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1.
Sci Total Environ ; 719: 137461, 2020 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-32114235

RESUMO

The re-integration of trees into the urban landscape is a veritable strategy for urban climate mitigation and adaptation. However, dysfunctional trees in terms of urban heat mitigation are dominant in many sub-tropical cities' landscapes due to the lack of scientific basis of tree selection. Therefore, this study proposes and evaluates a methodological framework as an approach for "right tree, right place" for urban heat mitigation through parametric ENVI-met simulations that involve the combination of 54 generic tree forms and 10 characteristic urban morphology - Sky-View Factor (SVF). Results show variable temperature regulation by tree forms (species) with varying magnitude in different urban morphology. Daytime and nighttime temperature regulation effects were between 0.3 °C - 1.0 °C and 0.0 °C - 2.0 °C, respectively depending on tree forms and SVF value. Furthermore, the Heat Reduction Potential (HRP) of trees forms were determined in terms of their human thermal comfort improvement. In general, we found a range of +5% and - 20% depending on SVF, negative and positive values imply heat reduction and increment, respectively. With the competing shading effect of buildings, the HRP of trees reduces from high to low SVF area with variable magnitude among tree forms (species). Hence, the proposed morphology-based tree selection approach was evaluated by comparison with two uninformed selection approaches in a realistic urban neighborhood in Hong Kong. Results clearly indicate the proposed approach's capability in improving human thermal comfort by up two times more than either of the other approaches. Finally, evidence-based recommendations were given for the reference of policy-makers when they make urban green development plan.

2.
Nat Commun ; 11(1): 1507, 2020 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-32198345

RESUMO

Tumor cells often reprogram their metabolism for rapid proliferation. The roles of long noncoding RNAs (lncRNAs) in metabolism remodeling and the underlying mechanisms remain elusive. Through screening, we found that the lncRNA Actin Gamma 1 Pseudogene (AGPG) is required for increased glycolysis activity and cell proliferation in esophageal squamous cell carcinoma (ESCC). Mechanistically, AGPG binds to and stabilizes 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3). By preventing APC/C-mediated ubiquitination, AGPG protects PFKFB3 from proteasomal degradation, leading to the accumulation of PFKFB3 in cancer cells, which subsequently activates glycolytic flux and promotes cell cycle progression. AGPG is also a transcriptional target of p53; loss or mutation of TP53 triggers the marked upregulation of AGPG. Notably, inhibiting AGPG dramatically impaired tumor growth in patient-derived xenograft (PDX) models. Clinically, AGPG is highly expressed in many cancers, and high AGPG expression levels are correlated with poor prognosis, suggesting that AGPG is a potential biomarker and cancer therapeutic target.

3.
Sensors (Basel) ; 20(5)2020 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-32111084

RESUMO

Remote sensing images have been widely used in many applications. However, the resolution of the obtained remote sensing images may not meet the increasing demands for some applications. In general, the sparse representation-based super-resolution (SR) method is one of the most popular methods to solve this issue. However, traditional sparse representation SR methods do not fully exploit the complementary constraints of images. Therefore, they cannot accurately reconstruct the unknown HR images. To address this issue, we propose a novel adaptive joint constraint (AJC) based on sparse representation for the single remote sensing image SR. First, we construct a nonlocal constraint by using the nonlocal self-similarity. Second, we propose a local structure filter according to the local gradient of the image and then construct a local constraint. Next, the nonlocal and local constraints are introduced into the sparse representation-based SR framework. Finally, the parameters of the joint constraint model are selected adaptively according to the level of image noise. We utilize the alternate iteration algorithm to tackle the minimization problem in AJC. Experimental results show that the proposed method achieves good SR performance in preserving image details and significantly improves the objective evaluation indices.

4.
Exp Mol Pathol ; 114: 104405, 2020 Feb 19.
Artigo em Inglês | MEDLINE | ID: mdl-32084395

RESUMO

BACKGROUND: Obesity is associated with the impairment of cardiac fitness and consequent ventricular dysfunction and heart failure. Ghrelin has been largely documented to be cardioprotective against ischaemia/reperfusion injury. However, the role of ghrelin in obesity-induced myocardial injury is largely unknown. This study sought to determine the cardiac effect of ghrelin against obesity-induced injury and the underlying mechanisms. METHODS: The effect of ghrelin was evaluated in a mouse model of obesity and a palmitic acid (PA)-treated cardiomyocyte cell line with or without ghrelin transfection. Gene and protein expression levels were determined by real-time PCR and western blot, respectively. Cell apoptosis was measured by flow cytometry analysis. RESULTS: In the present study, we found that both a high-fat diet (HFD) and PA treatment caused myocardial injury by increasing apoptosis and the expression of inflammatory cytokines. Overexpression of ghrelin reversed the effects induced by HFD or PA treatment. Knockdown of lncRNA H19 or overexpression of miR-29a abrogated the cardioprotective effects of ghrelin against apoptosis and inflammation. We also found that IGF-1 was a target gene of miR-29a and that H19 regulated IGF-1 expression via miR-29a. Overexpression of IGF-1 partially reversed the apoptosis and inflammation promoting effects of miR-29a. CONCLUSIONS: Our findings suggested that ghrelin protected against obesity-induced myocardial injury by regulating the H19/miR-29a/IGF-1 signalling axis, providing further evidence for the clinical application of ghrelin.

5.
BMJ Open ; 10(2): e030854, 2020 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-32029484

RESUMO

OBJECTIVES: We employed a comprehensive systematic review and meta-analysis to assess benefits and risks of a threshold of haemoglobin level below 7 g/dL versus liberal transfusion strategy among critically ill patients, and even patients with septic shock. DESIGN: Systematic review and meta-analysis. DATA SOURCES: We performed systematical searches for relevant randomised controlled trials (RCTs) in the Cochrane Library, EMBASE and PubMed databases up to 1 September 2019. ELIGIBILITY CRITERIA: RCTs among adult intensive care unit (ICU) patients comparing 7 g/dL as restrictive strategy with liberal transfusion were incorporated. DATA EXTRACTION AND SYNTHESIS: The clinical outcomes, including short-term mortality, length of hospital stay, length of ICU stay, myocardial infarction (MI) and ischaemic events, were screened and analysed after data collection. We applied odds ratios (ORs) to analyse dichotomous outcomes and standardised mean differences (SMDs) to analyse continuous outcomes with fixed or random effects models based on heterogeneity evaluation for each outcome. RESULTS: Eight RCTs with 3415 patients were included. Compared with a more liberal threshold, a red blood cell (RBC) transfusion threshold <7 g/dL haemoglobin showed no significant difference in short-term mortality (OR: 0.90, 95% CI: 0.67 to 1.21, p=0.48, I2=53%), length of hospital stay (SMD: -0.11, 95% CI: -0.30 to 0.07, p=0.24, I2=71%), length of ICU stay (SMD: -0.03, 95% CI: -0.14 to 0.08, p=0.54, I2=0%) or ischaemic events (OR: 0.80, 95% CI: 0.43 to 1.48, p=0.48, I2=51%). However, we found that the incidence of MI (OR: 0.54, 95% CI: 0.30 to 0.98, p=0.04, I2=0%) was lower in the group with the threshold <7 g/dL than that with the more liberal threshold. CONCLUSIONS: An RBC transfusion threshold <7 g/dL haemoglobin is incapable of decreasing short-term mortality in ICU patients according to currently published evidences, while it might have potential role in reducing MI incidence.

6.
Autophagy ; : 1-17, 2020 Feb 12.
Artigo em Inglês | MEDLINE | ID: mdl-32048886

RESUMO

The structural integrity and functional stability of organelles are prerequisites for the viability and responsiveness of cells. Dysfunction of multiple organelles is critically involved in the pathogenesis and progression of various diseases, such as chronic obstructive pulmonary disease, cardiovascular diseases, infection, and neurodegenerative diseases. In fact, those organelles synchronously present with evident structural derangement and aberrant function under exposure to different stimuli, which might accelerate the corruption of cells. Therefore, the quality control of multiple organelles is of great importance in maintaining the survival and function of cells and could be a potential therapeutic target for human diseases. Organelle-specific autophagy is one of the major subtypes of autophagy, selectively targeting different organelles for quality control. This type of autophagy includes mitophagy, pexophagy, reticulophagy (endoplasmic reticulum), ribophagy, lysophagy, and nucleophagy. These kinds of organelle-specific autophagy are reported to be beneficial for inflammatory disorders by eliminating damaged organelles and maintaining homeostasis. In this review, we summarized the recent findings and mechanisms covering different kinds of organelle-specific autophagy, as well as their involvement in various diseases, aiming to arouse concern about the significance of the quality control of multiple organelles in the treatment of inflammatory diseases.Abbreviations: ABCD3: ATP binding cassette subfamily D member 3; AD: Alzheimer disease; ALS: amyotrophic lateral sclerosis; AMBRA1: autophagy and beclin 1 regulator 1; AMPK: AMP-activated protein kinase; ARIH1: ariadne RBR E3 ubiquitin protein ligase 1; ATF: activating transcription factor; ATG: autophagy related; ATM: ATM serine/threonine kinase; BCL2: BCL2 apoptosis regulator; BCL2L11/BIM: BCL2 like 11; BCL2L13: BCL2 like 13; BECN1: beclin 1; BNIP3: BCL2 interacting protein 3; BNIP3L/NIX: BCL2 interacting protein 3 like; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CANX: calnexin; CAT: catalase; CCPG1: cell cycle progression 1; CHDH: choline dehydrogenase; COPD: chronic obstructive pulmonary disease; CSE: cigarette smoke exposure; CTSD: cathepsin D; DDIT3/CHOP: DNA-damage inducible transcript 3; DISC1: DISC1 scaffold protein; DNM1L/DRP1: dynamin 1 like; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; EIF2S1/eIF2α: eukaryotic translation initiation factor 2 alpha kinase 3; EMD: emerin; EPAS1/HIF-2α: endothelial PAS domain protein 1; ER: endoplasmic reticulum; ERAD: ER-associated degradation; ERN1/IRE1α: endoplasmic reticulum to nucleus signaling 1; FBXO27: F-box protein 27; FKBP8: FKBP prolyl isomerase 8; FTD: frontotemporal dementia; FUNDC1: FUN14 domain containing 1; G3BP1: G3BP stress granule assembly factor 1; GBA: glucocerebrosidase beta; HIF1A/HIF1: hypoxia inducible factor 1 subunit alpha; IMM: inner mitochondrial membrane; LCLAT1/ALCAT1: lysocardiolipin acyltransferase 1; LGALS3/Gal3: galectin 3; LIR: LC3-interacting region; LMNA: lamin A/C; LMNB1: lamin B1; LPS: lipopolysaccharide; MAPK8/JNK: mitogen-activated protein kinase 8; MAMs: mitochondria-associated membranes; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MFN1: mitofusin 1; MOD: multiple organelles dysfunction; MTPAP: mitochondrial poly(A) polymerase; MUL1: mitochondrial E3 ubiquitin protein ligase 1; NBR1: NBR1 autophagy cargo receptor; NLRP3: NLR family pyrin domain containing 3; NUFIP1: nuclear FMR1 interacting protein 1; OMM: outer mitochondrial membrane; OPTN: optineurin; PD: Parkinson disease; PARL: presenilin associated rhomboid like; PEX3: peroxisomal biogenesis factor 3; PGAM5: PGAM family member 5; PHB2: prohibitin 2; PINK1: PTEN induced putative kinase 1; PRKN: parkin RBR E3 ubiquitin protein ligase; RB1CC1/FIP200: RB1 inducible coiled-coil 1; RETREG1/FAM134B: reticulophagy regulator 1; RHOT1/MIRO1: ras homolog family member T1; RIPK3/RIP3: receptor interacting serine/threonine kinase 3; ROS: reactive oxygen species; RTN3: reticulon 3; SEC62: SEC62 homolog, preprotein translocation factor; SESN2: sestrin2; SIAH1: siah E3 ubiquitin protein ligase 1; SNCA: synuclein alpha; SNCAIP: synuclein alpha interacting protein; SQSTM1/p62: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TFEB: transcription factor EB; TICAM1/TRIF: toll-like receptor adaptor molecule 1; TIMM23: translocase of inner mitochondrial membrane 23; TNKS: tankyrase; TOMM: translocase of the outer mitochondrial membrane; TRIM: tripartite motif containing; UCP2: uncoupling protein 2; ULK1: unc-51 like autophagy activating kinase; UPR: unfolded protein response; USP10: ubiquitin specific peptidase 10; VCP/p97: valosin containing protein; VDAC: voltage dependent anion channels; XIAP: X-linked inhibitor of apoptosis; ZNHIT3: zinc finger HIT-type containing 3.

7.
Neuromolecular Med ; 2020 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-31933131

RESUMO

As a type of stress, maternal separation (MS) has been one of the most widely used models in neuropsychiatric research. An increasing number of studies has found that MS not only affects the function of the hypothalamic-pituitary-adrenal axis and hippocampal 5-hydroxytryptamine system, but also causes dysfunction of the central dopamine (DA) system and increases the susceptibility of dopaminergic neurons to pathogenic factors of Parkinson's disease (PD), for instance, 6-hydroxydopamine, thus impairing motor function. We reviewed the impact of MS on the DA system and its correlation with PD and found the following: (1) discrepant effects of MS on the DA system have been reported; (2) MS is a good model to study the impact of stress on the occurrence and development of PD, however, unified modeling criteria of MS are required; (3) correlation between MS and PD may involve the impact of MS on the DA system, which however is not the only connection; (4) intervening measures can block pathways between MS and PD, which provides reference for the prevention of PD in specific populations such as left-behind children.

8.
Clin Nucl Med ; 45(3): 246-247, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31977456

RESUMO

A 46-year-old man underwent Tc-pyrophosphate scan to evaluate possible infiltrative myocardiopathy revealed by echocardiography. The images did not show abnormal cardiac activity. However, diffuse abnormal activity in the liver and spleen was noted. Pathological examination from the specimen acquired from hepatic biopsy demonstrated amyloidosis, light chain type.

9.
ISA Trans ; 2020 Jan 22.
Artigo em Inglês | MEDLINE | ID: mdl-31983417

RESUMO

This paper presents a structure-improved extended state observer (SESO) based trajectory tracking control scheme with application to an omnidirectional mobile robot. To alleviate the initial peaking phenomenon of the traditional extended state observer (TESO), a SESO with reduced order is proposed by improving the structure of TESO. Moreover, the designed SESO can achieve superior estimation performances. The total disturbances are estimated by SESO and then compensated in the controller. Then a phase-based nonlinear proportional-differential controller with time-varying gains is applied for high trajectory tracking performance. The stability of SESO and the closed-loop system are analyzed, respectively. Finally, the effectiveness of the proposed control scheme is validated through simulations in both frequency domain and time domain as well as experimental tests.

10.
Medicine (Baltimore) ; 99(2): e18700, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31914074

RESUMO

BACKGROUND: Delirium is a commonly occurred complication in the critically ill. Melatonin is an endogenous hormone exerting multiple biological effects, mainly in regulating diurnal rhythms, also in inflammatory process and immune response. We aimed to assess the efficacy of exogenous melatonergics in prevention of delirium. METHODS: PubMed, Cochrane Library, and Embase will be searched to identify randomized controlled trials published from 1960 to April 2019. Critically ill adult patients administrated with melatonergics will be included. The primary outcome measure will be the incidence of delirium. The secondary outcome measure will be the length of stay in intensive care unit. The pooled effects of dichotomous outcomes will be analyzed as risk ratio, and that of continuous outcomes will be analyzed using weighted mean difference. Subgroup and sensitivity analyses will be conducted. Funnel plots and/or Egger test will be done for the examination of publication bias. The quality of evidence resulting from this study will be evaluated using the GRADE methodology. Trial sequential analysis (TSA) will be done to test whether the evidence in our meta-analysis is reliable and conclusive. RESULT: The evidence to date of the melatonergics in prevention of delirium will be systematically reviewed and meta-analyzed with the GRADE level reported and TSA examined. CONCLUSION: The stronger evidence for the efficacy of melatonergics in prevention of delirium in critically ill patients will be provided for intensive care physicians. PROSPERO REGISTRATION NUMBER: CRD42019138863.


Assuntos
Estado Terminal , Delírio/prevenção & controle , Melatonina/administração & dosagem , Projetos de Pesquisa , Humanos , Unidades de Terapia Intensiva , Tempo de Internação
11.
J Neuroinflammation ; 17(1): 14, 2020 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-31924221

RESUMO

Sepsis-associated encephalopathy (SAE) is commonly complicated by septic conditions, and is responsible for increased mortality and poor outcomes in septic patients. Uncontrolled neuroinflammation and ischemic injury are major contributors to brain dysfunction, which arises from intractable immune malfunction and the collapse of neuroendocrine immune networks, such as the cholinergic anti-inflammatory pathway, hypothalamic-pituitary-adrenal axis, and sympathetic nervous system. Dysfunction in these neuromodulatory mechanisms compromised by SAE jeopardizes systemic immune responses, including those of neutrophils, macrophages/monocytes, dendritic cells, and T lymphocytes, which ultimately results in a vicious cycle between brain injury and a progressively aberrant immune response. Deep insight into the crosstalk between SAE and peripheral immunity is of great importance in extending the knowledge of the pathogenesis and development of sepsis-induced immunosuppression, as well as in exploring its effective remedies.

12.
Cell Cycle ; 19(4): 391-404, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31916488

RESUMO

N6-methyladenosine (m6A) is the most prevalent epigenetic modification of messenger RNA (mRNA) in higher eukaryotes; this modification is mainly catalyzed by a methyltransferase complex including methyltransferase-like 3 (METTL3) as a key factor. Although m6A modification has been proven to play an essential role in diverse biological processes, our knowledge of Mettl3 is still limited because Mettl3 mutations are lethal to embryos in both mammals and plants. In this study, we knocked down Mettl3 by microinjection of its specific short interfering RNAs (siRNAs) or morpholino into fully grown germinal vesicle (GV) oocytes. As a result, we demonstrated that knocking down Mettl3 in female germ cells severely inhibited oocyte maturation by decreasing mRNA translation efficiency and led to defects in the maternal-to-zygotic transition, probably due to its interference in disrupting mRNA degradation. The discovery from this study suggests that the reversible m6A modification has vital functions in mammalian oocyte maturation and pre-implantation embryonic development processes.

13.
Int J Biol Sci ; 16(1): 27-37, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31892843

RESUMO

Introduction: Sepsis is an intractable disorder, which is associated with high risk of organ dysfunction and even death, while its pathogenesis remains largely unclear. Our study aims to study the research trend on sepsis and host immune response, and compare the contribution of publications from different countries, institutions, journals and authors. Materials and Methods: We extracted all relevant publications with regard to sepsis and immune response during 1999-2019 from Web of Science. GraphPad Prism 6, and VOSviewer software were used to collect and analyze the publication trend in related field. Results: We identified a total of 1225 publications with citation frequency of 40511 times up to March 30, 2019. The United States accounted for the largest number of publications (36.3%), 51.9% of total citations as well as the highest H-index (72). The sum of publications from China ranked the second, while the overall citations (1935) and H-index (22) ranked the eighth and the seventh, respectively. Journal of Shock had published most papers related to the topic on sepsis and immune response. Ayala A SA, has published the most papers in this field (31), while Hotchkiss RS presented with the most citation frequency (3532). The keyword "regulatory T cell" appeared most recently with an average appearing years of 2014.0. The "immunosuppression related research" seemed to be the hotspot in relevant scope. Conclusions: The United States made the most outstanding contribution within this important field. There is a mismatch between the quantity and quality of publications from China. Latest progress can be tracked in journal of Shock. Immunosuppression related researches may be hotspots in the near future.

14.
Insect Biochem Mol Biol ; 118: 103314, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31926881

RESUMO

C-type lectins participate in hemocytic encapsulation as pattern recognition receptors; however, the molecular mechanisms underlying their function remain unknown. In this study, we determined that the encapsulation-promoting function of a C-type lectin, IML-10, may be related to its interaction with hemocytes in the agricultural pest Ostrinia furnacalis. IML-10 possesses two carbohydrate-recognition domains (CRDs) containing EPN and QPD motifs with 4 and 6 conserved cysteine residues, respectively. IML-10 was found to mainly be secreted by the fat body into the larval plasma, and its expression was induced by Sephadex A-25 beads. Anti-IML-10 antibodies inhibited encapsulation-promoting function of IML-10 in the larval plasma. The encapsulation rate of Sephadex A-25 beads decreased from approximately 90%-30% when expression of IML-10 in O. furnacalis larvae was inhibited by RNAi. Moreover, the Sephadex bead-encapsulating ability of hemocytes decreased to almost zero in O. furnacalis larvae with IML-10 knocked out by CRISPR/Cas9, with IML-10 expression clearly decreasing compared to that of the control. Similar to the larval plasma, recombinant IML-10 promoted Sephadex bead encapsulation by hemocytes. Immunohistochemistry analysis showed that IML-10 was able to bind to the surface of both granulocytes and plasmatocytes but not to Sephadex beads as foreign objects. Furthermore, recombinant IML-10 promoted hemocyte aggregation but not adhesion. Therefore, we speculate that IML-10 binds to the surface of hemocytes to promote their aggregation and further improve their encapsulation capacity. These results contribute to clarifying the function of insect C-type lectins in encapsulation.

15.
Cancer Med ; 9(1): 151-159, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31724334

RESUMO

BACKGROUND: Monosialotetrahexosylganglioside (GM1) is a neuroprotective glycosphingolipid that repairs nerves. Oxaliplatin-based chemotherapy is neurotoxic. This study assessed the efficacy of GM1 for preventing oxaliplatin-induced peripheral neurotoxicity (OIPN) in colorectal cancer (CRC) patients receiving oxaliplatin-based chemotherapy. METHODS: In total, 196 patients with stage II/III CRC undergoing adjuvant chemotherapy with mFOLFOX6 were randomly assigned to intravenous GM1 or a placebo. The primary endpoint was the rate of grade 2 or worse cumulative neurotoxicity (NCI-CTCAE). The secondary endpoints were chronic cumulative neurotoxicity (EORTC QLQ-CIPN20), time to grade 2 neurotoxicity (NCI-CTCAE or the oxaliplatin-specific neuropathy scale), acute neurotoxicity (analog scale), rates of dose reduction or withdrawal due to OIPN, 3-year disease-free survival (DFS) and adverse events. RESULTS: There were no significant differences between the arms in the rate of NCI-CTCAE grade 2 or worse neurotoxicity (GM1: 33.7% vs placebo: 31.6%; P = .76) or neuropathy measured by the EORTC QLQ-CIPN20 or time to grade 2 neurotoxicity using NCI-CTCAE and the oxaliplatin-specific neuropathy scale. GM1 substantially decreased participant-reported acute neurotoxicity (sensitivity to cold items [P < .01], discomfort swallowing cold liquids [P < .01], throat discomfort [P < .01], muscle cramps [P < .01]). The rates of dose reduction or withdrawal were not significantly different between the arms (P = .08). The 3-year DFS rates were 85% and 83% in the GM1 and placebo arms, respectively (P = .19). There were no differences in toxicity between the arms. CONCLUSION: Patients receiving GM1 were less troubled by the symptoms of acute neuropathy. However, we do not support the use of GM1 to prevent cumulative neurotoxicity. (ClinicalTrials.gov number, NCT02251977).

16.
Neural Netw ; 122: 289-307, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31739268

RESUMO

The learning problem from imbalanced data sets poses a major challenge in data mining community. Although conventional support vector machine can generally show relatively robust performance in dealing with the classification problems of imbalanced data sets, it treats all training samples with the same contribution for learning, which results in the final decision boundary biasing toward the majority class especially in the presence of outliers or noises. In this paper, we propose a new affinity and class probability-based fuzzy support vector machine technique (ACFSVM). The affinity of a majority class sample is calculated according to support vector description domain (SVDD) model trained only by the given majority class training samples in kernel space similar to that used for FSVM learning. The obtained affinity can be used for identifying possible outliers and some border samples existing in the majority class training samples. In order to eliminate the effect of noises, we employ the kernel k-nearest neighbor method to determine the class probability of the majority class samples in the same kernel space as before. The samples with lower class probabilities are more likely to be noises and their contribution for learning seems to be reduced by their low memberships constructed by combining the affinities and the class probabilities. Thus, ACFSVM can pay more attention to the majority class samples with higher affinities and class probabilities while reducing their effects of the ones with lower affinities and class probabilities, eventually skewing the final classification boundary toward the majority class. In addition, the minority class samples are assigned relative high memberships to guarantee their importance for the model learning. The extensive experimental results on the different imbalanced datasets from UCI repository demonstrate that the proposed approach can achieve better generalization performance in terms of G-Mean, F-Measure, and AUC as compared to the other existing imbalanced dataset classification techniques.

17.
Biotechnol Bioeng ; 117(2): 318-329, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31631320

RESUMO

Protein engineering is a powerful tool for improving the properties of enzymes. However, large changes in enzyme properties are still challenging for traditional evolution strategies because they usually require multiple amino acid substitutions. In this study, a feasible evolution approach by a combination of fragment swapping and semi-rational design was developed for the engineering of nitrilase. A chimera BaNIT harboring 12 amino acid substitutions was obtained using nitrilase from Arabis alpine (AaNIT) and Brassica rapa (BrNIT) as parent enzymes, which exhibited higher enantioselectivity and activity toward isobutylsuccinonitrile for the biosynthesis of pregabalin precursor. The semi-rational design was executed on BaNIT to further generate variant BaNIT/L223Q/H263D/Q279E with the concurrent improvement of activity, enantioselectivity, and solubility. The robust nitrilase displayed a 5.4-fold increase in whole-cell activity and the enantiomeric ratio (E) increased from 180 to higher than 300. Molecular dynamics simulation and molecular docking demonstrated that the substitution of residues on the A and C surface contributed to the conformation alteration of nitrilase, leading to the simultaneous enhancement of enzyme properties. The results obtained not only successfully engineered the nitrilase with great industrial potential for the production of pregabalin precursor, but also provided a new perspective for the development of novel industrially important enzymes.

18.
J Environ Sci (China) ; 88: 209-216, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31862062

RESUMO

Cell wall polysaccharides play a vital role in binding with toxic metals such as copper (Cu) ions. However, it is still unclear whether the major binding site of Cu in the cell wall varies with different degrees of Cu stresses. Moreover, the contribution of each cell wall polysaccharide fraction to Cu sequestration with different degrees of Cu stresses also remains to be verified. The distribution of Cu in cell wall polysaccharide fractions of castor (Ricinus communis L.) root was investigated with various Cu concentrations in the hydroponic experiment. The results showed that the hemicellulose1 (HC1) fraction fixed 44.9%-67.8% of the total cell wall Cu under Cu stress. In addition, the pectin fraction and hemicelluloses2 (HC2) fraction also contributed to the Cu binding in root cell wall, accounting for 11.0%-25.9% and 14.1%-26.6% of the total cell wall Cu under Cu treatments, respectively. When the Cu levels were ≤25 µmol/L, pectin and HC2 contributed equally to Cu storage in root cell wall. However, when the Cu level was higher than 25 µmol/L, the ability of the pectin to bind Cu was easy to reach saturation. Much more Cu ions were bound on HC1 and HC2 fractions, and the HC2 played a much more important role in Cu binding than pectin. Combining fourier transform infrared (FT-IR) and two-dimensional correlation analysis (2D-COS) techniques, the hemicellulose components were showed not only to accumulate most of Cu in cell wall, but also respond fastest to Cu stress.

19.
PeerJ ; 7: e8101, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31824761

RESUMO

Background: Hepatocellular carcinoma (HCC) is the most common primary liver cancer in the world, with a high degree of malignancy and recurrence. The influence of the ceRNA network in tumor on the biological function of liver cancer is very important, It has been reported that many lncRNA play a key role in liver cancer development. In our study, integrated data analysis revealed potential eight novel lncRNA biomarkers in hepatocellular carcinoma. Methods: Transcriptome data and clinical data were downloaded from the The Cancer Genome Atlas (TCGA) data portal. Weighted gene co-expression network analysis was performed to identify the expression pattern of genes in liver cancer. Then, the ceRNA network was constructed using transcriptome data. Results: The integrated analysis of miRNA and RNAseq in the database show eight novel lncRNAs that may be involved in important biological pathways, including TNM and disease development in liver cancer. We performed function enrichment analysis of mRNAs affected by these lncRNAs. Conclusions: By identifying the ceRNA network and the lncRNAs that affect liver cancer, we showed that eight novel lncRNAs play an important role in the development and progress of liver cancer.

20.
Sci Rep ; 9(1): 18848, 2019 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-31827216

RESUMO

Local climate zone (LCZ) maps that describe the urban surface structure and cover with consistency and comparability across cities are gaining applications in studies of urban heat waves, sustainable urbanization and urban energy balance. Following the standard World Urban Database and Access Portal Tools (WUDAPT) method, we generated LCZ maps for over 20 individual cities and 3 major economic regions in China. Based on the confusion matrices constructed by manual comparison between the predicted classes and ground truths, we highlight the following: (1) notable variation in overall accuracies (i.e., 60%-89%) among cities were observed, which was mainly due to class incompleteness and distinct proportions of natural landscapes; (2) building classes in selected cities were poorly classified in general, with a mean accuracy of 48%; (3) the sparsely built class (i.e., LCZ 9), which is rare in the selected Chinese cities, had the lowest classification accuracy (32% on average), and the class of low plants had the widest accuracy range. The findings indicate that the standard WUDAPT method alone is insufficient for generating LCZ products that demonstrate practical value, especially for built-up areas in China, and the misclassification is largely caused by the lack of building height data. This result is confirmed by a refinement test, in which the urban DEM retrieved from Sentinel-1 data with radar interferometry technique was used. The study shows a detailed and comprehensive assessment of applying the WUDAPT method in China and a feasible refinement strategy to improve the classification accuracy, especially for the built-up types of LCZ. The study could serve as a useful reference for generating quality-ensured LCZ maps. This study also examines and explores the relationship between socio-economic status and LCZ products, which is essential for further implementations.

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