Commissioning and performance of the CMS silicon strip tracker with cosmic ray muons

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Analytic element modelling for strip aquifers

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Foraminiferal ecological zonation along a Brazilian mangrove transect: Diversity, morphotypes and the influence of subaerial exposure time.

Two foraminiferal associations comprising only arenaceous species define two distinct environments in a 340 m-long mangrove transect at Cardoso Island, Trapande Bay (Cananeia-Iguape estuarine system, SP, Brazil). The "lower muddy flat" (LMF), from the outer mangrove fringe inwards towards land (100 m), is positioned in the lower plain between 0.04 and 0.23 m above the mean sea level (msl), and remains subaerially exposed between 48.5 and 65.6% of the time. This environment is characterized by higher foraminiferal diversity and evenness (McIntosh's D = 0.54 [plus or minus] 0.21 and Pielou's E = 0.68 [plus or minus] 0.25, respectively) and is dominated by Arenoparrella mexicana and Trochammina inflata, and to a lesser extent by Ammotium directum and Textularia earlandi. The mangrove plant of this segment is a Rhizophoretum with average height of 8.4 [plus or minus] 1.2 m. The sediment is characterized by higher concentration of organic matter (93.5 [plus or minus] 32.3 g dm-3) and metals (e.g. V = 53.4 [plus or minus] 21.8 ppm and Zn = 46.4 [plus or minus] 21.3 ppm). The "upper sandy flat" (USF), 240 m wide along the transect, is positioned in the upper plain between 0.28 and 0.89 m above the msl, and remains subaerially exposed between 69.7 and 98.5% of the time. This environment is characterized by a lower diversity and evenness (D = 0.33 [plus or minus] 0.17 and E = 0.49 [plus or minus] 0.20, respectively). The association is dominated by species T. inflata and Miliammina fusca. The Rhizophoretum exhibits a lower average height of 3.6 [plus or minus] 0.6 m. The sediment is poorer in organic matter (39.3 [plus or minus] 15.0 g dm-3) and metals (e.g. V = 13.0 [plus or minus] 6.8 ppm and Zn = 6.9 [plus or minus] 3.7 ppm). Whereas "elongate" tests (uniserial, biserial and planospiral followed by a uniserial portion) are restricted to the LMF, "spiraled" species dominate the USF. Subaerial exposure time seems to exert a primary influence on species distribution, in addition to salinity and sediment type. Species may be adapted to different exposure times, a factor dependent on their position on the intertidal zone and the tidal regime, which should be taken into account in relative sea level reconstructions based on intertidal foraminifera. These patterns have important implications for studies investigating the ecology and paleoecology of foraminifera and subtle fluctuations in relative sea level during the Quaternary.

Effects of hand weeding strip and nitrogen fertilizer on corn plants

The objective of the present research was to evaluate effects of different strip weed control associated with nitrogen fertilizer on corn applied after planting. The experiment was set and conducted in Botucatu, São Paulo State, Brazil, and the hybrid planted was Dekalb 333-B. A completely randomized block design with four replications was used. Experimental plots were disposed as a factorial scheme 2 x 2 x 4, constituted by two types of weeding on row (with or without manual hoeing), two types of weeding on inter-row (with or without manual hoeing), and four nitrogen levels applied after planting (00, 60, 90, and 120 kg ha-1). Plots were composed by six rows with 5 m length. Nitrogen fertilizer was applied at 35 days after emergence (d.a.e). For weed community it was evaluated: weed density, dominancy, frequency, and relative importance. The main weed species were: Brachiaria plantiginea, Amaranthus retroflexus, Bidens pilosa, Cyperus rotunds, Brachiaria decumbens, Euphorbia heterofila, Oxalis latifolia, Acanthospermum hispidum, Commelina benghalensis. It was evaluated corn height at 40 and 100 d.a.e., first ear insertion height at 100 d.a.e., and final grain yield at harvesting. Plants and first ear insertion height were affected when nitrogen fertilizer was not applied. Treatments without weed control showed that weed interfered negatively with plants height. There were no correlation between weeds and nitrogen fertilizer for all parameters evaluated. Parcels without weed showed the highest ear weights and final grain production. Treatments that received nitrogen fertilizer, independently of studied arrangement, provided higher yields.

Performance of the CMS cathode strip chambers with cosmic rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47μm to 243μm. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns. © 2010 IOP Publishing Ltd and SISSA.

Low toxic effects of a whitening strip to cultured pulp cells

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Pesquisa de genes de resistência do M. tuberculosis a isoniazida e rifampicina por sequenciamento e pela tecnologia de DNA-STRIP

Tuberculose (TB), causada por Mycobacterium tuberculosis, é uma das doenças infecciosas que mais causam mortes. Estima-se que mais de dois bilhões de pessoas estejam infectadas no mundo. O tratamento da TB consite em associação de fármacos, isoniazida, rifampicina, pirazinamida e etambutol, nos primeiros 2 meses e 4 meses de isoniazida e de rifampicina. Internacionalmente, são consideradas cepas multi resistentes (MDR), as que apresentam resistência simultânea a isoniazida e a rifampicina. A rápida detecção de resistência é essencial para o controle e tratamento da TB, reduzindo, assim, o custo do tratamento e a transmissão da doença. Neste projeto, os isolados já identificados fenotipicamente como resistentes a isoniazida e/ou rifampicina, foram submetidos ao sequenciamento de Sanger para pesquisa de 3 genes relacionados a resistência a isoniazida (katG, inhA e ahpC) e 1 gene de resistência a rifampicina (rpoB). Foi realizada uma comparação destes genes mutados para a resistência utilizando o novo teste desenvolvido pela Biomérieux, denominado GenoType® MTBDRplus, que se baseia na tecnologia DNA-STRIP. Através deste novo teste, foi observada mutação em 22 isolados clínicos de M. tuberculosis para genes de resistência a isoniazida e/ou rifampicina, sendo 4 provenientes do MS e 18 de SP. Já pelo sequenciamento genético foi observada mutação em 24 isolados para genes de resistência a isoniazida e/ou rifampicina, sendo 6 provenientes do MS e 18 de SP. Portanto, através do sequenciamento de Sanger, foi possível detectar um número maior de isolados mutados e mais mutações quando comparado ao teste GenoType® MTBDRplus. Isso acontece porque na técnica de sequenciamento, um fragmento do gene como um todo é analisado e no caso do teste GenoType® MTBDRplus, é verificada apenas a ausência ou presença das mutações mais frequentes descritas na literatura, além de não ser analisado o gene ahpC. A grande ...

Low toxic effects of a whitening strip to cultured pup cells

Fundacao de Amparo a Pesquisa do Estado de sao Paulo (FAPESP)

Estimating abundance of killer whales in the nearshore waters of the Gulf of Alaska and Aleutian Islands using line-transect sampling

Killer whale (Orcinus orca Linnaeus, 1758) abundance in the North Pacific is known only for a few populations for which extensive longitudinal data are available, with little quantitative data from more remote regions. Line-transect ship surveys were conducted in July and August of 2001–2003 in coastal waters of the western Gulf of Alaska and the Aleutian Islands. Conventional and Multiple Covariate Distance Sampling methods were used to estimate the abundance of different killer whale ecotypes, which were distinguished based upon morphological and genetic data. Abundance was calculated separately for two data sets that differed in the method by which killer whale group size data were obtained. Initial group size (IGS) data corresponded to estimates of group size at the time of first sighting, and post-encounter group size (PEGS) corresponded to estimates made after closely approaching sighted groups.

Results from the April 2009 Gulf of Alaska Line Transect Survey (GOALS) in the Navy Training Exercise Area

Little is known about the present-day occurrence of cetaceans found in offshore waters in the Gulf of Alaska; however, whaling records and a few recent surveys have shown this area to be important habitat. The U.S. Navy maintains a maritime training area in the central Gulf of Alaska, east of Kodiak Island, and has requested additional information on marine mammal presence and use of this area. To describe the occurrence and distribution of marine mammals in and around the U.S. Navy training area, a line transect visual and acoustic survey was conducted 10-20 April 2009 from the NOAA ship Oscar Dyson. The primary survey area encompassed nearshore and offshore pelagic waters of the central Gulf of Alaska. Survey lines were designed to provide equal coverage of the nearshore and offshore habitat.

Double-Observer Line Transect Methods: Levels of Independence

Double-observer line transect methods are becoming increasingly widespread, especially for the estimation of marine mammal abundance from aerial and shipboard surveys when detection of animals on the line is uncertain. The resulting data supplement conventional distance sampling data with two-sample mark–recapture data. Like conventional mark–recapture data, these have inherent problems for estimating abundance in the presence of heterogeneity. Unlike conventional mark–recapture methods, line transect methods use knowledge of the distribution of a covariate, which affects detection probability (namely, distance from the transect line) in inference. This knowledge can be used to diagnose unmodeled heterogeneity in the mark–recapture component of the data. By modeling the covariance in detection probabilities with distance, we show how the estimation problem can be formulated in terms of different levels of independence. At one extreme, full independence is assumed, as in the Petersen estimator (which does not use distance data); at the other extreme, independence only occurs in the limit as detection probability tends to one. Between the two extremes, there is a range of models, including those currently in common use, which have intermediate levels of independence. We show how this framework can be used to provide more reliable analysis of double-observer line transect data. We test the methods by simulation, and by analysis of a dataset for which true abundance is known. We illustrate the approach through analysis of minke whale sightings data from the North Sea and adjacent waters.

Paleoclimate Reconstruction Along The Pole-Equator-Pole Transect of the Americas (PEP 1)

Examples are presented of inter-hemispheric comparison of instrumental climate and paleoclimate proxy records from the Americas for different temporal scales. Despite a certain symmetry of seasonal precipitation patterns along the PEP 1 transect, decadal variability of winter precipitation shows different characteristics in terms of amplitude and frequency in both the last 100 and last 1000 years. Such differences in variability are also seen in a comparison of time series of different El Nino/Southern Oscillation proxy records from North and South America, however, these differences do not appear to affect the spatial correlation with Pacific sea surface temperature patterns. Local and regional differences in response to climate change are even more pronounced for records with lower temporal resolution, and inter-hemispheric synchroneity may or may not be indicative of the same forcing. This aspect is illustrated in an inter-hemispheric comparison of the last 1000 years of glacier variability, and of the full- and late-glacial lake level history.

Vertical distribution of benthic invertebrate larvae during an upwelling event along a transect off the tropical Brazilian continental margin

Abundance and composition of marine benthic communities have been relatively well studied in the SE Brazilian coast, but little is known on patterns controlling the distribution of their planktonic larval stages. A survey of larval abundance in the continental margin, using a Multi-Plankton Sampler, was conducted in a cross-shelf transect off Cabo Frio (23 degrees S and 42 degrees W) during a costal upwelling event. Hydrographic conditions were monitored through discrete CDT casts. Chlorophyll-a in the top 100 m of the water column was determined and changes in surface chlorophyll-a was estimated using SeaWiFS images. Based on the larval abundances and the meso-scale hydrodynamics scenario, our results suggest two different processes affecting larval distributions. High larval densities were found nearshore due to the upwelling event associated with high chlorophyll a and strong along shore current. On the continental slope, high larval abundance was associated with a clockwise rotating meander, which may have entrapped larvae from a region located further north (Cabo de Sao Tome, 22 degrees S and 41 degrees W). In mid-shelf areas, our data suggests that vertical migration may likely occur as a response to avoid offshore transport by upwelling plumes and/or cyclonic meanders. The hydrodynamic scenario observed in the study area has two distinct yet extremely important consequences: larval retention on food-rich upwelling areas and the broadening of the tropical domain to southernmost subtropical areas. (C) 2009 Elsevier B.V. All rights reserved.

An algorithm for the strip packing problem using collision free region and exact fitting placement

The irregular shape packing problem is approached. The container has a fixed width and an open dimension to be minimized. The proposed algorithm constructively creates the solution using an ordered list of items and a placement heuristic. Simulated annealing is the adopted metaheuristic to solve the optimization problem. A two-level algorithm is used to minimize the open dimension of the container. To ensure feasible layouts, the concept of collision free region is used. A collision free region represents all possible translations for an item to be placed and may be degenerated. For a moving item, the proposed placement heuristic detects the presence of exact fits (when the item is fully constrained by its surroundings) and exact slides (when the item position is constrained in all but one direction). The relevance of these positions is analyzed and a new placement heuristic is proposed. Computational comparisons on benchmark problems show that the proposed algorithm generated highly competitive solutions. Moreover, our algorithm updated some best known results. (C) 2012 Elsevier Ltd. All rights reserved.

Can Roads Be Used as Transects for Primate Population Surveys?

Line transect distance sampling (LTDS) can be applied to either trails or roads. However, it is likely that sampling along roads might result in biased density estimates. In this paper, we compared the results obtained with LTDS applied on trails and roads for two primate species (Callithrix penicillata and Callicebus nigrifrons) to clarify whether roads are appropriate transects to estimate densities. We performed standard LTDS surveys in two nature reserves in south-eastern Brazil. Effective strip width and population density were different between trails and roads for C. penicillata, but not for C. nigrifrons. The results suggest that roads are not appropriate for use as transects in primate surveys, at least for some species. Further work is required to fully understand this issue, but in the meantime we recommend that researchers avoid using roads as transects or treat roads and trails as covariates when sampling on roads is unavoidable. Copyright (C) 2012 S. Karger AG, Basel