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Identifying essential proteins is very important for understanding the minimal requirements of cellular survival and development. Fast growth in the amount of available protein--protein interactions has produced unprecedented opportunities for detecting protein essentiality on network level. A series of centrality measures have been proposed to discover essential proteins based on network topology. Unfortunately, the protein--protein interactions produced by highthroughput experiments generally have high false positives. Moreover, most of centrality measures based on network topology are sensitive to false positives. We therefore propose a new method for evaluating the confidence of each interaction based on the combination of logistic regression-based model and function similarity. Nine standard centrality measures in weighted network were redefined in this paper. The experimental results on a yeast protein interaction network shows that the weighting method improved the performance of centrality measures considerably. More essential proteins were discovered by the weighted centrality measures than by the original centrality measures used in the unweighted network. Even about 20% improvements were obtained from closeness centrality and subgraph centrality. [ABSTRACT FROM AUTHOR]

Knocking is the main obstacle of increasing the compression ratio in order to improve the thermal efficiency of gasoline engines. This paper proposes a concept of a stratified stoichiometric mixture (SSM) with two-zone homogeneity (TZH)for suppressing knocking and validated the concept by means of a numerical simulation and an experimental study in a DISI engine. The results show that the SSM can effectively suppress knocking and the knocking intensity decreases when the zone around the spark plug is richer and the end-gas zone is leaner. The less rich zone (fuel/air equivalent ratio of Φ≤l .2) of the SSM can speed up the initial burning velocity in order to avoid a thermal efficiency decrease, while the over rich zone (Φ>1.2) would decrease the combustion velocity when knocking was suppressed. The SSM leads to higher CO and lower HC and NOx emissions, which can be effectively after-treated using a three-way catalyst. The SSM can also reduce the decrease of power output compared to the method of retarding spark timing for suppressing knocking and has better fuel economy and fewer emissions than the method of enriching the mixture. The TZH can effectively alleviate combustion deterioration and soot formation due to the stratified mixture combustion. As a result, the SSM with TZH suppresses knocking, thus simultaneously lowering fuel consumption and emissions. [ABSTRACT FROM AUTHOR]

Imidazo[1,5-a]pyrazines 1undergo regioselective C3-metalation and C5/C3-dimetalation to afford a range of functionalized derivatives 2a−2g(Table 1), and 4a−4d(Table 2). Under similar conditions, the C3-methyl derivatives 2aand 5undergo surprising regioselective C5-deprotonation to afford, after electrophile quench, products 4b and 6a−6p(Table 3), results that are rationalized by quantum mechanical calculations. Benzamide 7b, obtained from such metalation chemistry followed by Suzuki cross coupling, undergoes directed remote metalation-cyclization to afford 8, representing the hitherto unknown triazadibenzo[cd,f]azulen-7(6H)-one tricyclic ring system. [ABSTRACT FROM AUTHOR]

A general and efficient synthesis of 5-aryl imidazo[1,5- a]pyrazines by palladium-catalyzed coupling of the corresponding 8-substituted derivatives with aryl halides is described. The scope of this new reaction for the imidazo[1,5- a]pyrazine ring system was explored using three readily available 8-substituted precursors, X = NH 2, NMe 2, and OMe, as well as 8-aryl derivatives, X = Ar′. On the basis of these results as well as studies using a deuterated derivative, a Heck-like mechanism is proposed for this transformation. [ABSTRACT FROM AUTHOR]

Monoconidial isolates of 33 carbendazim-sensitive isolates and 31 carbendazim-resistant isolates of Fusarium graminearum were selected from three regions of China for vegetative compatibility group (VCG) analysis. A total of 213 and 224 nil mutants were recovered from the 33 sensitive and the 31 resistant isolates, respectively. Of all the nit mutants, the frequency of the different phenotypes was 44.6, 46.5, 5.7, and 3.2% for nit1, nit3, nitM, and nitA, respectively. VCG analysis identified 30 different VCOs among the 33 sensitive- and the 31 carbendazim-resistant isolates, with VCG diversity 0.91 and 0.97, respectively. Both, a car- bendazim-sensitive and a -resistant isolate from the same field belonged to the same VCG. In all then, a total of 59 VCGs were identified among the 64 isolates with an overall VCG diversity 0.92. Direct hyphal fusion was observed in six pairs of vegetatively compatible complements, which is evidence of heterokaryon formation. It was hypothesized that carbendazim resistance could not be transferred by hyphal fusion or there is a small chance to be transferred between two compatible isolates. Three stable sexual recombinants of F graminearum were randomly chosen from each of the three genetic crosses to study their biological properties. There were no significant differences in mycelial linear growth and pathogenicity between recombinants and their parents, but they differ in sporulation ability and capacity to produce perithecia. We concluded that sexual recombination presumably played a role in the development of carbendazim resistance under field conditions. [ABSTRACT FROM AUTHOR]

In this paper, a multimode combustion system was developed in a gasoline direct injection engine. A two-stage fuel-injection strategy, including flexible injection timings and flexible fuel quantity, is adopted as a main means to form desired mixture in the cylinder. The combustion system can realize five combustion modes. The homogeneous charge spark ignition (HCSI) mode was used at high load to achieve high-power output density; stratified charge spark ignition (SCSI) was adopted at intermediate load to get optimum fuel economy; stratified charge compression ignition (SCCI) was introduced at transient operation between SI and CI mode. Homogeneous charge compression ignition (HCCI) was utilized at part load to obtain ultralow emissions. Reformed charge compression ignition (RCCI) was imposed at low load to extend the HCCI operation range. In SI mode, the stratified concentration is formed by introducing a second fuel injection in the compression stroke. This kind of stratified mixture has a faster heat release than the homogeneous mixture and is primarily optimized to reduce the fuel consumption. In CI mode, the cam phase configurations are switched from positive valve overlap to negative valve overlap (NVO). The test results reveal that the CI combustion is featured with a high gradient pressure after ignition and has advantages in high thermal efficiency and low NOx emissions over SI combustion at part load. [ABSTRACT FROM AUTHOR]

Homogeneous Charge Compression Ignition (HCCI) has challenges of ignition control. In this paper, HCCI ignition timing and combustion rate were controlled by two-stage direct injection (TSDI) strategies on a four, stroke gasoline HCCI engine. TSDI strategy was proposed to solve the two major problems of HCCI application-ignition control and load extension. Both simulation and experiments were carried out on a gasoline HCCI engine with negative valve overlap (NVO). An engine model with detailed chemical kinetics was established to study the gas exchange process and the direct injection strategy in the gasoline HCCI engine with TSDI and NVO. Simulation results were compared with experiments and good agreement was achieved. The simulated and experimental results provided a detailed insight into the processes governing ignition in the HCCI engine. Using TSDI, the fuel concentration, temperature as well as chemical species can be controlled. The effects of different injection parameters, such as split injection ratio and start-of-injection (SOI) timing, were studied. The experimental results indicate that, two-stage direct injection is a practical technology to control the ignition timing and combustion rate effectively in four-stroke gasoline HCCI engines. Both the high load and low load limits of HCCI operation were extended. [ABSTRACT FROM AUTHOR]

Starting from commercially available (+)-sclareolide, the first synthesis of zerumin B was achieved by a concise, highly efficient pathway featuring stereoselective addition of a new silyloxyfuryltitanium reagent to an aldehyde intermediate and silyloxyfuran oxyfunctionalization as key steps. The synthesis established the relative and absolute configuration of zerumin B along with its identity with a purportedly new diterpenoid isolated from the plant Renealmia alpinia. [ABSTRACT FROM AUTHOR]

The effect of ethanol blended gasoline fuels on emissions and catalyst conversion efficiencies was investigated in a spark ignition engine with an electronic fuel injection (EFI) system. The addition of ethanol to gasoline fuel enhances the octane number of the blended fuels and changes distillation temperature. Ethanol can decrease engine-out regulated emissions. The fuel containing 30% ethanol by volume can drastically reduce engine-out total hydrocarbon emissions (THC) at operating conditions and engine-out THC, CO and NOx emissions at idle speed, but unburned ethanol and acetaldehyde emissions increase. Pt/Rh based three-way catalysts are effective in reducing acetaldehyde emissions, but the conversion of unburned ethanol is low. Tailpipe emissions of THC, CO and NOx have close relation to engine-out emissions, catalyst conversion efficiency, engine''s speed and load, air/fuel equivalence ratio. Moreover, the blended fuels can decrease brake specific energy consumption. [Copyright &y& Elsevier]

The structure of ottensinin, a recently reported constituent of the medicinal plant Zingiber ottensii, was revised by re-evaluation of available NMR data from α-ylidenebutenolide 1to γ-pyrone 2, whose rearranged labdane skeleton is unprecedented. Structure 2was proven by synthesis from (+)-sclareolide (nine steps, 27% overall yield) and was further validated by X-ray diffraction analysis of our synthetic sample. A plausible biosynthesis of 2is proposed. [ABSTRACT FROM AUTHOR]

Optimal disease management depends on the ability to monitor the development of fungicide resistance in plant pathogen populations. Benzimidazole resistance is caused by the point mutations of the P-tubulin gene in Botrytis cinerea, and three mutations (E198A, E198K, and E198V) at codon 198 account for more than 98% of all resistant strains. Although traditional methods remain a cornerstone in monitoring fungicide resistance, molecular methods that do not require the isolation of pathogens can detect resistance alleles present at low frequencies, and require less time and labor than traditional methods. In this study, we present an efficient, rapid, and highly specific method for detecting highly benzimidazole-resistant B. cinerea isolates based on loop-mediated isothermal amplification (LAMP). By using specific primers, we could simultaneously detect all three resistance-conferring mutations at codon 198. The LAMP reaction components and conditions were optimized, and the best reaction temperatures and times were 60 to 62°C and 45 min, respectively. When B. cinerea field isolates were assessed for benzimidazole resistance, similar results were obtained with LAMP, minimal inhibition concentration, and sequencing. The LAMP assay developed in the current study was highly suitable for detection of highly benzimidazoleresistant field isolates of B. cinerea. [ABSTRACT FROM AUTHOR]

Background: Identification of protein complexes is crucial for understanding principles of cellular organization and functions. As the size of protein-protein interaction set increases, a general trend is to represent the interactions as a network and to develop effective algorithms to detect significant complexes in such networks. Results: Based on the study of known complexes in protein networks, this paper proposes a new topological structure for protein complexes, which is a combination of subgraph diameter (or average vertex distance) and subgraph density. Following the approach of that of the previously proposed clustering algorithm DPClus which expands clusters starting from seeded vertices, we present a clustering algorithm IPCA based on the new topological structure for identifying complexes in large protein interaction networks. The algorithm IPCA is applied to the protein interaction network of Sacchromyces cerevisiae and identifies many well known complexes. Experimental results show that the algorithm IPCA recalls more known complexes than previously proposed clustering algorithms, including DPClus, CFinder, LCMA, MCODE, RNSC and STM. Conclusion: The proposed algorithm based on the new topological structure makes it possible to identify dense subgraphs in protein interaction networks, many of which correspond to known protein complexes. The algorithm is robust to the known high rate of false positives and false negatives in data from high-throughout interaction techniques. The program is available at http:// netlab.csu.edu.cn/bioinformatics/limin/IPCA. [ABSTRACT FROM AUTHOR]

This work investigates the effect of surface fields on the dynamic resistance of a planar HgCdTe mid-wavelength infrared photodiode from both theoretical and experimental aspects, considering a gated n-on-p diode with the surface potential of its p-region modulated. Theoretical models of the surface leakage current are developed, where the surface tunnelling current in the case of accumulation is expressed by modifying the formulation of bulk tunnelling currents, and the surface channel current for strong inversion is simulated with a transmission line method. Experimental data from the fabricated devices show a flat-band voltage of VFB = -5.7 V by capacitance-voltage measurement, and then the physical parameters for bulk properties are determined from the resistance-voltage characteristics of the diode working at a flat-band gate voltage. With proper values of the modeling parameters such as surface trap density and channel electron mobility, the theoretical R0A product and corresponding dark current calculated from the proposed model as functions of the gate voltage Vg demonstrate good consistency with the measured values. The R0A product remarkably degenerates when Vg is far below or above VFB because of the surface tunnelling current or channel current, respectively; and it attains the maximum value of 5:7 x 107 Ω ⋅ cm² around the transition between surface depletion and weak inversion when Vg ≈ -4 V, which might result from reduced generation-recombination current. [ABSTRACT FROM AUTHOR]

A generalized transmission line model (TLM) and a compatible numerical method have been proposed to characterize metal-semiconductor contacts that exhibit nonlinear properties. This model and method have been applied to the analysis of Au/Sn/p-HgCdTe contact and have realized determination of related physical parameters by fitting experimental data. Our model's merit of avoiding the overestimation of barrier height active contact area encountered in other methods without TLM scheme is discussed. In addition, only by using this model, the transfer length can be credibly determined in the case of nonlinear contacts. [ABSTRACT FROM AUTHOR]

Scandia-ceria-stabilized zirconia (ScCeSZ) is one of the most important electrolytes used for solid oxide fuel cells. However, it has not been reported for applications in electrolyte gated transistors. Here, a high room-temperature proton conductivity of ~8  ×  10−3 S cm−1 and a large electric-double-layer capacitance of ~1.5 μF cm−2 are observed for a tape-casted water-infiltrated ScCeSZ electrolyte. A laterally coupled indium-tin oxide transistor gated by such an electrolyte exhibits good electric performances at a low voltage of 1.5 V, such as the on/off ratio of above 1  ×  105, mobility of 2.2 cm2 Vs−1 and subthreshold swing of ~160 mV/dec. Furthermore, unique synergic proton modulation behaviors are observed and AND logic operation is demonstrated. The laterally-coupled oxide transistors with synergic proton gating effects may find potential applications in chemical sensors and artificial neuromorphic devices. [ABSTRACT FROM AUTHOR]

Background: The cause of idiopathic pulmonary fibrosis (IPF) remains unknown, yet gastro-esophageal reflux disease (GERD) is highly prevalent in this population. GERD prevalence was studied, and esophageal function tests (EFT) were assessed in Chinese IPF patients. Methods: We prospectively studied 69 IPF patients who undertook both stationary High Resolution esophageal Manometry/Impedance (HRiM) and 24-hour esophageal Multi-Channel Intraluminal Impedance with pH Recordings (MII/pH). Patients were divided into GERD+ and GERD- groups according to pH results. Controls were HRiM treated healthy volunteers, and patients without IPF received HRiM and MII/pH diagnosed with GERD. Results: 69 IPF patients, 62 healthy volunteers, and 88 IPF negative GERD patients were selected. GERD prevalence in IPF was 43/69 (62.3%), and 58.1% of patients presented with at least one typical symptom. Symptoms had a sensitivity of 58.1%, a specificity of 61.6%, a positive predictive value of 71.4% and a negative predictive of 47.1%. Compared with healthy volunteers, IPF patients had significantly decreased lower esophageal sphincter pressure (LESP), upper esophageal sphincter pressure (UESP) and complete bolus transit rate (CBTR). By contrast, IPF patients had increased total bolus transit time and prevalence of weak peristalsis. MII/pH showed that one third of IPF patients had abnormal distal and proximal reflux, especially non-acid reflux. Compared with GERD patients without IPF, GERD patients with IPF had significantly decreased CBTR and UESP with increased bolus exposure time. Conclusions: GERD prevalence in IPF was high, but symptoms alone were an unreliable predictor of reflux. IPF patients had lower LESP and UESP, impaired esophageal peristalsis and bolus clearance function with more proximal reflux events. [ABSTRACT FROM AUTHOR]

Water scarcity is a critical policy issue in the arid regions of northwest China. The local government has widely adopted integrated water resources management (IWRM), but lacks support from farmers and farm communities. We undertook a case study in the Minqin oasis of northwest China to examine farmers' responses to IWRM and understand why farmer water users' associations (WUAs) are not functioning effectively at the community level. Results of quantitative and qualitative surveys of 392 farmers in 27 administrative villages showed that over 70% of farmers disapprove of the IWRM market-based reforms. In particular, the failure of farmer WUAs can be attributed to overlapping organizational structures between the WUAs and the villagers' committees; mismatches between the organizational scale of the WUAs and practical irrigation management by the farmers themselves; marginalization of rural women in water decision-making processes; and the inflexibility of IWRM implementation. An important policy implication from this study is that rebuilding farmer WUAs is key to overcoming the difficulties of IWRM. The current water governance structure, which is dominated by administrative systems, must be thoroughly reviewed to break the vicious cycle of tension and distrust between farmers and the government. [ABSTRACT FROM AUTHOR]

The efficacy of carbendazim-8-oxyquinoline-copper (BCOC), which is a chelate of carbendazim (MBC) and oxine-copper (BHC), was compared with that of MBC and BHC for control of Fusarium graminearum. In vitro inhibition of MBC-resistant (MBCR) strains was greater with BCOC than with MBC or BHC, or the mixture of MBC and BHC; the minimum inhibitory concentration (MIC) of MBC-high-resistant strains for BCOC was 10 times lower than the MIC for MBC. Appearance of germ tubes of F. graminearum was similar after treating with BCOC or MBC. The EC50 of BCOC was 1.29±0.61 µmg/mL against 124 F. graminearum field strains collected in 2010 and 3.23±0.41 µg/mL against 127 F. graminearum MBCR field strains collected between 2000 and 2010. BCOC provided best protective and curative control of Fusarium head blight on wheat artificially inoculated with both MBCS (MBC sensitive) and MBCR strains in the field. To explain the high efficacy of BCOC, we hypothesize that the 8-oxyquinoline-copper in BCOC changes the molecule's structure and thereby increases the interaction between the carbendazim radical in BCOC and the β2-tubulin protein in F. graminearum. BCOC has substantial potential for the synthesis of new fungicides for disease control and resistance management. [ABSTRACT FROM AUTHOR]

Rice leaves with bacterial blight or bacterial leaf streak symptoms were collected in southern China in 2007 and 2008. Five hundred and thirty-four single-colony isolates of Xanthomonas oryzae pv. oryzae and 827 single-colony isolates of Xanthomonas oryzae pv. oryzicola were obtained and tested on plates for sensitivity to streptomycin. Four strains (0.75%) of X. oryzae pv. oryzae isolated from the same county of Province Yunnan were resistant to streptomycin, and the resistance factor (the ratio of the mean median effective concentration inhibiting growth of resistant isolates to that of sensitive isolates) was approximately 226. The resistant isolate also showed streptomycin resistance in vivo. In addition to resistant isolates, isolates of less sensitivity were also present in the population of X. oryzae pv. oryzae from Province Yunnan. However, no isolates with decreased streptomycin-sensitivity were obtained from the population of X. oryzae pv. oryzicola. Mutations in the rpsL (encoding S12 protein) and rrs genes (encoding 16S rRNA) and the presence of the strA gene accounting for streptomycin resistance in other phytopathogens or animal and human pathogenic bacteria were examined on sensitive and resistant strains of X. oryzae pv. oryzae by polymerase chain reaction amplification and sequencing. Neither the presence of the strA gene nor mutations in the rpsL or rrs were found, suggesting that different resistance mechanisms are involved in the resistant isolates of X. oryzae pv. oryzae. [ABSTRACT FROM AUTHOR]

Wheat head blight caused by Gibberella zeae (anamorph: Fusarium graminearum) is a threat to food safety in China because of mycotoxin contamination of the harvested grain, the frequent occurrence of the disease, and the failure of chemical control in some areas due to benzimidazole resistance in the pathogen population. The molecular resistance mechanism, however, of G. zeae to benzimidazole fungicides (especially carbendazim; active ingredient: methyl benzimidazol-2-yl carbamate [MBC]) is poorly understood. DNA sequences of a β-tubulin. gene (P2tub) (GenBank access number FG06611.1) in G. zeae were analyzed. Mutations in p2tub in moderately resistant strains (MBCMR) included TTT (Phe)→TAT (Tyr) at codon 167 or TTC (Phe)→ TAC (Tyr) at codon 200. A highly resistant strain (MBCHR) had two point mutations, one at codon 73, CAG (Gln) → CGG (Arg), and the other at codon 198, GAG (Glu)→CTG (Leu). To confirm that mutations in the B2tub confer resistance to benzimidazole fungicides, the entire β2Tub locus was deleted from MBCMR and MBCHR strains of G. zeae. The resulting Δβ2tub mutants from both MBCMR and MBCHR strains grew normally on MBC-free potato dextrose agar medium and were supersensitive to MBC. Complementation of the Δβ2tub mutants by transformation with a copy of the intact β2Tub locus from their parent strains exhibited less resistance than the original strains, and complementation of the Δβ2tub mutants by transformation with a copy of the intact β2Tub locus from sensitive strains restored MBC sensitivity. The results indicated that the mutations in the β2tub gene conferred resistance of G. zeae to benzimidazole fungicides and this gene can be used as a genetic marker in G. zeae. [ABSTRACT FROM AUTHOR]

Mycobacterium tuberculosis, the etiological agent of TB, possesses a cholesterol catabolic pathway implicated in pathogenesis. This pathway includes an iron-dependent extradiol dioxygenase, HsaC, that cleaves catechols. Immunocompromised mice infected with a DhsaC mutant of M. tuberculosis H37Rv survived 50% longer than mice infected with the wild-type strain. In guinea pigs, the mutant disseminated more slowly to the spleen, persisted less successfully in the lung, and caused little pathology. These data establish that, while cholesterol metabolism by M. tuberculosis appears to be most important during the chronic stage of infection, it begins much earlier and may contribute to the pathogen's dissemination within the host. Purified HsaC efficiently cleaved the catecholic cholesterol metabolite, DHSA (3,4-dihydroxy-9,10- seconandrost-1,3,5(10)-triene-9,17-dione; kcat/Km = 14.4±0.5 μM-1 s-1), and was inactivated by a halogenated substrate analogue (partition coefficient,50). Remarkably, cholesterol caused loss of viability in the DhsaC mutant, consistent with catechol toxicity. Structures of HsaC:DHSA binary complexes at 2.1 Å revealed two catechol-binding modes: bidentate binding to the active site iron, as has been reported in similar enzymes, and, unexpectedly, monodentate binding. The position of the bicyclo-alkanone moiety of DHSA was very similar in the two binding modes, suggesting that this interaction is a determinant in the initial substrate-binding event. These data provide insights into the binding of catechols by extradiol dioxygenases and facilitate inhibitor design. [ABSTRACT FROM AUTHOR]

The current study presents a rare case of an accessory spleen that manifested as a solid intrasplenic pseudo-tumor. The affected patient was previously healthy. Upon examination with computed tomography (CT), an ovoid, soft-tissue mass of ~4.1 cm in diameter was found on the upper pole of the spleen. Biochemical indices, such as blood routine and coagulation tests, and tumor marker analysis, revealed no abnormalities. Another CT scan was performed, but this failed to indicate whether the mass was benign or malignant. Therefore, the lesion was resected along with the spleen by laparoscopic surgery. The resected sample was subject to pathological examinations for final validation, and was finally diagnosed as an accessory spleen. The patient was followed up for six months with no signs of recurrence. [ABSTRACT FROM AUTHOR]