LATENT RANK CHANGE DETECTION FOR ANALYSIS OF SPLICE-JUNCTION MICROARRAYS WITH NONLINEAR EFFECTS

Alternative splicing of gene transcripts greatly expands the functional capacity of the genome, and certain splice isoforms may indicate specific disease states such as cancer. Splice junction microarrays interrogate thousands of splice junctions, but data analysis is difficult and error prone because of the increased complexity compared to differential gene expression analysis. We present Rank Change Detection (RCD) as a method to identify differential splicing events based upon a straightforward probabilistic model comparing the over-or underrepresentation of two or more competing isoforms. RCD has advantages over commonly used methods because it is robust to false positive errors due to nonlinear trends in microarray measurements. Further, RCD does not depend on prior knowledge of splice isoforms, yet it takes advantage of the inherent structure of mutually exclusive junctions, and it is conceptually generalizable to other types of splicing arrays or RNA-Seq. RCD specifically identifies the biologically important cases when a splice junction becomes more or less prevalent compared to other mutually exclusive junctions. The example data is from different cell lines of glioblastoma tumors assayed with Agilent microarrays.

Contrasting photoelectrochemical behaviour of two isomeric supramolecular dyes based on meso-tetra(pyridyl)porphyrin incorporating four (mu(3)-oxo)- triruthenium(III) clusters

A saddle shaped tetracluster porphyrin species containing four [Ru(3)O(OAc)(6)(py)(2)](+) clusters coordinated to the N-pyridyl atoms of 5,10,15,20-tetra(3-pyridyl)porphyrin, H(2)(3-TCPyP), has been investigated in comparison with the planar tetra(4-pyridyl) porphyrin analogue H(2)(4-TCPyP). The steric effects from the bulky peripheral complexes play a critical role in the H(2)(3-TCPyP) species, determining a non-planar configuration around the porphyrin centre and precluding any significant pi-electronic coupling, in contrast with the less hindered H(2)(4-TCPyP) species. Both systems exhibit a photoelectrochemical response in the presence of nanocrystalline TiO(2) films, involving the porphyrin excitation around 450 nm. However, only in the H(2)(4-TCPyP) case do the cluster moieties also contribute to the photoinduced electron injection process at 670 nm, reflecting the relevance of the electronic coupling between the porphyrin centre and the peripheral complexes.

The Amazon Frontier of Land-Use Change: Croplands and Consequences for Greenhouse Gas Emissions

The Brazilian Amazon is one of the most rapidly developing agricultural frontiers in the world. The authors assess changes in cropland area and the intensification of cropping in the Brazilian agricultural frontier state of Mato Grosso using remote sensing and develop a greenhouse gas emissions budget. The most common type of intensification in this region is a shift from single-to double-cropping patterns and associated changes in management, including increased fertilization. Using the enhanced vegetation index (EVI) from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor, the authors created a green-leaf phenology for 2001-06 that was temporally smoothed with a wavelet filter. The wavelet-smoothed green-leaf phenology was analyzed to detect cropland areas and their cropping patterns. The authors document cropland extensification and double-cropping intensification validated with field data with 85% accuracy for detecting croplands and 64% and 89% accuracy for detecting single-and double-cropping patterns, respectively. The results show that croplands more than doubled from 2001 to 2006 to cover about 100 000 km(2) and that new double-cropping intensification occurred on over 20% of croplands. Variations are seen in the annual rates of extensification and double-cropping intensification. Greenhouse gas emissions are estimated for the period 2001-06 due to conversion of natural vegetation and pastures to row-crop agriculture in Mato Grosso averaged 179 Tg CO(2)-e yr(-1),over half the typical fossil fuel emissions for the country in recent years.

Influence of land-use change on near-surface hydrological processes: Undisturbed forest to pasture

Soil compaction that follows the clearing of tropical forest for cattle pasture is associated with lower soil hydraulic conductivity and increased frequency and volume of overland flow. We investigated the frequency of perched water tables, overland flow and stormflow in an Amazon forest and in an adjacent 25-year-old pasture cleared from the same forest. We compared the results with the frequencies of these phenomena estimated from comparisons of rainfall intensity and soil hydraulic conductivity. The frequency of perched water tables based on rainfall intensity and soil hydraulic conductivity was expected to double in pasture compared with forest. This corresponded closely with an approximate doubling of the frequency of stormflow and overland flow in pasture. In contrast, the stormflow volume in pasture increased 17-fold. This disproportional increase of stormflow resulted from overland flow generation over large areas of pasture, while overland flow generation in the forest was spatially limited and was observed only very near the stream channel. In both catchments, stormflow was generated by saturation excess because of perched water tables and near-surface groundwater levels. Stormflow was occasionally generated in the forest by rapid return flow from macropores, while slow return flow from a continuous perched water table was more common in the pasture. These results suggest that deforestation for pasture alters fundamental mechanisms of stormflow generation and may increase runoff volumes over wide regions of Amazonia. (C) 2009 Elsevier B.V. All rights reserved.

Implications of long-term land-use change for the hydrology and solute budgets of small catchments in Amazonia

The replacement of undisturbed tropical forest with cattle pasture has the potential to greatly modify the hydrology of small watersheds and the fluxes of solutes. We examined the fluxes of water, Cl(-), NO(3)(-)-N: SO(4)(2--)-S, NH(4)(+)-N, Na(+), K(+), Mg(2+) and Ca(2+) in different flow paths in similar to 1 ha catchments of undisturbed open tropical rainforest and a 20 year-old pasture established from forest in the southwestern Brazilian Amazon state of Rondonia. Storm flow discharge was 18% of incident rainfall in pasture, but only 1% in forest. Quickflow predominated over baseflow in both catchments and in both wet and dry seasons. In the pasture, groundwater and quickflow were important flow paths for the export of all solutes. In the forest, quickflow was important for NO(3)(-)-N export, but all other solutes were exported primarily by groundwater outflow. Both catchments were sinks for SO(4)(2-)-S and Ca(2+), and sources of Na(+). The pasture catchment also lost K(+) and Mg(2+) because of higher overland flow frequency and volume and to cattle excrement. These results show that forest clearing dramatically influences small watershed hydrology by increasing quickflow and water export to streams. They also indicate that tropical forest watersheds are highly conservative for most solutes but that pastures continue to lose important cations even decades after deforestation and pasture establishment. (c) 2008 Elsevier B.V. All rights reserved.

Runoff sources and land cover change in the Amazon: an end-member mixing analysis from small watersheds

The flowpaths by which water moves from watersheds to streams has important consequences for the runoff dynamics and biogeochemistry of surface waters in the Amazon Basin. The clearing of Amazon forest to cattle pasture has the potential to change runoff sources to streams by shifting runoff to more surficial flow pathways. We applied end-member mixing analysis (EMMA) to 10 small watersheds throughout the Amazon in which solute composition of streamwater and groundwater, overland flow, soil solution, throughfall and rainwater were measured, largely as part of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia. We found a range in the extent to which streamwater samples fell within the mixing space determined by potential flowpath end-members, suggesting that some water sources to streams were not sampled. The contribution of overland flow as a source of stream flow was greater in pasture watersheds than in forest watersheds of comparable size. Increases in overland flow contribution to pasture streams ranged in some cases from 0% in forest to 27-28% in pasture and were broadly consistent with results from hydrometric sampling of Amazon forest and pasture watersheds that indicate 17- to 18-fold increase in the overland flow contribution to stream flow in pastures. In forest, overland flow was an important contribution to stream flow (45-57%) in ephemeral streams where flows were dominated by stormflow. Overland flow contribution to stream flow decreased in importance with increasing watershed area, from 21 to 57% in forest and 60-89% in pasture watersheds of less than 10 ha to 0% in forest and 27-28% in pastures in watersheds greater than 100 ha. Soil solution contributions to stream flow were similar across watershed area and groundwater inputs generally increased in proportion to decreases in overland flow. Application of EMMA across multiple watersheds indicated patterns across gradients of stream size and land cover that were consistent with patterns determined by detailed hydrometric sampling.

Change in central kinin B2 receptor density after exercise training in rats

Cardiovascular responses elicited by the stimulation of kinin B2 receptors in the IV cerebral ventricle paratrigeminal nucleus or in the thoracic spinal cord are similar to those observed during an exercise bout Considering that the kalikrein-kinin system (KKS) could act on the cardiovascular modulation during behavioral responses as physical exercise or stress this study evaluated the central B2 receptor densities of Wistar (W) and spontani ously hypertensive rats (SHR) after chronic moderate exercise Animals we re exercise-trained for ten weeks on a treadmill Afterwards systolic blood pressure decreased in both trained strains Animals were killed and the medulla and spinal cord extracted for B2 receptor autoradiography Trained animals were compared to their sedentary controls Sedentary groups showed specific binding sites for Hoe-140 (fmol/mg of tissue) in laminas 1 and 2 of the spinal cord nucleus of the solitary tract (NTS) area postrema (AP) spinal trigeminal tract (sp5) and paratrigeminal nucleus (Pa5) In trained W a significant increase (p<0 05) in specific binding was observed in the Pa5 (31 3%) and NTS (28 2%) Trained SHR showed a significant decrease in n ceptor density in lamina 2 (21 9%) of the thoracic spinal cord and an increase in specific binding in Pa5 (36 1%) We suggest that in the medulla chronic exercise could hyper stimulate the KKS enhancing their efficiency through the increase of B2 receptor density involving this receptor in central cardiovascular control during exercise or stress In the lamina 2 B2 receptor might be involved in the exercise-induced hypotension (C) 2010 Elsevier BV All rights reserved

Cardiac and peripheral adjustments induced by early exercise training intervention were associated with autonomic improvement in infarcted rats: role in functional capacity and mortality

Aims To test the effects of early exercise training (ET) on left ventricular (LV) and autonomic functions, haemodynamics, tissues blood flows (BFs), maximal oxygen consumption (VO(2) max), and mortality after myocardial infarction (MI) in rats. Methods and results Male Wistar rats were divided into: control (C), sedentary-infarcted (SI), and trained-infarcted (TI). One week after MI, TI group underwent an ET protocol (90 days, 50-70% VO2 max). Left ventricular function was evaluated noninvasively and invasively. Baroreflex sensitivity, heart rate variability, and pulse interval were measured. Cardiac output (CO) and regional BFs were determined using coloured microspheres. Infarcted area was reduced in TI (19 +/- 6%) compared with SI (34 +/- 5%) after ET. Exercise training improved the LV and autonomic functions, the CO and regional BF changes induced by MI, as well as increased SERCA2 expression and mRNA vascular endothelial growth factor levels. These changes brought about by ET resulted in mortality rate reduction in the TI (13%) group compared with the SI (54%) group. Conclusion Early aerobic ET reduced cardiac and peripheral dysfunctions and preserved cardiovascular autonomic control after MI in trained rats. Consequently, these ET-induced changes resulted in improved functional capacity and survival after MI.

Clinic and ambulatory blood pressure responses after resistance exercise

Queiroz, ACC, Gagliardi, JFL, Forjaz, CLM, and Rezk, CC. Clinic and ambulatory blood pressure responses after resistance exercise. J Strength Cond Res 23(2): 571-578, 2009-This study investigated clinic and ambulatory blood pressure (BP) responses after a single bout of low-intensity resistance exercise in normotensive subjects. Fifteen healthy subjects underwent 2 experimental sessions: control-40 minutes of seated rest, and exercise-6 resistance exercises, with 3 sets of as many repetitions as possible until moderate fatigue, with an intensity of 50% of 1-repetition maximum (1RM). Before and for 60 minutes after interventions, clinic BP was measured by auscultatory and oscillometric methods. Postintervention ambulatory BP levels were also measured for 24 hours. In comparison with preintervention values, clinic systolic BP, as measured by the auscultatory method, did not change in the control group, but it decreased after exercise (-3.7 +/- 1.6 mm Hg, p < 0.05). Diastolic and mean BP levels increased after intervention in the control group (+3.4 +/- 1.0 and +3.0 +/- 0.8 mm Hg, respectively, p, 0.05) and decreased in the exercise group (-3.6 +/- 1.7 and -3.4 +/- 1.4 mm Hg, respectively, p < 0.05). Systolic and mean oscillometric BP levels did not change after interventions either in the control or exercise sessions, whereas diastolic BP increased after intervention in the control group (+5.0 +/- 1.7 mm Hg, p < 0.05) but not change after exercise. Ambulatory BP behaviors after interventions were similar in the control and exercise sessions. Significant and positive correlations were observed between preexercise values and postexercise clinic and ambulatory BP decreases. In conclusion, in the whole sample, a single bout of low-intensity resistance exercise decreased postexercise BP under clinic, but not ambulatory, conditions. However, considering individual responses, postexercise clinic and ambulatory hypotensive effects were greater in subjects with higher preexercise BP levels.

Behaviour of biofuel addition on metallurgical properties of sinter

Blast furnace gas yield is essentially controlled by a gas-solid reaction phenomenon, which strongly influences hot metal manufacturing costs. As a result of rising prices for reducing agents on the international market, Companhia Siderurgica Nacional decided to inject natural gas into its blast furnaces. With more gas inside the furnace, the burden permeability became even more critical. To improve blast furnace gas yield, a new technological approach was adopted; raising the metallic burden reaction surface. To that end, a special sinter was developed with permeability being controlled by adding micropore nucleus forming agents, cellulignin coal, without, however, degrading its mechanical properties. This paper shows the main process parameters and the results from physicochemical characterisation of a sinter with controlled permeability, on a pilot scale, compared to those of conventional sinter. Gas flow laboratory simulations have conclusively corroborated the positive effects of micropore nucleus forming agents on enhancing sinter permeability.

Wetting behaviour of silicon nitride ceramics by Ti-Cu alloys

The wetting of Ti-Cu alloys on Si3N4 was analyzed by the sessile drop method, using an imaging system with a CCD camera during the heating under argon flow. The contact angle was measured as a function of temperature and time. The samples were cut transversally and characterized by scanning electron microscopy and energy dispersive spectrometry (SEM/EDS). Wettability of the Ti-Cu alloy on Si3N4 is influenced by the reaction between the Ti and the ceramic. The TC1 and TC2 alloys presented low final contact angle values around 2 degrees and 26 degrees, respectively, indicating good wetting on Si3N4. (c) 2006 Elsevier Ltd and Techna Group S.r.l. All rights reserved.

Crystallisation behaviour and glass-forming ability in Al-La-Ni system

The crystallisation behaviour for alloys in the Al-rich corner in the Al-La-Ni system is reported in this paper Alloys were selected based on the topological instability criterion (lambda criterion) calculated from the alloy composition and metallic radii of the alloying elements and aluminum Amorphous ribbons were produced by melt-spinning and the crystallisation reactions were analysed by X-ray diffraction and calorimetry The results showed that increasing the values of lambda from 0.072 to 0.16 resulted in the following changes in the crystallisation behaviour, as predicted by the lambda criterion (a) nanocrystallisation of alpha-Al for the alloy composition corresponding to lambda = 0 072 and (b) detection of the glass transition temperature, T(g), for the alloys with composition close to lambda approximate to 0.1 line. For compositions corresponding to both ends of the lambda approximate to 0 1 line (near the binaries lines) T(g) could be detected only in the ""intermediary"" central region, and the alloy we produced in this region was considered the best glass former for the Al-rich corner Also, except for the alloys with the highest NI content, crystallisation proceeded by two distinct exothermic peaks which are typical of nanocrystallisation transformation. These behaviours are discussed in terms of compositional (lambda parameter) and topological aspects to account for cluster formation in the amorphous phase. Crown Copyright (C) 2009 Published by Elsevier B V All rights reserved

The effects of skin-to-skin contact during acute pain in preterm newborns

Background and purpose: Several promising non-pharmacological interventions have been developed to reduce acute pain in preterm infants including skin-to-skin contact between a mother and her infant. However, variability in physiological outcomes of existing studies on skin-to-skin makes it difficult to determine treatment effects of this naturalistic approach for the preterm infant. The aim of this study was to test the efficacy of mother and infant skin-to-skin contact during heel prick in premature infants. Method: Fifty nine stable preterm infants (born at least 30 weeks gestational age) who were undergoing routine heel lance were randomly assigned to either 15 min of skin-to-skin contact before, during and following heel prick (n = 31, treatment group), or to regular care (n = 28, control group). Throughout the heel lance procedure, all infants were assessed for change in facial action (NFCS), behavioral state, crying, and heart rate. Results: Statistically significant differences were noted between the treatment and control groups during the puncture, heel squeeze and the post phases of heel prick. Infants who received skin-to-skin contact were more likely to show lower NFCS scores throughout the procedure. Both groups of infants cried and showed increased heart rate during puncture and heel squeeze although changes in these measures were less for the treated infants. Conclusions: Skin-to-skin contact promoted reduction in behavioral measures and less physiological increase during procedure. It is recommended that skin-to-skin contact be used as a non-pharmacologic intervention to relieve acute pain in stable premature infants born 30 weeks gestational age or older. (C) 2007 European Federation of Chapters of the International Association for the Study of Pain. Published by Elsevier Ltd. All rights reserved.

Experimental Analysis of Structural Change and Rheological Behavior of Macromolecular Solutions with Guar and Xanthan Gums in Crossflow Microfiltration Processing

The present paper reports on the structural change and rheological behavior of mixtures of macromolecular suspensions (guar and xanthan gums) in crossflow microfiltration processing. Mixtures in suspension of guar and xanthan gums at low concentrations (1,000 ppm) and different proportions were processed by microfiltration with membrane of nominal pore size of 0.4 mu m. The rheological behavior of the mixtures was investigated in rotational viscometers at two different temperatures, 25 and 40 C, at the beginning and at the end of each experiment. The shear stress (t) in function of the shear rate (gamma) was fitted and analyzed with the power-law model. All the mixtures showed flow behavior index values (n) lower than 1, characterizing non-Newtonian fluids (pseudoplastic). The samples of both mixtures and permeates were also analyzed by absorbency spectroscopy in infrared radiation. The absorbency analysis showed that there is good synergism between xanthan and guar gums without structure modifications or gel formation in the concentration process by microfiltration.

A discussion on volume change in the plastic phase

This technical note discusses the possibility of using a more simplified scheme to estimate the plastic multiplier when some material shows volume changes, e.g. soil, balsa wood foam and other similar materials. Two procedures regarding volume changes during the plastic phase are discussed here. The first one is the classic procedure applied to non-associative plasticity, for which a Drucker-Prager-like surface is adopted to represent the plastic potential. For the second procedure, the plastic potential is not explicitly known, however, its orthogonal direction is chosen respecting a plastic volume change parameter similar to Poisson`s ratio. Copyright (C) 2007 John Wiley & Sons, Ltd.