A Study of Archiving Strategies in Multi-Objective PSO for Molecular Docking

Molecular docking is a complex optimization problem aimed at predicting the position of a ligand molecule in the active site of a receptor with the lowest binding energy. This problem can be formulated as a bi-objective optimization problem by minimizing the binding energy and the Root Mean Square Deviation (RMSD) difference in the coordinates of ligands. In this context, the SMPSO multi-objective swarm-intelligence algorithm has shown a remarkable performance. SMPSO is characterized by having an external archive used to store the non-dominated solutions and also as the basis of the leader selection strategy. In this paper, we analyze several SMPSO variants based on different archiving strategies in the scope of a benchmark of molecular docking instances. Our study reveals that the SMPSOhv, which uses an hypervolume contribution based archive, shows the overall best performance.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

A critical experimental study of the classical tactile threshold theory

<p>Abstract</p> <p>Background</p> <p>The tactile sense is being used in a variety of applications involving tactile human-machine interfaces. In a significant number of publications the classical threshold concept plays a central role in modelling and explaining psychophysical experimental results such as in stochastic resonance (SR) phenomena. In SR, noise enhances detection of sub-threshold stimuli and the phenomenon is explained stating that the required amplitude to exceed the sensory threshold barrier can be reached by adding noise to a sub-threshold stimulus. We designed an experiment to test the validity of the classical vibrotactile threshold. Using a second choice experiment, we show that individuals can order sensorial events below the level known as the classical threshold. If the observer's sensorial system is not activated by stimuli below the threshold, then a second choice could not be above the chance level. Nevertheless, our experimental results are above that chance level contradicting the definition of the classical tactile threshold.</p> <p>Results</p> <p>We performed a three alternative forced choice detection experiment on 6 subjects asking them first and second choices. In each trial, only one of the intervals contained a stimulus and the others contained only noise. According to the classical threshold assumptions, a correct second choice response corresponds to a guess attempt with a statistical frequency of 50%. Results show an average of 67.35% (STD = 1.41%) for the second choice response that is not explained by the classical threshold definition. Additionally, for low stimulus amplitudes, second choice correct detection is above chance level for any detectability level.</p> <p>Conclusions</p> <p>Using a second choice experiment, we show that individuals can order sensorial events below the level known as a classical threshold. If the observer's sensorial system is not activated by stimuli below the threshold, then a second choice could not be above the chance level. Nevertheless, our experimental results are above that chance level. Therefore, if detection exists below the classical threshold level, then the model to explain the SR phenomenon or any other tactile perception phenomena based on the psychophysical classical threshold is not valid. We conclude that a more suitable model of the tactile sensory system is needed.</p

Evaluation of Xpert® MTB/RIF and ustar easyNAT™ TB IAD for diagnosis of tuberculous lymphadenitis of children in Tanzania : a prospective descriptive study

Fine needle aspiration biopsy has become a standard approach for diagnosis of peripheral tuberculous lymphadenitis. The aim of this study was to compare the performance of Xpert MTB/RIF and Ustar EasyNAT TB IAD nucleic acid amplification assays, against acid-fast bacilli microscopy, cytology and mycobacterial culture for the diagnosis of TB lymphadenitis in children from a TB-endemic setting in Tanzania.; Children of 8 weeks to 16 years of age, suspected of having TB lymphadenitis, were recruited at a district hospital in Tanzania. Fine needle aspirates of lymph nodes were analysed using acid-fast bacilli microscopy, liquid TB culture, cytology, Xpert MTB/RIF and EasyNAT. Latent class analysis and comparison against a composite reference standard comprising "culture and/or cytology" was done, to assess the performance of Xpert MTB/RIF and EasyNAT for the diagnosis of TB lymphadenitis.; Seventy-nine children were recruited; 4 were excluded from analysis. Against a composite reference standard of culture and/or cytology, Xpert MTB/RIF and EasyNAT had a sensitivity and specificity of 58 % and 93 %; and 19 % and 100 % respectively. Relative to latent class definitions, cytology had a sensitivity of 100 % and specificity of 94.7 %.; Combining clinical assessment, cytology and Xpert MTB/RIF may allow for a rapid and accurate diagnosis of childhood TB lymphadenitis. Larger diagnostic evaluation studies are recommended to validate these findings and on Xpert MTB/RIF to assess its use as a solitary initial test for TB lymphadenitis in children

Screening a variable germplasm collection of Cucumis melo L. for seedling resistance to Macrophomina phaseolina

[EN] We evaluate the seedling resistance to charcoal rot caused by Macrophomina phaseolina in ninety-seven Cucumis melo accessions, from different geographical origins and five F1 generations, derived from crosses of five accessions selected for their resistance. Artificial inoculations with the toothpick method, previously reported to be useful for predicting shoot resistance, were performed, and plants were scored using a scale of disease severity. The average disease severity was calculated for each accession and was used to cluster the accession in five reaction classes. The screening revealed that sources of natural resistance to this fungus are limited. However, seedlings of seven accessions of different botanic groups displayed a resistant response to the stem inoculation, one cantaloup from Israel, one conomon accession from Korea, two wild agrestis and one acidulus from Africa, and two dudaim accessions from Middle East. The response of the F1 progenies varied from susceptibility to high resistance, the latter in progenies from the two agrestis wild types. These results suggest differences in the genetic basis of the resistance in the different selected sources. The resistant accessions are suggested to be screened under field conditions to confirm the level of resistance at adult plant stage and under stressful conditions.This work has been partially funded by the Project No 294/13 of the Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior CAPES (Brazil). M. M. Q. Ambrosio and A. C. A. Dantas thank CAPES for their research fellowships. B.Pico thanks the Programa Hispano-Brasileno de Cooperacion Universitaria HBP2012-008 and PHBP14/00021 and to the MINECO project AGL2014-53398-C2-2-R.Ambrosio, MM.; Dantas, AC.; Martinez Perez, EM.; Medeiros, AC.; Sousa Nunes, GHD.; Picó Sirvent, MB. (2015). Screening a variable germplasm collection of Cucumis melo L. for seedling resistance to Macrophomina phaseolina. Euphytica. 206(2):287-300. https://doi.org/10.1007/s10681-015-1452-xS2873002062Aegerter BJ, Gordon TR, Davis RM (2000) Occurrence and pathogenicity of fungi associated with melon root rot and vine decline in California. Plant Dis 84:224–230Almeida AMR, Abdelnoor RV, Arias CAA, Carvalho VP, Jacoud Filho DS, Marin SRR, Benato LC, Pinto MC, Carvalho CGP (2003) Genotypic diversity among Brazilian isolates of Macrophomina phaseolina revealed by RAPD. Fitopatol Bras 28:279–285Almeida AMRA, Seixas CDSS, Farias JRBF, Oliveira MCN, Franchini JC, Debiasi H, Costa JM, Gaudêncio CA (2014) Macrophomina phaseolina em soja. Embrapa Soja, Londrina, p 30pAmbrósio MMQ, Bueno CJ, Padovani CR, Souza NL (2009) Sobrevivência de fungos fitopatogênicos habitantes do solo, em microcosmo, simulando solarização com prévia incorporação de materiais orgânicos. Summa Phytopathol 35(1):20–25Andrade DEGT, Michereff SJ, Biondi CM, Nascimento CWA, Sales R Jr (2005) Frequência de fungos associados ao colapso do meloeiro e relação com características físicas, químicas e microbiológicas dos solos. Summa Phytopathol 31(4):327–333Bedendo IP (2011) Podridões de raiz e de colo. In: Amorin L, Rezende JAM, Bergamin Filho A (eds) Manual de Fitopatologia: Princípios e conceitos. Agronômica Ceres, São Paulo, pp 443–448Bramel-Cox PJ, Stein IS, Rodgers DM, Claflin LE (1988) Inheritance of resistance to Macrophomina phaseolina (Tassi) Goid. and Fusarium moniliforme Sheldom in Sorghum. Crop Sci 28(1):37–40Bruton BD, Miller E (1997) Occurrence of vine decline diseases of melons in Honduras. Plant Dis 81(6):696Bruton BD, Jeger MD, Reuveni R (1987) Macrophomina phaseolina infection and vine decline in cantaloupe in relation to planting date, soil environment, and maturation. Plant Dis 71(3):259–263Burger Y, Katzir N, Tzuri G, Portnoy V, Saar U, Shriber S, Perl-Treves R, Cohen R (2003) Variation in the response of melon genotypes to Fusarium oxysporum f. sp. melonis race 1 determined by inoculation tests and molecular markers. Plant Pathol 52:204–211Chamorro M, Miranda L, Domínguez P, Medina JJ, Soria C, Romero F, López Aranda JM, De los Santos B (2015) Evaluation of biosolarization for the control of charcoal rot disease (Macrophomina phaseolina) in strawberry. Crop Prot 67:279–286Cohen R (1993) A leaf disk assay for detection of resistance of melons to Sphaerotheca fuliginea race 1. Plant Dis 77(5):513–517Cohen R, Katzir N, Schreiber S, Greenberg R (1996) Occurrence of Shaerotheca fuliginea Race 3 on Cucurbits in Israel. Plant Dis 80:334Cohen R, Omari N, Porat A, Edelstein M (2012) Management of Macrophomina wilt in melons using grafting or fungicide soil application: pathological, horticultural and economical aspects. Crop Prot 35:58–63Cohen R, Tyutyunik J, Fallik E, Oka Y, Tadmor Y, Edelstein M (2014) Phytopathological evaluation of exotic watermelon germplasm as a basic for rootstock breeding. Sci Hortic 165:203–210Dantas AMM, Ambrósio MMQ, Nascimento SRC, Senhor RF, Cézar MA, Lima JSS (2013) Incorporation of plant materials in the control of root pathogens in mushmelon. Revista Agro@ambiente on-line 7(3):338–344Davis RM, Turini TA, Aegerter BJ, Stapleton JJ (2009) Cucurbits charcoal rot, pathogen: Macrophomina phaseolina. UC IPM online. http://www.totoagriculture.org/PDFs/PlantDiseasesPests/1026.pdf . Accessed 25 Feb 2015Dias RCS, Picó B, Espinos A, Nuez F (2004) Resistance to melón vine decline derived from Cucumis melo ssp. agrestis: genetic analysis of root structure and root response. Plant Breed 123:66–72Diourte M, Starr JL, Jegger MJ, Stack JP, Rosenow DT (1995) Charcoal rot (Macrophomina phaseolina) resistance and the effect of water stress on disease development in Sorghum. Plant Pathol 44:196–202Esteras C, Pascual B, Nuez F, Picó MB (2009) Use of ecotilling to identify natural allelic variants of melon candidate genes involved in fuit ripening. 8th Plant Genomics European Meeting (Plant GEM 8) Istambul, 213Esteras C, Formisano G, Roig C, Díaz A, Blanca J, Garcia-Mas J, Gómez-Guillamón ML, López-Sesé AI, Lázaro A, Monforte AJ, Picó B (2013) SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium. Theor Appl Genet 126(5):1285–1303. doi: 10.1007/s00122-013-2053-5Fang X, Phillips D, Li H, Sivasithamparama K, Barbettia MJ (2011) Comparisons of virulence of pathogens associated with crown and root diseases of strawberry in Western Australia with special reference to the effect of temperature. Sci Hortic 131(22):39–48Food and Agriculture Organization (2014) Faostat. http://faostat.fao.org/site/567/default.aspx#ancor . Accessed 11 Nov 2011García-Jiménez J, Martínez-Ferrer G, Armengol J, Velazquez MT, Orts M, Juárez M, Ortega A, Jordá MC, Alfaro A (1993) Agentes asociados al colapso del melón en distintas zonas españolas. Bol San Veg Plagas 19:401–423Grezes-Besset B, Lucante N, Kelechian V, Dargent R, Muller H (1996) Evaluation of castor bean resistance to sclerotial wilt disease caused by Macrophomina phaseolina. Plant Dis 80(8):842–846Hutcheson SW (1998) Current concepts of active defense in plants. Annu Rev Phytopathol 36:59–90Iglesias A, Picó B, Nuez F (2000) A temporal genetic analysis of disease resistance genes resistance to melon vine decline derived from Cucumis melo var. agrestis. Plant Breed 119:329–334Islam MS, Haque MS, Islam MM, Emdad EM, Halim A, Hossen QMM, Hossain MZ, Ahmed B, Rahim S, Rahman MS, Alam MM, Hou S, Wan X, Saito JÁ, Alam M (2012) Tools to kill: genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina. BMC Genomic 13(493):1–16Jacob CJ, Krarup C, Díaz A, Latorre BA (2013) A severe outbreak of charcoal rot in cantaloupe melon caused by Macrophomina phaseolina in Chile. Plant Dis 97(1):141Kaur S, Dhillon GS, Brar SK, Vallad GE, Chand R, Chauhan VB (2012) Emerging phytopathogen Macrophomina phaseolina: biology, economic importance and current diagnostic trends. Crit Rev Microbiol 38(1):136–151Keeling A (1982) Seedling test for resistance to soybean stem canker caused by diaporthe phaseolorum var. caulivora. Phytopathology 72(7):807–809Khan SN (2007) Macrophomina phaseolina as causal agent for charcoal rot of sunflower. Mycopath 5(2):111–118Khan SH, Shuaib M (2007) Identification of sources of resistance in Mung bean (Vigna radiata L.) against Charcoal Rot Macrophomina phaseolina (Tassi) Goid. Afr Crop Sci 8:2101–2102Krikun J, Orion D, Nachmias A, Reuveni R (1982) The role of soilborne pathogens under conditions of intensive agricultura. Phytoparasitica 10(4):247–258Mahmoudi SB, Ghashghaie S (2013) Reaction of sugar beet S1 lines and cultivars to different isolates of Macrophomina phaseolina and Rhizoctonia solani AG-2-2IIIB. Euphytica 190:39–445. doi: 10.1007/s10681-012-0832-8Mertely J, Seijo T, Peres N (2005) First report of Macrophomina phaseolina causing a crown rot of strawberry in Florida. Plant Dis 89(4):434Mughogho LK, Pande S (1984) Charcoal Rot of Sorghum. In: Mughogho LK, Rosenberg G (eds) Sorghum root and stalk rots, a critical review: proceedings of the consultative group discussion on research needs and strategies for control of sorghum root and stalk rot diseases. Icrisat, Bellagio, pp 11–24Nischwitz C, Olsen M, Rasmussen S (2004) Effect of irrigation type on inoculum density of Macrophomina phaseolina in melon fields in Arizona. J Phytopathol 152(3):133–137Noling JW, Becker JO (1994) The challenge of research and extension to define and implement alternatives to methyl bromide. J Nematol 26(4S):573–586Pitrat M (2008) Melon. In: Prohens J, Nuez F (eds) Handbook of plant breeding. Springer, New York, pp 283–315Purkayastha S, Kaur B, Dilbaghi N, Chaudhury A (2006) Characterization of Macrophomina phaseolina, the charcoal rot pathogen of cluster bean, using conventional techniques and PCR-based molecular markers. Plant Pathol 55:106–116. doi: 10.1111/j.1365-3059.2005.01317.xRadwan O, Rouhana LV, Hartman GL, Korban SS (2014) Genetic mechanisms of host-pathogen interactions for charcoal rot in soybean. Plant Mol Biol Report 32(3):617–629Ravf BA, Ahmad I (1998) Studies on correlation of seed infection to field incidence of Alternaria alternate and Macrophomina phaseolina in Sunflower. 13th Iranian Plant Protection Congress-Karaj, p 113Roustaee A, Reyhan MK, Jafari M (2011) Study of interaction between salinity and charcoal rot diseases of melon (Macrophomina phaseolina) in Semnan and Garmsar. Desert 16(2):175–218Salari M, Panjehkeh N, Nasirpoor Z, Abkhoo J (2012) Reaction of melón (Cucumis melo L.) cultivars to soil-borne plant pathogenic fungi in Iran. Afr J Biotecnol 11(87):15324–15329Sales R Jr, Oliveira OF, Medeiros EV, Guimarães IM, Correia KC, Michereff SJ (2012) Ervas daninhas como hospedeiras alternativas de patógenos causadores do colapso do meloeiro. Rev Ciênc Agron 43(1):195–198Sas Institute (2000) Sas/Stat user´s guide: statistics, version 8.01, v. 2, 4. SAS Institute, Inc, CaryScandiani MM, Ruberti DS, Giorda LM, Pioli RN, Luque AG, Bottai H, Ivancovich JJ, Aoki T, O´Donnell K (2011) Comparison of inoculation methods for characterizing relative aggressiveness of two soybean sudden-death syndrome pathogens, Fusarium virguliforme and F. tucumaniae. Trop Plant Pathol 36(3):133–140Scott AJ, Knott MA (1974) Cluster analysis method for grouping means in the analysis of variance. Biometrics 30(3):507–512Sebastian P, Schaefer H, Telford IRH, Renner SS (2010) Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia. Proc Natl Acad Sci 107:14269–14273Sharmishtha P, Bhavneet K, Neeraj D, Ashok C (2006) Evaluation of cluster bean genotypes for resistance to charcoal rot caused by Macrophomina phaseolina using different host inoculation methods pages. J Crop Improv 15(1):67–79Shekhar M, Sharma RC, Singh L, Dutta R (2006) Morphological and pathogenic variability of Macrophomina phaseolina (Tassi.) Goid Incitant of charcoal rot of maize in India. Indian Phytopath 59(3):294–298Stapleton JJ (2000) Soil solarization in various agricultural production systems. Crop Prot 19:837–841Twizeyimana M, Hill CB, Pawlowski M, Paul C, Hartman GL (2012) A cut-stem inoculation technique to evaluate soybean for resistance to Macrophomina phaseolina. Plant Dis 96(8):1210–1215Watson A, Napier T (2009) Disease of cucurbit vegetables. Primefact 832:1–6Wolukau JN, Zhou XH, Li Y, Zhang Y, Chen J (2007) Resistance to gummy stem blight in melon (Cucumis melo L.) germplasm and inheritance of resistance from plant introductions 157076, 420145, and 323498. HortScience 42(2):215–221Wrather JA, Anderson TR, Arsyad DM, Tan Y, Ploper LD, Porta-Puglia A, Ram HH, Yorinori JT (2001) Soybean disease loss estimates for the top ten soybean-producing countries in 1998. Can J Plant Pathol 23:115–12

Preoperative external beam radiotherapy and reduced dose brachytherapy for carcinoma of the cervix: survival and pathological response

PURPOSE: To evaluate the pathologic response of cervical carcinoma to external beam radiotherapy (EBRT) and high dose rate brachytherapy (HDRB) and outcome. MATERIALS AND METHODS: Between 1992 and 2001, 67 patients with cervical carcinoma were submitted to preoperative radiotherapy. Sixty-five patients were stage IIb. Preoperative treatment included 45 Gy EBRT and 12 Gy HDRB. Patients were submitted to surgery after a mean time of 82 days. Lymphadenectomy was performed in 81% of patients. Eleven patients with residual cervix residual disease on pathological specimen were submitted to 2 additional insertions of HDRB. RESULTS: median follow up was 72 months. Five-year cause specific survival was 75%, overall survival 65%, local control 95%. Complete pelvic pathological response was seen in 40%. Surgery performed later than 80 days was associated with pathological response. Pelvic nodal involvement was found in 12%. Complete pelvic pathological response and negative lymphnodes were associated with better outcome (p = .03 and p = .005). Late grade 3 and 4 urinary and intestinal adverse effects were seen in 12 and 2% of patients. CONCLUSION: Time allowed between RT and surgery correlated with pathological response. Pelvic pathological response was associated with improved outcome. Postoperative additional HDRB did not improve therapeutic results. Treatment was well tolerated

Scoping review of measures of treatment burden in patients with multimorbidity: advancements and current gaps

Objectives: To identify, assess, and summarize the measures to assess burden of treatment in patients with multimorbidity (BoT-MMs) and their measurement properties. Study Design and Setting: MEDLINE via PubMed was searched from inception until May 2021. Independent reviewers extracted data from studies in which BoT-MMs were developed, validated, or reported as used, including an assessment of their measurement properties (e.g., validity and reliability) using the COnsensus-based Standards for the selection of health Measurement INstruments. Results: Eight BoT-MMs were identified across 72 studies. Most studies were performed in English (68%), in high-income countries (90%), without noting urban-rural settings (90%). No BoT-MMs had both sufficient content validity and internal consistency; some measurement properties were either insufficient or uncertain (e.g., responsiveness). Other frequent limitations of BoT-MMs included absent recall time, presence of floor effects, and unclear rationale for categorizing and interpreting raw scores. Conclusion: The evidence needed for use of extant BoT-MMs in patients with multimorbidity remains insufficiently developed, including that of suitability for their development, measurement properties, interpretability of scores, and use in low-resource settings. This review summarizes this evidence and identifies issues needing attention for using BoT-MMs in research and clinical practice

Applications of Direct Injection Soft Chemical Ionisation-Mass Spectrometry for the Detection of Pre-blast Smokeless Powder Organic Additives

Analysis of smokeless powders is of interest from forensics and security perspectives. This article reports the detection of smokeless powder organic additives (in their pre-detonation condition), namely the stabiliser diphenylamine and its derivatives 2-nitrodiphenylamine and 4-nitrodiphenylamine, and the additives (used both as stabilisers and plasticisers) methyl centralite and ethyl centralite, by means of swab sampling followed by thermal desorption and direct injection soft chemical ionisation-mass spectrometry. Investigations on the product ions resulting from the reactions of the reagent ions H3O+ and O2+ with additives as a function of reduced electric field are reported. The method was comprehensively evaluated in terms of linearity, sensitivity and precision. For H3O+, the limits of detection (LoD) are in the range of 41-88 pg of additive, for which the accuracy varied between 1.5 and 3.2%, precision varied between 3.7 and 7.3% and linearity showed R20.9991. For O2+, LoD are in the range of 72 to 1.4 ng, with an accuracy of between 2.8 and 4.9% and a precision between 4.5 and 8.6% and R20.9914. The validated methodology was applied to the analysis of commercial pre-blast gun powders from different manufacturers.(VLID)4826148Accepted versio

Spin structure and first-order transition of GdIn(3): Near-surface magnetism, buried amplitude-modulated phase, and interface delocalization

A resonant x-ray magnetic diffraction study was performed for pure and (Cd,Ga)-doped GdIn(3) single crystals with cubic structure. All studied samples show an equal-magnitude antiferromagnetic spin structure with propagation vector (tau) over right arrow=[1/2, 1/2,0] at low temperatures, corresponding to a parallel spin propagation along the (c) over right arrow direction (normal to the studied surfaces) and antiparallel propagation along (a) over right arrow and (b) over right arrow. A complex magnetic behavior in the submicrometric near-surface region (NSR) was found close to T(N)(bulk) similar to 44 K. For both pure and substituted samples, a fairly strong signal from the equal-magnitude magnetic phase was found to survive above T(N)(bulk) and abruptly disappears at T(N)(NSR) similar to T(N)(bulk)+ 0.7 K, indicating that the NSR may show a larger T(N) than the bulk for all studied samples. For the pure compound only, satellite peaks consistent with an amplitude-modulated magnetic phase with a wavelength of 380 angstrom were found between T(N)(bulk) and T(N)(NSR). A successful fit of the scattering profile around several magnetic Bragg positions and photon energies, using a simple phase coexistence model, confirmed that the amplitude-modulated phase develops underneath the most superficial region showing the equal magnitude structure. The evolution of the magnetic scattering profile on cooling indicates that the interface between equal-magnitude and amplitude-modulated phases diverges towards the bulk as T -> T(N)(bulk) from above. A detailed analysis of the magnetic scattering, as well as the existence of a single bulk transition within the experimental sensitivity of our specific heat and magnetic susceptibility measurements, in contrast to the rich behavior shown by the near-surface region, indicates that the amplitude-modulated phase is not bulk representative, being actually sandwiched between the bulk paramagnetic and the equal-magnitude phases. Depth-temperature phase diagrams for pure and (Ga,Cd)-doped GdIn(3) are drawn on the basis of our results, which are discussed in terms of a three-phase coexistence scenario theoretically proposed for first-order transitions in the NSR.77