)], quantum mechanical (QM) calculation is applied to deal with short-range non-neighboring interactions replacing the classical treatment. Numerical studies are carried out for proteins up to 3837 atoms at the HF?6-31G? level. As compared to standard full system CPCM calculations, EE-GMFCC-CPCM shows clear improvement over the MFCC-CPCM method for both the total electrostatic solvation energy and its components (the polarized solute-solvent reaction field energy and wavefunction distortion energy of the solute). For large proteins with 1000-4000 atoms, where the standard full system ab initio CPCM calculations are not affordable, the EE-GMFCC-CPCM gives larger relative wavefunction distortion energies and weaker relative electrostatic solvation energies for proteins, as compared to the corresponding energies calculated by the Divide-and-Conquer Poisson-Boltzmann (D&C-PB) method. Notwithstanding, a high correlation between EE-GMFCC-CPCM and D&C-PB is observed. This study demonstrates that the linear-scaling EE-GMFCC-CPCM approach is an accurate and also efficient method for the calculation of electrostatic solvation energy of proteins.
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RBOH1-dependent H2O2 production and subsequent activation of MPK1/2 play an important role in acclimation-induced cross-tolerance in tomato.
J. Exp. Bot.
PUBLISHED: 12-09-2013
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H2O2 and mitogen-activated protein kinase (MAPK) cascades play important functions in plant stress responses, but their roles in acclimation response remain unclear. This study examined the functions of H2O2 and MPK1/2 in acclimation-induced cross-tolerance in tomato plants. Mild cold, paraquat, and drought as acclimation stimuli enhanced tolerance to more severe subsequent chilling, photooxidative, and drought stresses. Acclimation-induced cross-tolerance was associated with increased transcript levels of RBOH1 and stress- and defence-related genes, elevated apoplastic H2O2 accumulation, increased activity of NADPH oxidase and antioxidant enzymes, reduced glutathione redox state, and activation of MPK1/2 in tomato. Virus-induced gene silencing of RBOH1, MPK1, and MPK2 or MPK1/2 all compromised acclimation-induced cross-tolerance and associated stress responses. Taken together, these results strongly suggest that acclimation-induced cross-tolerance is largely attributed to RBOH1-dependent H2O2 production at the apoplast, which may subsequently activate MPK1/2 to induce stress responses.
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Species-specific toxicity of ceria nanoparticles to Lactuca plants.
Nanotoxicology
PUBLISHED: 11-22-2013
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Abstract Species-specific differences in the toxicity of manufactured nanoparticles (MNPs) have been reported, but the underlying mechanisms are unknown. We previously found that CeO2 NPs inhibited root elongation of head lettuce, whereas no toxic effect was observed on other plants (such as wheat, cucumber and radish). In this study, interactions between Lactuca plants and three types of CeO2 NPs (lab-synthesized 7 and 25?nm CeO2 NPs, and a commercial CeO2 NPs) were investigated. It was found that CeO2 NPs were toxic to three kinds of Lactuca genus plants and different CeO2 NPs showed different degrees of toxicity. The results of X-ray absorption near edge fine structure indicate that small parts of CeO2 NPs were transformed from Ce(IV) to Ce(III) in roots of the plants that were treated with CeO2 NPs during the seed germination stage. But the high sensitivity of Lactuca plants to the released Ce(3+) ions caused the species-specific phytotoxicity of CeO2 NPs. Differences in sizes and zeta potentials among three types of CeO2 NPs resulted in their different degrees of biotransformation which accounted for the discrepancy in the toxicity to Lactuca plants. This study is among the few, and may indeed the first, that addresses the relation between the physicochemical properties of nanoparticles and its species-specific phytotoxicity.
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[Relationship between colorectal adenocarcinoma with invasive micropapillary carcinoma component and lymph node metastasis].
Zhonghua Bing Li Xue Za Zhi
PUBLISHED: 11-20-2013
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To investigate the relationship between colorectal adenocarcinoma with invasive micropapillary carcinoma (IMPC) component, lymphovascular invasion, and lymph node metastasis.
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Pulmonary toxicity of ceria nanoparticles in mice after intratracheal instillation.
J Nanosci Nanotechnol
PUBLISHED: 11-20-2013
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Ceria nanoparticles (nano-ceria) are widely used for various applications such as catalytic converters for automobile exhaust, ultraviolet absorber, and electrolyte in fuel cells. Their potential impacts on the environment and human health have also drawn peoples attention. The present study was designed to explore the pulmonary toxicity of nano-ceria in mice after an acute intratracheal instillation. CD-1 mice were exposed to 0.04, 0.4, 4 and 40 microg nano-ceria (corresponding to 10, 100, 1000 and 10000 times of the maximum exposure dose, respectively) and sacrificed at 1, 7, and 28 d post-exposure. Lung injury was assessed by bronchoalveolar ravage fluid (BALF) analysis, cell counts, biochemical analysis of lung homogenate, and histopathology. Cell differential analysis of the BALF show that the numbers of neutrophils and lymphocytes increased significantly in the mice exposed to 40 microg nano-ceria at 1 d after instillation, and returned to control levels by 7 d. The lactate dehydrogenate activity in the BALF from the 40 microg group increased significantly during the whole experimental period. Pathological changes were only found in the lung tissues from the mice of 40 microg nano-ceria group. The changes were most obvious by 7 d post-exposure, and returned to normal by 28 d. No other changes were found. The results of the present study suggest that exposure to nano-ceria at the current levels in the ambient air may not cause respiratory toxicity.
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Changes in BMI and waist circumference among primary and secondary school students from 2005 to 2010 in Anhui, China.
Ann. Hum. Biol.
PUBLISHED: 10-11-2013
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Abstract Aim: To examine the change in Body Mass Index (BMI) and waist circumference (WC) among primary and secondary school students aged 7-18 in Anhui Province between 2005-2010. Subjects and methods: A total of 15 812 primary and secondary school students aged 7-18 were included in two national surveys on students constitution and health in 2005 and 2010 in Anhui Province. Measurements of height, weight and WC were taken by trained investigators. BMI was calculated for each subject. Results: The mean BMI and WC were significantly increased from 2005 to 2010. For boys, mean increases were 0.85?kg/m(2) and 2.01?cm or 0.08 and 0.34 SD score units, while for girls those were 0.39?kg/m(2) and 2.10?cm or 0.20 and 0.39 SD score units (all p?
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Baseline obesity status modifies effectiveness of adapted diabetes prevention program lifestyle interventions for weight management in primary care.
Biomed Res Int
PUBLISHED: 09-30-2013
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Objective. To examine whether baseline obesity severity modifies the effects of two different, primary care-based, technology-enhanced lifestyle interventions among overweight or obese adults with prediabetes and/or metabolic syndrome. Patients and Methods. We compared mean differences in changes from baseline to 15 months in clinical measures of general and central obesity among participants randomized to usual care alone (n = 81) or usual care plus a coach-led group (n = 79) or self-directed individual (n = 81) intervention, stratified by baseline body mass index (BMI) category. Results. Participants with baseline BMI 35+ had greater reductions in mean BMI, body weight (as percentage change), and waist circumference in the coach-led group intervention, compared to usual care and the self-directed individual intervention (P < 0.05 for all). In contrast, the self-directed intervention was more effective than usual care only among participants with baseline BMIs between 25 ? 35. Mean weight loss exceeded 5% in the coach-led intervention regardless of baseline BMI category, but this was achieved only among self-directed intervention participants with baseline BMIs <35. Conclusions. Baseline BMI may influence behavioral weight-loss treatment effectiveness. Researchers and clinicians should take an individuals baseline BMI into account when developing or recommending lifestyle focused treatment strategy. This trial is registered with ClinicalTrials.gov NCT00842426.
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Imbalance of interleukin-17+ T-cell and foxp3+ regulatory T-cell dynamics in rat periapical lesions.
J Endod
PUBLISHED: 09-09-2013
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Interleukin (IL)-17(+) T-helper (Th17) cells and Foxp3(+) regulatory T (Treg) cells are CD4(+) T-helper cells with reciprocal functions in immunology and bone metabolism. The present study aimed to investigate the expression dynamics of Th17 and Treg cells in rat periapical lesions as well as their correlation with bone resorption.
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A cytotoxicity study of fluorescent carbon nanodots using human bronchial epithelial cells.
J Nanosci Nanotechnol
PUBLISHED: 07-26-2013
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The labeling of living cells with carbon nanoparticles has been increasingly studied both in vivo and in vitro, but concerns about the potential cytotoxicity of these nanoprobes are also increasing. In this study, the fluorescent carbon dots (CDs) without surface modification was synthesized and evaluated for its cytotoxicity. Indicators including cell viability, total reactive oxygen species (ROS), glutathione, malondialdehyde and lactate dehydrogenase were assessed using human bronchial epithelial (16HBE) cell line. Our results showed that CDs preferred to locate on the surface of cells, which significantly increased the membrane permeability of 16HBE cells. CDs exposure could further induce oxidative stress, exhaust the antioxidant defenses of cells and finally lead to decreased cell viability. Therefore, surface modification of CDs is needed to minimize its cytotoxicity. The present work is useful for the development of new strategies towards the in vitro and in vivo applications of CDs for optical imaging and drug delivery.
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On the Kohn-Luttinger conundrum.
J Chem Phys
PUBLISHED: 06-08-2013
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Kohn and Luttinger [Phys. Rev. 118, 41 (1960)] showed that the conventional finite-temperature extension of the second-order many-body perturbation theory had the incorrect zero-temperature limit in metals and, on this basis, argued that the theory was incorrect. We show that this inconsistency arises from the noninclusion of the temperature effect in the energies of the zeroth-order eigenstates of the perturbation theory, which causes not only the Kohn-Luttinger conundrum but also another inconsistency with the zero-temperature many-body perturbation theory, namely, the different rates of divergence of the correlation energy in a homogeneous electron gas (HEG). We propose a renormalized many-body perturbation theory derivable from the finite-temperature extension of the normal-ordered second quantization applied to the denominators of the energy expression, which involves the energies of the zeroth-order states, as well as to the numerators. The renormalized theory is shown to have the correct zero-temperature limit and the same rate of divergence in a HEG as the zero-temperature counterpart, and is, therefore, the correct finite-temperature many-body perturbation theory.
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Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization.
J Chem Inf Model
PUBLISHED: 05-20-2013
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Docking programs that use scoring functions to estimate binding affinities of small molecules to biological targets are widely applied in drug design and drug screening with partial success. But accurate and efficient scoring functions for protein-ligand binding affinity still present a grand challenge to computational chemists. In this study, the polarized protein-specific charge model (PPC) is incorporated into the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method to rescore the binding poses of some protein-ligand complexes, for which docking programs, such as Autodock, could not predict their binding modes correctly. Different sampling techniques (single minimized conformation and multiple molecular dynamics (MD) snapshots) are used to test the performance of MM/PBSA combined with the PPC model. Our results show the availability and effectiveness of this approach in correctly ranking the binding poses. More importantly, the bridging water molecules are found to play an important role in correctly determining the protein-ligand binding modes. Explicitly including these bridging water molecules in MM/PBSA calculations improves the prediction accuracy significantly. Our study sheds light on the importance of both bridging water molecules and the electronic polarization in the development of more reliable scoring functions for predicting molecular docking and protein-ligand binding affinity.
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Transmembrane Protein 214 (TMEM214) mediates endoplasmic reticulum stress-induced caspase 4 enzyme activation and apoptosis.
J. Biol. Chem.
PUBLISHED: 05-09-2013
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Endoplasmic reticulum (ER) stress caused by excessive aggregation of misfolded proteins induces apoptosis. Although ER stress-induced apoptosis has been implicated in many diseases, the detailed mechanisms are not well understood. Here, we identified human transmembrane protein 214 (TMEM214) as a critical mediator of ER stress-induced apoptosis. Overexpression of TMEM214 induced apoptosis, whereas knockdown of TMEM214 inhibited ER stress-induced apoptosis. TMEM214 was localized on the outer membrane of the ER and constitutively associated with procaspase 4, which was also critical for ER stress-induced apoptosis. TMEM214-induced apoptosis was abolished by a dominant negative mutant of procaspase 4, whereas caspase 4-induced apoptosis was inhibited by knockdown of TMEM214. Furthermore, knockdown of TMEM214 inhibited the activation and cleavage of procaspase 4 by impairing its recruitment to the ER. Our findings suggest that TMEM214 is essential for ER stress-induced apoptosis by acting as an anchor for recruitment of procaspase 4 to the ER and its subsequent activation.
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Neuroimaging of six neurosyphilis cases mimicking viral encephalitis.
J. Neurol. Sci.
PUBLISHED: 05-08-2013
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Neurosyphilis is known as "the great imitator" due to its wide range of clinical symptoms and abnormalities upon magnetic resonance imaging (MRI). Typical findings of both neurosyphilis and viral encephalitis include unilateral or bilateral MR hyperintensities in mesiotemporal lobes upon T2-weighted imaging or fluid attenuation inversion recovery (FLAIR) imaging. Accordingly, patients with neurosyphilis are frequently misdiagnosed with viral encephalitis, which prevents them from receiving appropriate treatment and often results in greater neurologic damage.
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Thermal transparency with the concept of neutral inclusion.
Phys Rev E Stat Nonlin Soft Matter Phys
PUBLISHED: 04-25-2013
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The concept of the electromagnetic wave transparency is introduced into the thermal field. The conditions of the thermal transparency for a multilayered sphere with isotropic coatings, a coated spheroid with an isotropic coating, and a coated sphere with a radial anisotropic core or a radial anisotropic coat are deduced with the help of the idea of the neutral inclusion. The thermal transparency can be achieved by making the effective thermal conductivity of the composite inclusion equal to the thermal conductivity of the surrounding matrix. The validity of the theoretical analysis is checked by the corresponding simulated results, which indicate that the designed neutral inclusion can be transparent perfectly. A specific case of interest of the thermal transparency is its application to cancel the thermal stress concentration resulting from the existence of the inclusions in the particle (even the thermal-insulated particle) -reinforced composites.
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Predicting mutation-induced Stark shifts in the active site of a protein with a polarized force field.
J Phys Chem A
PUBLISHED: 04-05-2013
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The electric field inside a protein has a significant effect on the protein structure, function, and dynamics. Recent experimental developments have offered a direct approach to measure the electric field by utilizing a nitrile-containing inhibitor as a probe that can deliver a unique vibration to the specific site of interest in the protein. The observed frequency shift of the nitrile stretching vibration exhibits a linear dependence on the electric field at the nitrile site, thus providing a direct measurement of the relative electric field. In the present work, molecular dynamics simulations were carried out to compute the electric field shift in human aldose reductase (hALR2) using a polarized protein-specific charge (PPC) model derived from fragment-based quantum-chemistry calculations in implicit solvent. Calculated changes of electric field in the active site of hALR2 between the wild type and mutants were directly compared with measured vibrational frequency shifts (Stark shifts). Our study demonstrates that the Stark shifts calculated using the PPC model are in much better agreement with the experimental data than widely used nonpolarizable force fields, indicating that the electronic polarization effect is important for the accurate prediction of changes in the electric field inside proteins.
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A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.
J Mol Model
PUBLISHED: 03-29-2013
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Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.
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Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy.
J Phys Chem A
PUBLISHED: 03-27-2013
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An electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method is developed for efficient linear-scaling quantum mechanical (QM) calculation of protein energy. This approach is based on our previously proposed GMFCC/MM method (He; et al. J. Chem. Phys. 2006, 124, 184703), In this EE-GMFCC scheme, the total energy of protein is calculated by taking a linear combination of the QM energy of the neighboring residues and the two-body QM interaction energy between non-neighboring residues that are spatially in close contact. All the fragment calculations are embedded in a field of point charges representing the remaining protein environment, which is the major improvement over our previous GMFCC/MM approach. Numerical studies are carried out to calculate the total energies of 18 real three-dimensional proteins of up to 1142 atoms using the EE-GMFCC approach at the HF/6-31G* level. The overall mean unsigned error of EE-GMFCC for the 18 proteins is 2.39 kcal/mol with reference to the full system HF/6-31G* energies. The EE-GMFCC approach is also applied for proteins at the levels of the density functional theory (DFT) and second-order many-body perturbation theory (MP2), also showing only a few kcal/mol deviation from the corresponding full system result. The EE-GMFCC method is linear-scaling with a low prefactor, trivially parallel, and can be readily applied to routinely perform structural optimization of proteins and molecular dynamics simulation with high level ab initio electronic structure theories.
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Effect of acupuncture on target tissue distribution of Schisandra lignans.
Acupunct Med
PUBLISHED: 02-28-2013
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Recently, the combination of acupuncture and Chinese medicine as a practical strategy to treat diseases is receiving considerable attention worldwide as they are usually found to exhibit intriguing therapeutic effectiveness. The current study aimed to study the adjunct effect of acupuncture on target tissue distribution of schisandra lignans when acupuncture is combined with Schisandra chinensis.
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Inherited cardiomyopathies caused by troponin mutations.
J Geriatr Cardiol
PUBLISHED: 01-30-2013
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Genetic investigations of cardiomyopathy in the recent two decades have revealed a large number of mutations in the genes encoding sarcomeric proteins as a cause of inherited hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), or restrictive cardiomyopathy (RCM). Most functional analyses of the effects of mutations on cardiac muscle contraction have revealed significant changes in the Ca(2+)-regulatory mechanism, in which cardiac troponin (cTn) plays important structural and functional roles as a key regulatory protein. Over a hundred mutations have been identified in all three subunits of cTn, i.e., cardiac troponins T, I, and C. Recent studies on cTn mutations have provided plenty of evidence that HCM- and RCM-linked mutations increase cardiac myofilament Ca(2+) sensitivity, while DCM-linked mutations decrease it. This review focuses on the functional consequences of mutations found in cTn in terms of cardiac myofilament Ca(2+) sensitivity, ATPase activity, force generation, and cardiac troponin I phosphorylation, to understand potential molecular and cellular pathogenic mechanisms of the three types of inherited cardiomyopathy.
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Plant-soil feedbacks and soil sickness: from mechanisms to application in agriculture.
J. Chem. Ecol.
PUBLISHED: 01-15-2013
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Negative plant-soil feedbacks play an important role in soil sickness, which is one of the factors limiting the sustainable development of intensive agriculture. Various factors, such as the buildup of pests in the soil, disorder in physico-chemical soil properties, autotoxicity, and other unknown factors may contribute to soil sickness. A range of autotoxins have been identified, and these exhibit their allelopathic potential by influencing cell division, water and ion uptake, dark respiration, ATP synthesis, redox homeostasis, gene expression, and defense responses. Meanwhile, there are great interspecific and intraspecific differences in the uptake and accumulation of autotoxins, which contribute to the specific differences in growth in response to different autotoxins. Importantly, the autotoxins also influence soil microbes and vice versa, leading to an increased or decreased degree of soil sickness. In many cases, autotoxins may enhance soilborne diseases by predisposing the roots to infection by soilborne pathogens through a direct biochemical and physiological effect. Some approaches, such as screening for low autotoxic potential and disease-resistant genotypes, proper rotation and intercropping, proper soil and plant residue management, adoption of resistant plant species as rootstocks, introduction of beneficial microbes, physical removal of phytotoxins, and soil sterilization, are proposed. We discuss the challenges that we are facing and possible approaches to these.
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Brassinosteroid alleviates polychlorinated biphenyls-induced oxidative stress by enhancing antioxidant enzymes activity in tomato.
Chemosphere
PUBLISHED: 01-03-2013
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Polychlorinated biphenyls (PCBs) are persistent organic pollutants often found in the atmosphere. Phytoremediation of airborne PCBs is an emerging new concept to minimize potential human exposure. However, effects of atmospheric PCBs on plant growth, photosynthesis and antioxidant defence system are poorly understood area. Brassinosteroids have been reported to alleviate different abiotic stresses including organic pollutants-induced stress. Hence, we studied the effects of PCBs and 24-epibrassinolide (EBR) on biomass accumulation, photosynthetic machinery and antioxidant system in tomato plants. PCBs (0.4, 2.0 and 10 ?g/l) mist spray significantly decreased dry weight, photosynthesis, chlorophyll contents in a dose dependent manner. Both stomatal and non-stomatal factors were involved in PCBs-induced photosynthetic inhibition. Likewise, the maximal photochemical efficiency of PSII (Fv/Fm), the quantum efficiency of PSII photochemistry (?(PSII)) and photochemical quenching coefficient were increasingly decreased by various levels of PCBs, suggesting an induction of photoinhibition. Increased accumulation of H(2)O(2) and O(2)(-) accompanied with high lipid peroxidation confirmed occurrence of oxidative stress upon PCBs exposure. Meanwhile, antioxidant enzymes activity was decreased following exposure to PCBs. Foliar application of EBR (100 nM) increased biomass, photosynthetic capacity, chlorophyll contents and alleviated photoinhibition by enhancing Fv/Fm, ?(PSII) and qP. EBR significantly decreased harmful ROS accumulation and lipid peroxidation through the induction of antioxidant enzymes activity. Our results suggest a protective role of EBR against PCBs stress which may strengthen phytoremediation approaches by enhancing plant tolerance.
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The first complete genomic characterization of an Amur virus isolate from China.
Arch. Virol.
PUBLISHED: 01-02-2013
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Amur virus (AMRV) is a member of the genus Hantavirus in the family Bunyaviridae. In this study, we determined for the first time the complete genome sequence of the AMRV H8205 strain, which was isolated from a patient with hemorrhagic fever with renal syndrome (HFRS) in China. The complete nucleotide sequence of the S segment of AMRV H8205 is 1699 nt long, with a 5 noncoding region (5NC) of 36 nt, followed by a coding sequence of 1290 nt and a 3NC of 373 nt. The complete sequence of the M segment is 3615 nt long, with a 5NC of 40 nt, followed by a coding sequence of 3408 nt and a 3NC of 167 nt. The complete sequence of the L segment is 6536 nt long, with a 5NC of 37 nt, followed by a coding sequence of 6453 nt and a 3NC of 40 nt. The major open reading frame (ORF) of each of the three segments (S, nt 37-1326; M, nt 41-3445; L, nt 38-6490) has a coding capacity of 430 aa, 1135 aa, 2151 aa, respectively. Phylogenetic analysis of the nucleotide sequences using the NJ method indicated that H8205 virus, together with the Amur strains isolated from Far-Eastern Russia and Korea, forms a well-supported lineage. Our results will provide insights into the genetic diversity of hantaviruses (HNTV).
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The role of hydrogen peroxide and nitric oxide in the induction of plant-encoded RNA-dependent RNA polymerase 1 in the basal defense against Tobacco mosaic virus.
PLoS ONE
PUBLISHED: 01-01-2013
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Plant RNA-dependent RNA Polymerase 1 (RDR1) is an important element of the RNA silencing pathway in the plant defense against viruses. RDR1 expression can be elicited by viral infection and salicylic acid (SA), but the mechanisms of signaling during this process remains undefined. The involvement of hydrogen peroxide (H2O2) and nitric oxide (NO) in RDR1 induction in the compatible interactions between Tobacco mosaic tobamovirus (TMV) and Nicotiana tabacum, Nicotiana benthamiana, and Arabidopsis thaliana was examined. TMV inoculation onto the lower leaves of N. tabacum induced the rapid accumulation of H2O2 and NO followed by the increased accumulation of RDR1 transcripts in the non-inoculated upper leaves. Pretreatment with exogenous H2O2 and NO on upper leaf led to increased RDR1 expression and systemic TMV resistance. Conversely, dimethylthiourea (an H2O2 scavenger) and 2-(4-carboxyphenyl)- 4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (an NO scavenger) partly blocked TMV- and SA-induced RDR1 expression and increased TMV susceptibility, whereas pretreatment with exogenous H2O2 and NO failed to diminish TMV infection in N. benthamiana plants with naturally occurring RDR1 loss-of-function. Furthermore, in N. tabacum and A. thaliana, TMV-induced H2O2 accumulation was NO-dependent, whereas NO generation was not affected by H2O2. These results suggest that, in response to TMV infection, H2O2 acts downstream of NO to mediate induction of RDR1, which plays a critical role in strengthening RNA silencing to restrict systemic viral infection.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.