Mixing of Non-Newtonian Fluids in Steadily Forced Systems

We investigate mixing in a viscoelastic and shear-thinning fluid—a very common combination in polymers and suspensions. We find that competition between elastic and viscous forces generates self-similar mixing, lobe transport, and other characteristics of chaos. The mechanism by which chaos is produced is evaluated both in experiments and in a simple model. We find that chaotic flow is generated by spontaneous oscillations, the magnitude and frequency of which govern the extent of chaos and mixing

Nuclear astrophysics with radioactive ions at FAIR

The nucleosynthesis of elements beyond iron is dominated by neutron captures in the s and r processes. However, 32 stable, proton-rich isotopes cannot be formed during those processes, because they are shielded from the s-process flow and r-process beta-decay chains. These nuclei are attributed to the p and rp process. For all those processes, current research in nuclear astrophysics addresses the need for more precise reaction data involving radioactive isotopes. Depending on the particular reaction, direct or inverse kinematics, forward or time-reversed direction are investigated to determine or at least to constrain the desired reaction cross sections. The Facility for Antiproton and Ion Research (FAIR) will offer unique, unprecedented opportunities to investigate many of the important reactions. The high yield of radioactive isotopes, even far away from the valley of stability, allows the investigation of isotopes involved in processes as exotic as the r or rp processes

Arquitectura ANFIS del Proceso de Fermentación de Aceitunas Negras Naturales

En el proceso de obtención de aceitunas negras naturales, las condiciones inciden sobre la calidad del fruto fermentado y éstas difieren a distintas escalas. El objetivo del trabajo es generar modelos matemáticos que caractericen las propiedades de las aceitunas negras naturales obtenidas a gran escala, a partir de datos del proceso a escala piloto. Se crearon arquitecturas ANFIS con parámetros físico-químicos como entradas, y de textura y color como salidas. Dichas estructuras se entrenaron con datos obtenidos a escala piloto y se validaron con los industriales. Las redes que demostraron mejor desempeño poseen dos funciones de membresia por entrada incorporada, en forma de campana generalizada y una de salida. Las estructuras logradas demostraron habilidad para predecir la evolución del proceso a escala industrial luego de los primeros días de fermentación. Para incrementar su aptitud, sería conveniente probar otros modelos para el tratamiento de datos, tales como las redes neuronales artificiales

Precave: Immediate neoadjuvant instillation of chemotherapy for the prevention of non-muscle invasive bladder carcinoma recurrence: A prospective randomized clinical trial protocol

Introduction and objectives: Recurrence rates for patients presenting with non-muscle invasive bladder carcinoma (NMIBC) can be as high as 60% during the first year after a transurethral resection of bladder tumor (TURBT). Currently, an immediate postoperative instillation of chemotherapy (IPOIC) is recommended for the prevention of recurrences in patients with low to intermediate risk disease. Although in real clinical practice this specific instillation of chemotherapy has many difficulties to be standardized, including its contraindications (suspected or confirmed bladder perforation, wide or extensive resection and, continuous bladder irrigation requirement), which will only make it feasible for around 30% of patients. We propose in this controlled study, to administer an immediate neoadjuvant instillation of chemotherapy (INAIC), which can be applied technically to all patients, no matter the surgical outcomes and compare it with a control group. We expect to find a reduction in the recurrence rate in the experimental group of at least 15%. Methods: We designed a phase IV, randomized, controlled, open label clinical trial. Main inclusion criteria are: patients with a clinical diagnosis of localized, papillary-type bladder cancer (suspected low to intermediate risk) with a disease-free interval of at least 6 months. Eligible patients will be allocated into group A (INAIC plus TURBT) or group B (TURBT) using a computer-generated block randomization sequence/ratio 1:1. Time to recurrence of both groups will be analyzed and compared using Kaplan- Meier estimates, log-rank tests and, Cox-regression. Univariate and multivariate analyzes will be performed to determine factors which influence recurrence. The study has received the approval of the Ethics Committee for Drug Research (CEIm) of La Paz University Hospital and the Spanish Agency for Medicines and Health ProductsThis study received funding from grants ‘‘Rafael Molla y Rodrigo” from the Foundation for Research in Urology (Spanish Urological Association) and Immunothercan-CM(B2017/BM D3733) from the Local Government of the Community of Madrid, Madrid, Spain

Invasive management of renal cell carcinoma in von hippel-lindau disease

Introduction Patients affected by von Hippel-Lindau (VHL) disease experience an increased risk for bi-lateral, synchronous, and metachronous renal cell carcinoma (RCC). Oncologic and functional outcomes are the main goals in the management of renal masses. We present our protocol for patients with VHL disease-associated RCC alongside functional and oncologic results observed in our series. Material and methods We performed a retrospective analysis of our clinical database of patients with VHL disease-associated RCC referred to our department between June 2005 and December 2017. We offer surveillance for lesions <2 cm and active management with radiofrequency ablation (RFA) for lesions 2–3 cm, and nephron-sparing surgery (NSS), RFA or embolization techniques for lesions >3 cm or growth rate >1 cm/year. Results Our series comprises 14 patients, of whom 13 had undergone at least one invasive procedure for RCC, mean age at first intervention was 27 years (range 18–60). Overall, 30 interventions were performed in 21 kidneys: four radical nephrectomies, 13 RFAs, 12 NSSs, and one embolization. During follow-up (median time: 41 months, range: 6–149), eight patients (57%) presented with new lesions that required treatment, with a mean time between treatments of 32 ±18.5 months. No metastatic progression or need for dialysis was recorded; the success rate for RFA was 85%. Conclusions Management of VHL kidney disease by NSS is the standard of care with a cut-off at 3 cm, ablative procedures should be offered to lesions ranging 2–3 cm in size. Follow-up should be done strictly in referral centers that can provide all treatment options to renal function and control oncologic progression.This research was funded by Madrid Regional Government Research Grant [S2010/BMD-2326 IMMUNOTHERCAN-CM (B2017/BMD-3733)/FEDE

Arabidopsis Heat Stress-Induced Proteins Are Enriched in Electrostatically Charged Amino Acids and Intrinsically Disordered Regions

[EN] Comparison of the proteins of thermophilic, mesophilic, and psychrophilic prokaryotes has revealed several features characteristic to proteins adapted to high temperatures, which increase their thermostability. These characteristics include a profusion of disulfide bonds, salt bridges, hydrogen bonds, and hydrophobic interactions, and a depletion in intrinsically disordered regions. It is unclear, however, whether such differences can also be observed in eukaryotic proteins or when comparing proteins that are adapted to temperatures that are more subtly different. When an organism is exposed to high temperatures, a subset of its proteins is overexpressed (heat-induced proteins), whereas others are either repressed (heat-repressed proteins) or remain unaffected. Here, we determine the expression levels of all genes in the eukaryotic model system Arabidopsis thaliana at 22 and 37 degrees C, and compare both the amino acid compositions and levels of intrinsic disorder of heat-induced and heat-repressed proteins. We show that, compared to heat-repressed proteins, heat-induced proteins are enriched in electrostatically charged amino acids and depleted in polar amino acids, mirroring thermophile proteins. However, in contrast with thermophile proteins, heat-induced proteins are enriched in intrinsically disordered regions, and depleted in hydrophobic amino acids. Our results indicate that temperature adaptation at the level of amino acid composition and intrinsic disorder can be observed not only in proteins of thermophilic organisms, but also in eukaryotic heat-induced proteins; the underlying adaptation pathways, however, are similar but not the same.D.A.-P. and F.F. were supported by funds from the University of Nevada, Reno, and by pilot grants from Nevada INBRE (P20GM103440) and the Smooth Muscle Plasticity COBRE from the University of Nevada, Reno (5P30GM110767-04), both funded by the National Institute of General Medical Sciences (National Institutes of Health). M.X.R.-G. and M.A.F. were supported by grants from Science Foundation Ireland (12/IP/1637) and the Spanish Ministerio de Economia y Competitividad, Spain (MINECO-FEDER; BFU201236346 and BFU2015-66073-P) to MAF. MXRG was supported by a JAE DOC fellowship from the MINECO, Spain. F.V.-S. and M.A.P.-A. were supported by grant BIO2014-55946-P from MINECO-FEDER.Alvarez-Ponce, D.; Ruiz-González, M.; Vera Sirera, FJ.; Feyertag, F.; Perez Amador, MA.; Fares Riaño, MA. (2018). Arabidopsis Heat Stress-Induced Proteins Are Enriched in Electrostatically Charged Amino Acids and Intrinsically Disordered Regions. International Journal of Molecular Sciences. 19(8). https://doi.org/10.3390/ijms19082276S198Karshikoff, A., & Ladenstein, R. (2001). Ion pairs and the thermotolerance of proteins from hyperthermophiles: a ‘traffic rule’ for hot roads. Trends in Biochemical Sciences, 26(9), 550-557. doi:10.1016/s0968-0004(01)01918-1Strop, P., & Mayo, S. L. (2000). Contribution of Surface Salt Bridges to Protein Stability†,‡. Biochemistry, 39(6), 1251-1255. doi:10.1021/bi992257jPERUTZ, M. F., & RAIDT, H. (1975). Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2. Nature, 255(5505), 256-259. doi:10.1038/255256a0Argos, P., Rossmann, M. G., Grau, U. M., Zuber, H., Frank, G., & Tratschin, J. D. (1979). Thermal stability and protein structure. Biochemistry, 18(25), 5698-5703. doi:10.1021/bi00592a028Beeby, M., O’Connor, B. D., Ryttersgaard, C., Boutz, D. R., Perry, L. J., & Yeates, T. O. (2005). The Genomics of Disulfide Bonding and Protein Stabilization in Thermophiles. PLoS Biology, 3(9), e309. doi:10.1371/journal.pbio.0030309Haney, P. J., Badger, J. H., Buldak, G. L., Reich, C. I., Woese, C. R., & Olsen, G. J. (1999). Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proceedings of the National Academy of Sciences, 96(7), 3578-3583. doi:10.1073/pnas.96.7.3578Kreil, D. P. (2001). Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Research, 29(7), 1608-1615. doi:10.1093/nar/29.7.1608Tekaia, F., Yeramian, E., & Dujon, B. (2002). Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis. Gene, 297(1-2), 51-60. doi:10.1016/s0378-1119(02)00871-5Zeldovich, K. B., Berezovsky, I. N., & Shakhnovich, E. I. (2007). Protein and DNA Sequence Determinants of Thermophilic Adaptation. PLoS Computational Biology, 3(1), e5. doi:10.1371/journal.pcbi.0030005Chakravarty, S., & Varadarajan, R. (2000). Elucidation of determinants of protein stability through genome sequence analysis. FEBS Letters, 470(1), 65-69. doi:10.1016/s0014-5793(00)01267-9Cambillau, C., & Claverie, J.-M. (2000). Structural and Genomic Correlates of Hyperthermostability. Journal of Biological Chemistry, 275(42), 32383-32386. doi:10.1074/jbc.c000497200Burra, P. V., Kalmar, L., & Tompa, P. (2010). Reduction in Structural Disorder and Functional Complexity in the Thermal Adaptation of Prokaryotes. PLoS ONE, 5(8), e12069. doi:10.1371/journal.pone.0012069Wang, J., Yang, Y., Cao, Z., Li, Z., Zhao, H., & Zhou, Y. (2013). The Role of Semidisorder in Temperature Adaptation of Bacterial FlgM Proteins. Biophysical Journal, 105(11), 2598-2605. doi:10.1016/j.bpj.2013.10.026Vicedo, E., Schlessinger, A., & Rost, B. (2015). Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes. PLOS ONE, 10(8), e0133990. doi:10.1371/journal.pone.0133990Galea, C. A., High, A. A., Obenauer, J. C., Mishra, A., Park, C.-G., Punta, M., … Kriwacki, R. W. (2009). Large-Scale Analysis of Thermostable, Mammalian Proteins Provides Insights into the Intrinsically Disordered Proteome. Journal of Proteome Research, 8(1), 211-226. doi:10.1021/pr800308vTsvetkov, P., Myers, N., Moscovitz, O., Sharon, M., Prilusky, J., & Shaul, Y. (2012). Thermo-resistant intrinsically disordered proteins are efficient 20S proteasome substrates. Mol. BioSyst., 8(1), 368-373. doi:10.1039/c1mb05283gGalea, C. A., Nourse, A., Wang, Y., Sivakolundu, S. G., Heller, W. T., & Kriwacki, R. W. (2008). Role of Intrinsic Flexibility in Signal Transduction Mediated by the Cell Cycle Regulator, p27Kip1. Journal of Molecular Biology, 376(3), 827-838. doi:10.1016/j.jmb.2007.12.016Van Noort, V., Bradatsch, B., Arumugam, M., Amlacher, S., Bange, G., Creevey, C., … Bork, P. (2013). Consistent mutational paths predict eukaryotic thermostability. BMC Evolutionary Biology, 13(1), 7. doi:10.1186/1471-2148-13-7Wang, G.-Z., & Lercher, M. J. (2010). Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes. BMC Evolutionary Biology, 10(1), 263. doi:10.1186/1471-2148-10-263Windisch, H. S., Lucassen, M., & Frickenhaus, S. (2012). Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes. BMC Genomics, 13(1), 549. doi:10.1186/1471-2164-13-549Albanèse, V., Yam, A. Y.-W., Baughman, J., Parnot, C., & Frydman, J. (2006). Systems Analyses Reveal Two Chaperone Networks with Distinct Functions in Eukaryotic Cells. Cell, 124(1), 75-88. doi:10.1016/j.cell.2005.11.039Berry, J., & Bjorkman, O. (1980). Photosynthetic Response and Adaptation to Temperature in Higher Plants. Annual Review of Plant Physiology, 31(1), 491-543. doi:10.1146/annurev.pp.31.060180.002423Sueoka, N. (1961). CORRELATION BETWEEN BASE COMPOSITION OF DEOXYRIBONUCLEIC ACID AND AMINO ACID COMPOSITION OF PROTEIN. Proceedings of the National Academy of Sciences, 47(8), 1141-1149. doi:10.1073/pnas.47.8.1141Cherry, J. L. (2009). Highly Expressed and Slowly Evolving Proteins Share Compositional Properties with Thermophilic Proteins. Molecular Biology and Evolution, 27(3), 735-741. doi:10.1093/molbev/msp270The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins. (1992). FEBS Letters, 303(2-3), 141-146. doi:10.1016/0014-5793(92)80506-cNakashima, H., & Nishikawa, K. (1994). Discrimination of Intracellular and Extracellular Proteins Using Amino Acid Composition and Residue-pair Frequencies. Journal of Molecular Biology, 238(1), 54-61. doi:10.1006/jmbi.1994.1267Dosztanyi, Z., Csizmok, V., Tompa, P., & Simon, I. (2005). IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21(16), 3433-3434. doi:10.1093/bioinformatics/bti541Peng, Z., Uversky, V. N., & Kurgan, L. (2016). Genes encoding intrinsic disorder in Eukaryota have high GC content. Intrinsically Disordered Proteins, 4(1), e1262225. doi:10.1080/21690707.2016.1262225Yruela, I., & Contreras-Moreira, B. (2013). Genetic recombination is associated with intrinsic disorder in plant proteomes. BMC Genomics, 14(1), 772. doi:10.1186/1471-2164-14-772Paliy, O., Gargac, S. M., Cheng, Y., Uversky, V. N., & Dunker, A. K. (2008). Protein Disorder Is Positively Correlated with Gene Expression inEscherichia coli. Journal of Proteome Research, 7(6), 2234-2245. doi:10.1021/pr800055rSingh, G. P., & Dash, D. (2008). How expression level influences the disorderness of proteins. Biochemical and Biophysical Research Communications, 371(3), 401-404. doi:10.1016/j.bbrc.2008.04.072Yang, J.-R., Liao, B.-Y., Zhuang, S.-M., & Zhang, J. (2012). Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. Proceedings of the National Academy of Sciences, 109(14), E831-E840. doi:10.1073/pnas.1117408109Hendsch, Z. S., & Tidor, B. (1994). Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Science, 3(2), 211-226. doi:10.1002/pro.5560030206Zhou, X.-X., Wang, Y.-B., Pan, Y.-J., & Li, W.-F. (2007). Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins. Amino Acids, 34(1), 25-33. doi:10.1007/s00726-007-0589-xCatanzano, F., Barone, G., Graziano, G., & Capasso, S. (1997). Thermodynamic analysis of the effect of selective monodeamidation at asparagine 67 in ribonuclease A. Protein Science, 6(8), 1682-1693. doi:10.1002/pro.5560060808Charlesworth, B. (2009). Effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics, 10(3), 195-205. doi:10.1038/nrg2526Bolser, D., Staines, D. M., Pritchard, E., & Kersey, P. (2016). Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data. Methods in Molecular Biology, 115-140. doi:10.1007/978-1-4939-3167-5_6Kasprzyk, A. (2003). EnsMart: A Generic System for Fast and Flexible Access to Biological Data. Genome Research, 14(1), 160-169. doi:10.1101/gr.1645104Hooper, C. M., Castleden, I. R., Tanz, S. K., Aryamanesh, N., & Millar, A. H. (2016). SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations. Nucleic Acids Research, 45(D1), D1064-D1074. doi:10.1093/nar/gkw1041R: A language and environment for statistical computing. R Foundation for Statistical Computinghttp://www.R-project.org/Kim, S. (2015). ppcor: An R Package for a Fast Calculation to Semi-partial Correlation Coefficients. Communications for Statistical Applications and Methods, 22(6), 665-674. doi:10.5351/csam.2015.22.6.66

A Feasibility Study on Disasters and Disaster Risk Reduction Factors Awareness of LSPU Students

This study determined the students' degree of awareness at Laguna State Polytechnic University (LSPU) Sta. Cruz, Laguna in terms of disaster risk reduction and its significance, which was the basis of the LSPU DRRM Center construct. This employed a descriptive- correlational study and used a purposive sampling technique. The results revealed that the respondents had experienced various types of disasters. They are slightly aware, at least, of risk reduction factors anchoring on political commitment, while they are no less than slightly aware of the particulars related to risk reduction measures. Moreover, the results of χ² Tests of Independence revealed that the awareness of Disaster Risk Reduction Factors depends on the individual's exposure to a single or a combination of natural disasters. On the contrary, the extent of awareness of those factors does not depend on the respondent's exposure or experience with global viral diseases and man-made disasters

Decoherence time in self-induced decoherence

A general method for obtaining the decoherence time in self-induced decoherence is presented. In particular, it is shown that such a time can be computed from the poles of the resolvent or of the initial conditions in the complex extension of the Hamiltonian's spectrum. Several decoherence times are estimated: $10^{-13}-$ $10^{-15}s$ for microscopic systems, and $10^{-37}-10^{-39}s$ for macroscopic bodies. For the particular case of a thermal bath, our results agree with those obtained by the einselection (environment-induced decoherence) approach.Comment: 11 page