Frequency distribution of TATA Box and extension sequences on human promoters

BACKGROUND: TATA box is one of the most important transcription factor binding sites. But the exact sequences of TATA box are still not very clear. RESULTS: In this study, we conduct a dedicated analysis on the frequency distribution of TATA Box and its extension sequences on human promoters. Sixteen TATA elements derived from the TATA Box motif, TATAWAWN, are classified into three distribution patterns: peak, bottom-peak, and bottom. Fourteen TATA extension sequences are predicted to be the new TATA Box elements due to their high motif factors, which indicate their statistical significance. Statistical analysis on the promoters of mice, zebrafish and drosophila melanogaster verifies seven of these elements. It is also observed that the distribution of TATA elements on the promoters of housekeeping genes are very similar with their distribution on the promoters of tissue specific genes in human. CONCLUSION: The dedicated statistical analysis on TATA box and its extension sequences yields new TATA elements. The statistical significance of these elements has been verified on random data sets by calculating their p values

?2-Microglobulin Amyloid Fibril-Induced Membrane Disruption Is Enhanced by Endosomal Lipids and Acidic pH

Although the molecular mechanisms underlying the pathology of amyloidoses are not well understood, the interaction between amyloid proteins and cell membranes is thought to play a role in several amyloid diseases. Amyloid fibrils of ?2-microglobulin (?2m), associated with dialysis-related amyloidosis (DRA), have been shown to cause disruption of anionic lipid bilayers in vitro. However, the effect of lipid composition and the chemical environment in which ?2m-lipid interactions occur have not been investigated previously. Here we examine membrane damage resulting from the interaction of ?2m monomers and fibrils with lipid bilayers. Using dye release, tryptophan fluorescence quenching and fluorescence confocal microscopy assays we investigate the effect of anionic lipid composition and pH on the susceptibility of liposomes to fibril-induced membrane damage. We show that ?2m fibril-induced membrane disruption is modulated by anionic lipid composition and is enhanced by acidic pH. Most strikingly, the greatest degree of membrane disruption is observed for liposomes containing bis(monoacylglycero)phosphate (BMP) at acidic pH, conditions likely to reflect those encountered in the endocytic pathway. The results suggest that the interaction between ?2m fibrils and membranes of endosomal origin may play a role in the molecular mechanism of ?2m amyloid-associated osteoarticular tissue destruction in DRA

Water Policies and Conflict Resolution of Public Participation Decision-Making Processes Using Prioritized Ordered Weighted Averaging (OWA) Operators

[EN] There is a growing interest in environmental policies about how to implement public participation engagement in the context of water resources management. This paper presents a robust methodology, based on ordered weighted averaging (OWA) operators, to conflict resolution decision-making problems under uncertain environments due to both information and stakeholders' preferences. The methodology allows integrating heterogeneous interests of the general public and stakeholders on account of their different degree of acceptance or preference and level of influence or power regarding the measures and policies to be adopted, and also of their level of involvement (i.e., information supply, consultation and active involvement). These considerations lead to different environmental and socio-economic outcomes, and levels of stakeholders' satisfaction. The methodology establishes a prioritization relationship over the stakeholders. The individual stakeholders' preferences are aggregated through their associated weights, which depend on the satisfaction of the higher priority decision maker. The methodology ranks the optimal management strategies to maximize the stakeholders' satisfaction. It has been successfully applied to a real case study, providing greater fairness, transparency, social equity and consensus among actors. Furthermore, it provides support to environmental policies, such as the EU Water Framework Directive (WFD), improving integrated water management while covering a wide range of objectives, management alternatives and stakeholders.Llopis Albert, C.; Merigó-Lindahl, JM.; Liao, H.; Xu, Y.; Grima-Olmedo, J.; Grima-Olmedo, C. (2018). Water Policies and Conflict Resolution of Public Participation Decision-Making Processes Using Prioritized Ordered Weighted Averaging (OWA) Operators. Water Resources Management. 32(2):497-510. https://doi.org/10.1007/s11269-017-1823-2S497510322Amin GR, Sadeghi H (2010) Application of prioritized aggregation operators in preference voting. Int J Intell Syst 25(10):1027–1034Chen TY (2014) A prioritized aggregation operator-based approach to multiple criteria decision making using interval-valued intuitionistic fuzzy sets: A comparative perspective. Inf Sci 281:97–112Chen LH, Xu ZS (2014) A prioritized aggregation operator based on the OWA operator and prioritized measures. J Intell Fuzzy Syst 27:1297–1307Chen LH, Xu ZS, Yu XH (2014a) Prioritized measure-guided aggregation operators. IEEE Trans Fuzzy Syst 22:1127–1138Chen LH, Xu ZS, Yu XH (2014b) Weakly prioritized measure aggregation in prioritized multicriteria decision making. Int J Intell Syst 29:439–461CHJ (2016). Júcar river basin authority http://www.chj.es/CHS (2016). Segura river basin authority http://www.chsegura.es/Dong JY, Wan SP (2016) A new method for prioritized multi-criteria group decision making with triangular intuitionistic fuzzy numbers. J Intell Fuzzy Syst 30:1719–1733EC (2000). Directive 2000/60/EC of the European Parliament and of the Council of October 23 2000 Establishing a Framework for Community Action in the Field of Water Policy. Official Journal of the European Communities, L327/1eL327/72 22.12.2000Jackson S, Tan P-L, Nolan S (2012) Tools to enhance public participation and confidence in the development of the Howard East aquifer water plan, Northern Territory. J Hydrol 474:22–28Jin FF, Ni ZW, Chen HY (2016) Note on “Hesitant fuzzy prioritized operators and their application to multiple attribute decision making”. Knowl-Based Syst 96:115–119Kentel E, Aral MM (2007) Fuzzy Multiobjective Decision-Making Approach for Groundwater Resources Management. J Hydrol Eng 12(2):206–217. https://doi.org/10.1061/(ASCE)1084-0699(2007)12:2(206).Kirchherr J, Charles KJ, Walton MJ (2016) Multi-causal pathways of public opposition to dam project in Asia: A fuzzy set qualitative comparative analysis (fsQCA). Glob Environ Chang 41:33–45. https://doi.org/10.1016/j.gloenvcha.2016.08.001Llopis-Albert C, Pulido-Velazquez D (2015) Using MODFLOW code to approach transient hydraulic head with a sharp-interface solution. Hydrol Process 29(8):2052–2064. https://doi.org/10.1002/hyp.10354Llopis-Albert C, Palacios-Marqués D, Soto-Acosta P (2015) Decision-making and stakeholders constructive participation in environmental projects. J Bus Res 68:1641–1644. https://doi.org/10.1016/j.jbusres.2015.02.010Llopis-Albert C, Merigó JM, Xu Y, Huchang L (2017) Improving regional climate projections by prioritized aggregation via ordered weighted averaging operators. Environ Eng Sci. https://doi.org/10.1089/ees.2016.0546Maia R (2017) The WFD Implementation in the European Member States. Water Resour Manag 31(10):3043–3060. https://doi.org/10.1007/s11269-017-1723-5Malczewski J, Chapman T, Flegel C, Walters D, Shrubsole D, Healy MA (2003) GIS - multicriteria evaluation with ordered weighted averaging (OWA): case study of developing watershed management strategies. Environ Plan A 35:1769–1784. https://doi.org/10.1068/a35156Merigó JM, Casanovas M (2011) The uncertain generalized owa operator and its application to financial decision making. Int J Inf Technol Decis Mak 10(2):211–230Merigó JM, Yager RR (2013) Generalized moving averages, distance measures and OWA operators. Int J Uncertain, Fuzziness Knowl-Based Syst 21(4):533–559Merigó JM, Palacios-Marqués D, Ribeiro-Navarrete B (2015) Aggregation systems for sales forecasting. J Bus Res 68:2299–2304Mesiar R, Stupnanová A, Yager RR (2015) Generalizations of OWA Operators. IEEE Trans Fuzzy Syst 23(6):2154–2162O’Hagan M (1988) Aggregating Template Rule Antecedents in Real-time Expert Systems with Fuzzy Set Logic. In: Proceedings of 22nd annual IEEE Asilomar Conference on Signals. IEEE and Maple Press, Pacific Grove, Systems and Computers, pp 681–689Rahmani MA, Zarghami M (2013) A new approach to combine climate change projections by ordered weighting averaging operator; applications to northwestern provinces of Iran. Glob Planet Chang 102:41–50Ran LG, Wei GW (2015) Uncertain prioritized operators and their application to multiple attribute group decision making. Technol Econ Dev Econ 21:118–139Ruiz-Villaverde, A., García-Rubio, M.A. (2017). Public Participation in European Water Management: from Theory to Practice. Water Resour Manag 31(8), 2479–2495. https://doi.org/10.1007/s11269-016-1355-1Sadiq R, Tesfamariam S (2007) Probability density functions based weights for ordered weighted averaging (OWA) operators: An example of water quality indices. Eur J Oper Res 182:1350–1368Sadiq R, Rodríguez MJ, Tesfamariam S (2010) Integrating indicators for performance assessment of small water utilities using ordered weighted averaging (OWA) operators. Expert Syst Appl 37:4881–4891Verma R, Sharma B (2016) Prioritized information fusion method for triangular fuzzy information and its application to multiple attribute decision making. Int J Uncertain, Fuzziness Knowl-Based Syst 24:265–290Wang HM, Xu YJ, Merigó JM (2014) Prioritized aggregation for non-homogeneous group decision making in water resource management. Econ Comput Econ Cybern Stud Res 48(1):247–258Wei GW (2012) Hesitant fuzzy prioritized operators. Knowl-Based Syst 31:176–182Wei CP, Tang XJ (2012) Generalized prioritized aggregation operators. Int J Intell Syst 27:578–589Xu ZS (2005) An Overview of Methods for Determining OWA Weights. Int J Intell Syst 20:843–865Yager RR (1988) On ordered weighted averaging aggregation operators in multi-criteria decision making, IEEE Transactions on Systems. Man Cybern B 18(1988):183–190Yager RR (2008) Prioritized Aggregation Operators. Int J Approx Reason 48:263–274Yan H-B, Huynh V-N, Nakamori Y, Murai T (2011) On prioritized weighted aggregation in multi-criteria decision making. Expert Syst Appl 38(1):812–823Ye J (2014) Prioritized aggregation operators of trapezoidal intuitionistic fuzzy sets and their application to multicriteria decision-making. Neural Comput & Applic 25:1447–1454Yu XH, Xu ZS, Liu SS (2013) Prioritized multi-criteria decision making based on preference relations. Comput Ind Eng 66:104–115Zadeh LA (1983) A Computational Approach to Fuzzy Quantifiers in Natural Languages. Comput Math Appl 9:149–184Zarghami M, Szidarovszky F (2009) Revising the OWA operator for multi criteria decision making problems under uncertainty. Eur J Oper Res 198:259–265Zarghami M, Ardakanian R, Memariani A, Szidarovszky F (2008) Extended OWA Operator for Group Decision Making on Water Resources Projects. J Water Resour Plan Manag 134(3):266–275. https://doi.org/10.1061/(ASCE)0733-9496(2008)134:3(266)Zarghami M, Szidarovszky F, Ardakanian R (2009) Multi-attribute decision making on inter-basin water transfer projects. Transaction E. Ind Eng 16(1):73–80Zhao XF, Li QX, Wei GW (2014) Some prioritized aggregating operators with linguistic information and their application to multiple attribute group decision making. J Intell Fuzzy Syst 26:1619–1630Zhao N, Xu ZS, Ren ZL (2016) On typical hesitant fuzzy prioritized “or” operator in multi-attribute decision making. Int J Intell Syst 31:73–100Zhou LY, Lin R, Zhao XF, Wei GW (2013) Uncertain linguistic prioritized aggregation operators and their application to multiple attribute group decision making. Int J Uncertain, Fuzziness Knowl-Based Syst 21:603–627Zhou LG, Merigó JM, Chen HY, Liu JP (2016) The optimal group continuous logarithm compatibility measure for interval multiplicative preference relations based on the COWGA operator. Inf Sci 328:250–26

Imperfection works: Survival, transmission and persistence in the system of Heliothis virescens ascovirus 3h (HvAV-3h), Microplitis similis and Spodoptera exigua

Ascoviruses are insect-specific large DNA viruses that mainly infect noctuid larvae, and are transmitted by parasitoids in the fields. Heliothis virescens ascovirus 3h (HvAV-3h) has been recently isolated from Spodoptera exigua, without parasitoid vector identified previously. Here we report that Microplitis similis, a solitary endoparasitoid wasp, could transmit HvAV-3h between S. exigua larvae in the laboratory. When the female parasitoid wasp acquired the virus and served as a vector, the period of virion viability on the ovipositor was 4.1 ± 1.4 days. Infected host larvae were still acceptable for egg laying by parasitoids, and the parasitoids thereafter transmitted virus to healthy hosts. Virus acquisition occurred only from donor hosts between 3 and 9 days post infection. The peak of virus acquisition (80.9 ± 6.3%) was found when M. similis wasps oviposited in larvae that had been inoculated with the virus 7 days previously. When virus infection of the host took place during the life cycle of the parasitoid wasp, it caused 1- to 4-day-old immature parasitoids death in the host, whilst a small proportion of 5- to 6-day-old and the majority of 7-day-old parasitoids larvae survived from the virus-infected hosts. Viral contamination did not reduce the life span or fecundity of female M. similis

Synthesis and Photoluminescence Property of Silicon Carbide Nanowires Via Carbothermic Reduction of Silica

Silicon carbide nanowires have been synthesized at 1400 °C by carbothermic reduction of silica with bamboo carbon under normal atmosphere pressure without metallic catalyst. X-ray diffraction, scanning electron microscopy, energy-dispersive spectroscopy, transmission electron microscopy and Fourier transformed infrared spectroscopy were used to characterize the silicon carbide nanowires. The results show that the silicon carbide nanowires have a core–shell structure and grow along <111> direction. The diameter of silicon carbide nanowires is about 50–200 nm and the length from tens to hundreds of micrometers. The vapor–solid mechanism is proposed to elucidate the growth process. The photoluminescence of the synthesized silicon carbide nanowires shows significant blueshifts, which is resulted from the existence of oxygen defects in amorphous layer and the special rough core–shell interface

Dramatic pain relief and resolution of bone inflammation following pamidronate in 9 pediatric patients with persistent chronic recurrent multifocal osteomyelitis (CRMO)

<p>Abstract</p> <p>Background</p> <p>Chronic recurrent multifocal osteomyelitis (CRMO) is an inflammatory, non-infectious osteopathy that affects predominantly patients ≤ 18 years of age. There is no uniformly effective treatment. Our objective is to describe clinical, magnetic resonance imaging (MRI), and bone resorption response to intravenous pamidronate in pediatric CRMO.</p> <p>Methods</p> <p>We report our prospectively documented experience with all CRMO patients treated with pamidronate between 2003 and 2008 at a tertiary pediatric centre. Pamidronate was administered as intravenous cycles. The dose of pamidronate varied among subjects but was given as monthly to every 3 monthly cycles depending on the distance the patient lived from the infusion center. Maximum cumulative dose was ≤ 11.5 mg/kg/year. Pamidronate treatment was continued until resolution of MRI documented bone inflammation. Visual analog scale for pain (VAS) and bone resorption marker urine N-telopeptide/urine creatinine (uNTX/uCr) were measured at baseline, preceding each subsequent pamidronate treatment, at final follow-up, and/or at time of MRI confirmed CRMO flare. MRI of the affected site(s) was obtained at baseline, preceding every 2^ndtreatment, and with suspected CRMO recurrence.</p> <p>Results</p> <p>Nine patients (5 F: 4 M) were treated, with a median (range) age at treatment of 12.9 (4.5–16.3) years, and median (range) duration of symptoms of 18 (6–36) months. VAS decreased from 10/10 to 0–3/10 by the end of first 3–day treatment for all patients. The mean (range) time to complete MRI resolution of bone inflammation was 6.0 (2–12) months. The mean (confidence interval (CI)) baseline uNTX/uCr was 738.83 (CI 464.25, 1013.42)nmol/mmol/creatinine and the mean (CI) decrease from baseline to pamidronate discontinuation was 522.17 (CI 299.77, 744.56)nmol/mmol/creatinine. Median (range) of follow-up was 31.4 (24–54) months. Four patients had MRI confirmed CRMO recurrence, which responded to one pamidronate re-treatment. The mean (range) uNTX/uCr change as a monthly rate from the time of pamidronate discontinuation to flare was 9.41 (1.38–19.85)nmol/mmol/creatinine compared to -29.88 (-96.83–2.01)nmol/mmol/creatinine for patients who did not flare by the time of final follow-up.</p> <p>Conclusion</p> <p>Pamidronate resulted in resolution of pain and MRI documented inflammation in all patients. No patient flared while his/her uNTX/uCr remained suppressed. We propose that pamidronate is an effective second-line therapy in persistent CRMO.</p