W–SPSA in Practice: Approximation of Weight Matrices and Calibration of Traffic Simulation Models

The development and calibration of complex traffic models demands parsimonious techniques, because such models often involve hundreds of thousands of unknown parameters. The Weighted Simultaneous Perturbation Stochastic Approximation (W-SPSA) algorithm has been proven more efficient than its predecessor SPSA (Spall, 1998), particularly in situations where the correlation structure of the variables is not homogeneous. This is crucial in traffic simulation models where effectively some variables (e.g. readings from certain sensors) are strongly correlated, both in time and space, with some other variables (e.g. certain OD flows). In situations with reasonably sized traffic networks, the difference is relevant considering computational constraints. However, W-SPSA relies on determining a proper weight matrix (W) that represents those correlations, and such a process has been so far an open problem, and only heuristic approaches to obtain it have been considered. This paper presents W-SPSA in a formally comprehensive way, where effectively SPSA becomes an instance of W-SPSA, and explores alternative approaches for determining the matrix W. We demonstrate that, relying on a few simplifications that marginally affect the final solution, we can obtain W matrices that considerably outperform SPSA. We analyse the performance of our proposed algorithm in two applications in motorway networks in Singapore and Portugal, using a dynamic traffic assignment model and a microscopic traffic simulator, respectively. Keywords: calibration algorithms; dynamic traffic assignment; microscopic traffic simulation; large–scale applications; optimisation; heuristic

Biochemical Basis of Topoisomerase I Relaxation Activity Reduction by Nonenzymatic Lysine Acetylation

The relaxation activity of topoisomerase I is required for regulation of global and local DNA supercoiling. The in vivo topoisomerase I enzyme activity is sensitive to lysine acetylation⁻deacetylation and can affect DNA supercoiling and growth as a result. Nonenzymatic lysine acetylation by acetyl phosphate has been shown to reduce the relaxation activity of topoisomerase I. In this work, the biochemical consequence of topoisomerase I modification by acetyl phosphate with enzymatic assays was studied. Results showed that noncovalent binding to DNA and DNA cleavage by the enzyme were reduced as a result of the acetylation, with greater effect on DNA cleavage. Four lysine acetylation sites were identified using bottom-up proteomics: Lys13, Lys45, Lys346, and Lys488. The Lys13 residue modified by acetyl phosphate has not been reported previously as a lysine acetylation site for topoisomerase I. We discuss the potential biochemical consequence of lysine acetylation at this strictly conserved lysine and other lysine residues on the enzyme based on available genetic and structural information

Fast, ultra-trace detection of juvenile hormone III from mosquitoes using mass spectrometry

In the present work, a new protocol for fast separation and quantification of JH III from biological samples using liquid chromatography coupled to electrospray tandem mass spectrometry is described. In particular, the proposed protocol improves existing methodologies by combining a limited number of sample preparation steps with fast LC-MS/MS detection, providing lower limits of detection and demonstrated matrix effect control, together with high inter and intraday reproducibility. A limit of detection of 8 pg/mL (0.32 pg on column) was achieved, representing a 15-fold gain in sensitivity with respect to previous LC-MS based protocols. The performance of the LC-MS/MS protocol is comparable to previously described JH III quantitation protocol based on fluorescence detection, with the added advantage that quantification is independent of the availability of fluorescent tags that are often unavailable or show quite diverse responses on a batch-to-batch basis. Additionally, a detailed description of the JH III fragmentation pathway is provided for the first time, based on isolation of the molecular ion and their intermediate fragments using in-source MS/MS, MS/MSn and FT-ICR MS/MS measurements. The JH III workflow was evaluated as a function of developmental changes, sugar feeding and farnesoic acid stimulation in mosquitoes and can be applied to the detection of other juvenile hormones

Transgene inheritances and genetic similarities of near isogenic lines of genetically modifi ed common beans

O objetivo do presente trabalho foi determinar a herança e a estabilidade de transgenes de uma linhagem de feijoeiro-comum com expressão dos genes rep-trap-ren, do Bean golden mosaic virus, e do gene bar. Foram realizados cruzamentos entre a linhagem transgênica e quatro cultivares comerciais de feijão, seguidos de quatro retrocruzamentos. As progênies de cada cruzamento foram avaliadas quanto à presença dos transgenes, com aplicação do glifosinato de amônia nas folhas e por meio da reação da polimerase em cadeia com uso de oligonucleotídeos específicos. O vírus do mosaico comum necrótico do feijoeiro, Bean common mosaic necrosis virus (BCMNV), foi inoculado mecanicamente nas gerações avançadas. Os transgenes foram herdados em padrão mendeliano nos quatro cruzamentos estudados. As linhagens analisadas apresentaram cerca de 80% das características do parental recorrente, conforme determinado por análises com uso de marcadores de DNA, além de manter caracteres importantes, tais como resistência ao BCMNV. A presença do transgene não causou efeitos indesejáveis que pudessem ser detectados nas progênies avaliadas.The objective of the present work was to determine the inheritance and stability of transgenes of a transgenic bean line expressing the genes rep-trap-ren from Bean golden mosaic virus and the bar gene. Crosses were done between the transgenic line and four commercial bean cultivars, followed by four backcrosses to the commercial cultivars. Progenies from each cross were evaluated for the presence of the transgenes by brushing the leaves with glufosinate ammonium and by polymerase chain reaction using specific oligonucleotides. Advanced generations were rub-inoculated with an isolate of Bean common mosaic necrosis virus (BCMNV). The transgenes were inherited consistently in a Mendelian pattern in the four crosses studied. The analyzed lines recovered close to 80% of the characteristics of the recurrent parent, as determined by the random amplified DNA markers used, besides maintaining important traits such as resistance to BCMNV. The presence of the transgene did not cause any detectable undesirable effect in the evaluated progenies

Lack of Association between Serum Serotonin, Eating Patterns, and Depression in Obese Women

Objective: The objective of this study was to determine the association between circulating serotonin concentrations, depressive symptoms, and dietary patterns in obese women. Methods: We studied 47 patients using the Beck Depression Scale, the 24-hour food registry, biochemical tests, and serum serotonin levels by high-performance liquid chromatography (HPLC). Results: The mean age of patients was 41.0 ± 10.0 years and their body mass index (BMI) was 36.9 ± 6.2 kg/m2. Depression was present in 34.0% of patients. There were no significant differences in serum serotonin concentrations between patients with or without depression (156.4 ± 63.5 vs. 147.7 ± 71.2 ng/mL; p = 0.357). The percentage of patients with abnormal serum serotonin concentrations and the presence of depression according to the degree of obesity were as follows: Class I 56.5% and 30.4%, Class II 54.5% and 36.5%, Class III 38.5% and 38.5%; p = .5 and p = .9, respectively). There were no significant correlations between serum serotonin concentrations and eating patterns related to calorie intake (r = 0.09, p = 0.5), carbohydrate intake (r = 0.03, p = 0.8), fat intake (r = 0.1, p = 0.2), or protein intake (r = 0.24, p = 0.09). Conclusion: We found that in adult women with obesity, there were no relationships between serum serotonin and nutrient intake, the presence of depression, or obesity severity

Sazonalidade no nicho trófico da abelha-sem-ferrão Frieseomelitta meadewaldoi (Cockerell, 1915) (Hymenoptera, Apidae)

Pollen samples collected by Frieseomelitta meadewaldoi were analyzed to determine the plants used and their pollen frequency and diversity, and thus test whether there is a correlation between its diversity with temperature or rainfall. In the rainy season, F. meadewaldoi explored 27 floral sources, with greater richness of pollen types from Fabaceae and Myrtaceae. In the dry season, 34 pollen types were recorded, with a great richness associated with Fabaceae, Rubiaceae, Anacardiaceae, and Myrtaceae. Sources of important floral resources and temporary specialization events occurred in both seasons, mainly Coutobea, Eucalyptus, Ligaria teretiflora, Mimosa pudica, Mollugo verticillata, Myrcia, Richardia grandiflora, and Tapirira guianensis. There was no correlation between the diversity of pollen resources and temperature or rainfall, as it depends on the availability of sources of floral resources. Thus, pollen diversity did not differ between months or seasons, as F. meadewaldoi foraging is similar throughout the year.Muestras de polen de Frieseomelitta meadewaldoi fueron analizadas para determinación de las plantas utilizadas y sus respectivas frecuencias de ocurrencia y diversidad, y así evaluar si existe correlación entre la diversidad de recursos con la temperatura y la pluviosidad. En la estación lluviosa, F. meadewaldoi visitó 27 fuentes florales, con mayor riqueza de tipos polínicos de Fabaceae y Myrtaceae. En la estación seca, fueron registrados 34 tipos polínicos, con mayor riqueza asociada a Fabaceae, Rubiaceae, Anacardiaceae y Myrtaceae. Fuentes de recursos florales importantes y eventos de especialización temporaria ocurrieron en ambas estaciones, con destaque para Coutobea, Eucalyptus, Ligaria teretiflora, Mimosa pudica, Mollugo, verticillata, Myrcia, Richardia grandiflora y Tapirira guianensis. No hubo correlación entre las diversidades de recurso polínico y la temperatura o la pluviosidad, pues depende de la disponibilidad de fuentes de recursos florales. Así, esa diversidad no difirió entre los meses o estaciones, pues el forrajeo de F. meadewaldoi es semejante a lo largo del año.Amostras de pólen de Frieseomelitta meadewaldoi foram analisadas para determinação das plantas utilizadas e respectivas frequências de ocorrência e diversidade, e assim testar se há correlação entre a diversidade de recursos com a temperatura ou a pluviosidade. Na estação chuvosa, F. meadewaldoi explorou 27 fontes florais, com maior riqueza de tipos polínicos de Fabaceae e Myrtaceae. Na estação seca, foram registrados 34 tipos polínicas, com maior riqueza associada a Fabaceae, Rubiaceae, Anacardiaceae e Myrtaceae. Fontes de recursos florais importantes e eventos de especialização temporária ocorreram em ambas as estações, com destaque para Coutobea, Eucalyptus, Ligaria teretiflora, Mimosa pudica, Mollugo verticillata, Myrcia, Richardia grandiflora e Tapirira guianensis. Não houve correlação entre diversidade de recursos polínicos e a temperatura ou pluviosidade, pois depende da disponibilidade de fontes de recursos florais. Assim, essa diversidade não diferiu entre os meses ou estações, pois o forrageio de F. meadewaldoi é semelhante ao longo do ano