Ultra-Deep Sequencing Reveals the microRNA Expression Pattern of the Human Stomach

Background: While microRNAs (miRNAs) play important roles in tissue differentiation and in maintaining basal physiology, little is known about the miRNA expression levels in stomach tissue. Alterations in the miRNA profile can lead to cell deregulation, which can induce neoplasia. Methodology/Principal Findings: A small RNA library of stomach tissue was sequenced using high-throughput SOLiD sequencing technology. We obtained 261,274 quality reads with perfect matches to the human miRnome, and 42% of known miRNAs were identified. Digital Gene Expression profiling (DGE) was performed based on read abundance and showed that fifteen miRNAs were highly expressed in gastric tissue. Subsequently, the expression of these miRNAs was validated in 10 healthy individuals by RT-PCR showed a significant correlation of 83.97% (P<0.05). Six miRNAs showed a low variable pattern of expression (miR-29b, miR-29c, miR-19b, miR-31, miR-148a, miR-451) and could be considered part of the expression pattern of the healthy gastric tissue. Conclusions/Significance: This study aimed to validate normal miRNA profiles of human gastric tissue to establish a reference profile for healthy individuals. Determining the regulatory processes acting in the stomach will be important in the fight against gastric cancer, which is the second-leading cause of cancer mortality worldwide.

Ablation Rate and Morphology of Superficial and Deep Dentin Irradiated with Different Er:YAG Laser Energy Levels

Objective: In this study we evaluated the ablation rate of superficial and deep dentin irradiated with different Er:YAG laser energy levels, and observed the micromorphological aspects of the lased substrates with a scanning electron microscope (SEM). Background Data: Little is known about the effect of Er: YAG laser irradiation on different dentin depths. Materials and Methods: Sixty molar crowns were bisected, providing 120 specimens, which were randomly assigned into two groups ( superficial or deep dentin), and later into five subgroups (160, 200, 260, 300, or 360 mJ). Initial masses of the specimens were obtained. After laser irradiation, the final masses were obtained and mass losses were calculated followed by the preparation of specimens for SEM examination. Mass-loss values were subjected to two-way ANOVA and Fisher's least significant difference multiple-comparison tests (p < 0.05). Results: There was no difference between superficial and deep dentin. A significant and gradual increase in the mass-loss values was reached when energies were raised, regardless of the dentin depth. The energy level of 360 mJ showed the highest values and was statistically significantly different from the other energy levels. The SEM images showed that deep dentin was more selectively ablated, especially intertubular dentin, promoting tubule protrusion. At 360 mJ the micromorphological features were similar for both dentin depths. Conclusion: The ablation rate did not depend on the depth of the dentin, and an energy level lower than 360 mJ is recommended to ablate both superficial and deep dentin effectively without causing tissue damage.

Deep sequencing of New World screw-worm transcripts to discover genes involved in insecticide resistance

Background: The New World screw-worm (NWS), Cochliomyia hominivorax, is one of the most important myiasis-causing flies, causing severe losses to the livestock industry. In its current geographical distribution, this species has been controlled by the application of insecticides, mainly organophosphate (OP) compounds, but a number of lineages have been identified that are resistant to such chemicals. Despite its economic importance, only limited genetic information is available for the NWS. Here, as a part of an effort to characterize the C. hominivorax genome and identify putative genes involved in insecticide resistance, we sampled its transcriptome by deep sequencing of polyadenylated transcripts using the 454 sequencing technology. Results: Deep sequencing on the 454 platform of three normalized libraries (larval, adult male and adult female) generated a total of 548,940 reads. Eighteen candidate genes coding for three metabolic detoxification enzyme families, cytochrome P450 monooxygenases, glutathione S transferases and carboxyl/cholinesterases were selected and gene expression levels were measured using quantitative real-time polymerase chain reaction (qRT-PCR). Of the investigated candidates, only one gene was expressed differently between control and resistant larvae with, at least, a 10-fold down-regulation in the resistant larvae. The presence of mutations in the acetylcholinesterase (target site) and carboxylesterase E3 genes was investigated and all of the resistant flies presented E3 mutations previously associated with insecticide resistance. Conclusions: Here, we provided the largest database of NWS expressed sequence tags that is an important resource, not only for further studies on the molecular basis of the OP resistance in NWS fly, but also for functional and comparative studies among Calliphoridae flies. Among our candidates, only one gene was found differentially expressed in resistant individuals, and its role on insecticide resistance should be further investigated. Furthermore, the absence of mutations in the OP target site and the high frequency of mutant carboxylesterase E3 indicate that metabolic resistance mechanisms have evolved predominantly in this species.

Crystallization, data collection and data processing of maltose-binding protein (MalE) from the phytopathogen Xanthomonas axonopodis pv. citri

Maltose-binding protein is the periplasmic component of the ABC transporter responsible for the uptake of maltose/maltodextrins. The Xanthomonas axonopodis pv. citri maltose-binding protein MalE has been crystallized at 293 Kusing the hanging-drop vapour-diffusion method. The crystal belonged to the primitive hexagonal space group P6(1)22, with unit-cell parameters a = 123.59, b = 123.59, c = 304.20 angstrom, and contained two molecules in the asymetric unit. It diffracted to 2.24 angstrom resolution.

Robust relations between CCN and the vertical evolution of cloud drop size distribution in deep convective clouds

In-situ measurements in convective clouds (up to the freezing level) over the Amazon basin show that smoke from deforestation fires prevents clouds from precipitating until they acquire a vertical development of at least 4 km, compared to only 1-2 km in clean clouds. The average cloud depth required for the onset of warm rain increased by similar to 350 m for each additional 100 cloud condensation nuclei per cm(3) at a super-saturation of 0.5% (CCN0.5%). In polluted clouds, the diameter of modal liquid water content grows much slower with cloud depth (at least by a factor of similar to 2), due to the large number of droplets that compete for available water and to the suppressed coalescence processes. Contrary to what other studies have suggested, we did not observe this effect to reach saturation at 3000 or more accumulation mode particles per cm(3). The CCN0.5% concentration was found to be a very good predictor for the cloud depth required for the onset of warm precipitation and other microphysical factors, leaving only a secondary role for the updraft velocities in determining the cloud drop size distributions. The effective radius of the cloud droplets (r(e)) was found to be a quite robust parameter for a given environment and cloud depth, showing only a small effect of partial droplet evaporation from the cloud's mixing with its drier environment. This supports one of the basic assumptions of satellite analysis of cloud microphysical processes: the ability to look at different cloud top heights in the same region and regard their r(e) as if they had been measured inside one well developed cloud. The dependence of r(e) on the adiabatic fraction decreased higher in the clouds, especially for cleaner conditions, and disappeared at r(e)>=similar to 10 mu m. We propose that droplet coalescence, which is at its peak when warm rain is formed in the cloud at r(e)=similar to 10 mu m, continues to be significant during the cloud's mixing with the entrained air, cancelling out the decrease in r(e) due to evaporation.

Heavy quark production in deep inelastic electron-nucleus scattering

Heavy quark production has been very well studied over the last years both theoretically and experimentally. Theory has been used to study heavy quark production in ep collisions at HERA, in pp collisions at Tevatron and RHIC, in pA and dA collisions at RHIC, and in AA collisions at CERN-SPS and RHIC. However, to the best of our knowledge, heavy quark production in eA has received almost no attention. With the possible construction of a high energy electron-ion collider, updated estimates of heavy quark production are needed. We address the subject from the perspective of saturation physics and compute the heavy quark production cross section with the dipole model. We isolate shadowing and nonlinear effects, showing their impact on the charm structure function and on the transverse momentum spectrum.

Polarity-Dependent Transcranial Direct Current Stimulation Effects on Central Auditory Processing

Given the polarity dependent effects of transcranial direct current stimulation (tDCS) in facilitating or inhibiting neuronal processing, and tDCS effects on pitch perception, we tested the effects of tDCS on temporal aspects of auditory processing. We aimed to change baseline activity of the auditory cortex using tDCS as to modulate temporal aspects of auditory processing in healthy subjects without hearing impairment. Eleven subjects received 2mA bilateral anodal, cathodal and sham tDCS over auditory cortex in a randomized and counterbalanced order. Subjects were evaluated by the Random Gap Detection Test (RGDT), a test measuring temporal processing abilities in the auditory domain, before and during the stimulation. Statistical analysis revealed a significant interaction effect of time vs. tDCS condition for 4000 Hz and for clicks. Post-hoc tests showed significant differences according to stimulation polarity on RGDT performance: anodal improved 22.5% and cathodal decreased 54.5% subjects' performance, as compared to baseline. For clicks, anodal also increased performance in 29.4% when compared to baseline. tDCS presented polarity-dependent effects on the activity of the auditory cortex, which results in a positive or negative impact in a temporal resolution task performance. These results encourage further studies exploring tDCS in central auditory processing disorders.

Improvements on ICA mixture models for image pre-processing and segmentation

Today several different unsupervised classification algorithms are commonly used to cluster similar patterns in a data set based only on its statistical properties. Specially in image data applications, self-organizing methods for unsupervised classification have been successfully applied for clustering pixels or group of pixels in order to perform segmentation tasks. The first important contribution of this paper refers to the development of a self-organizing method for data classification, named Enhanced Independent Component Analysis Mixture Model (EICAMM), which was built by proposing some modifications in the Independent Component Analysis Mixture Model (ICAMM). Such improvements were proposed by considering some of the model limitations as well as by analyzing how it should be improved in order to become more efficient. Moreover, a pre-processing methodology was also proposed, which is based on combining the Sparse Code Shrinkage (SCS) for image denoising and the Sobel edge detector. In the experiments of this work, the EICAMM and other self-organizing models were applied for segmenting images in their original and pre-processed versions. A comparative analysis showed satisfactory and competitive image segmentation results obtained by the proposals presented herein. (C) 2008 Published by Elsevier B.V.

Deep weathering and landscape evolution in a tropical plateau

The thick weathering profiles of humid tropical areas are an important, yet generally neglected, source of information on landscape evolution. Six complete profiles of the weathering mantle were sampled by drilling on the three stepped levels of the Campos do Jordao Plateau, on the NW flank of the Continental Rift of Southeastern Brazil. Mineralogical and micromorphological analyses of drill core samples, complemented by geochemical interpretations and by previous data on the upper saprolite, indicate continuity of a general lateritic trend during the entire process of mantle formation. Lateritization phases of different intensity were defined and considered to reflect adjustment to changes in environmental conditions created by the gradual uplift of the plateau to its present position. Older and more superficial materials related to intense lateritic weathering are characterized by allitization with direct formation of gibbsite from silicates, probably related to tropical climates existing immediately before the formation of the continental rift, during the Paleogene, and also before any significant increase in altitude. Monosialitization phase with general kaolinitization and restricted indirect formation of gibbsite from silicates could be associated to less aggressive climates that followed the Neogene (Miocene?) accentuation of uplift rates along the continental rift. The changes produced by uplift in the tropical climate eventually favored the development of a podzolization trend in soils above 1800m. (C) 2011 Elsevier BM. All rights reserved.

New perspectives on the processing and release of public information

This article discusses issues related to the organization and reception of information in the context of services and public information systems driven by technology. It stems from the assumption that in a ""technologized"" society, the distance between users and information is almost always of cognitive and socio-cultural nature, a product of our effort to design communication. In this context, we favor the approach of the information sign, seeking to answer how a documentary message turns into information, i.e. a structure recognized as socially useful. Observing the structural, cognitive and communicative aspects of the documentary message, based on Documentary Linguistics, Terminology, as well as on Textual Linguistics, the policy of knowledge management and innovation of the Government of the State of Sao Paulo is analyzed, which authorizes the use of Web 2.0, also questioning to what extent this initiative represents innovation in the environment of libraries.

Fermentation of cellulosic hydrolysates obtained by enzymatic saccharification of sugarcane bagasse pretreated by hydrothermal processing

This work aims to evaluate the fermentability of cellulosic hydrolysates obtained by enzymatic saccharification of sugarcane bagasse pretreated by hydrothermal processing using Candida guilliermondii FTI 20037 yeast. The inoculum was obtained from yeast culture in a medium containing glucose as a carbon source supplemented with rice bran extract, CaCl(2)center dot 2H(2)O and (NH(4))(2)SO(4) in 50 mL Erlenmeyer flasks, containing 20 mL of medium, initial 5.5 pH under agitation of an orbital shaker (200 rpm) at 30A degrees C for 24 h. The cellulosic hydrolysates, prior to being used as a fermentation medium, were autoclaved for 15 min at 0.5 atm and supplemented with the same nutrients employed for the inoculum, except the glucose, using the same conditions for the inoculum, but with a period of 48 h. Preliminary results showed the highest consumption of glucose (97%) for all the hydrolysates, at 28 h of fermentation. The highest concentration of ethanol (20.5 g/L) was found in the procedure of sugarcane bagasse pretreated by hydrothermal processing (195A degrees C/10 min in 20 L reactor) and delignificated with NaOH 1.0% (w/v), 100A degrees C, 1 h in 500 mL stainless steel ampoules immersed in an oil bath.

Noise reduction in biomedical speech signal processing based on time and frequency Kalman filtering combined with spectral subtraction

The goal of this paper is to study and propose a new technique for noise reduction used during the reconstruction of speech signals, particularly for biomedical applications. The proposed method is based on Kalman filtering in the time domain combined with spectral subtraction. Comparison with discrete Kalman filter in the frequency domain shows better performance of the proposed technique. The performance is evaluated by using the segmental signal-to-noise ratio and the Itakura-Saito`s distance. Results have shown that Kalman`s filter in time combined with spectral subtraction is more robust and efficient, improving the Itakura-Saito`s distance by up to four times. (C) 2007 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.

Relationship between installation torque and uplift capacity of deep helical piles in sand

Le facteur empirique de correlation du torque K(T), qui represente la capacite de soulevement du torque d`installation de pieux helicoidaux, est generalement utilise comme instrument de controle de la qualite sur le terrain pour ce type de fondations. Dans cet article, une relation theorique entre la capacite de soulevement et le torque d`installation de pieux helicoidaux places profondement dans du sable est presentee. Un programme experimental, qui comprend des essais centrifuge et de cisaillement direct a l`interface, a ete effectue dans le but de valider cette relation theorique. Les resultats experimentaux ont ete compares aux resultats predits par l`approche suggeree, et les resultats montrent une bonne concordance. Puisque le modele developpe depend de l`angle de friction residuel a l`interface delta(r) entre la surface de l`helice du pieu et le sable, les resultats de delta(r) obtenus a partir de differents echantillons de sable sont presentes afin d`etre utilises lors de l`application sur le terrain de la relation theorique proposee. De plus, les valeurs de K(T) obtenues dans ces travaux ont ete comparees a celles reportees dans la litterature; celles-ci ayant ete obtenues lors d`essais sur le terrain et en laboratoire sur des pieux helicoidaux dans le sable. Cette analyse a permis de demontrer que les valeurs mesurees de K(T) diminuent lorsque la dimension des pieux augmente, ainsi qu`avec une augmentation de l`angle de friction du sable, dans la plupart des cas. Ces derniers resultats ont aussi ete demontres avec le modele presente.

Failure Mechanisms in Sand over a Deep Active Trapdoor

An experimental testing program was undertaken to investigate failure mechanisms induced by the active movement of a deep rectangular trapdoor underlying a granular soil. Reduced-scale models were tested under normal gravity as well as under an increased gravitational field using a centrifuge facility. Some models were used to evaluate the performance of both flexible and rigid pipes undergoing a localized loss of support. Failure mechanisms in the longitudinal direction of the models were characterized by a single, well-defined failure surface that developed within the limits of the trapdoor. However, failure mechanisms in the transverse direction of the models were characterized by multiple failure surfaces extending outside the limits of the trapdoor. Significant dilation of the soil located immediately above the trapdoor was identified in the failure of the models. The pattern of the failure mechanisms was found to be affected by the stress level and backfill density. Higher stress levels were found to lead to well-developed failure zones. The influence of backfill density was found to be more relevant in models involving flexible pipes. Pipes embedded within loose backfill were severely damaged after loss of support, while pipes embedded in dense backfill experienced negligible deformations. These results indicate that damage to pipelines caused by ground loss of support can be significantly minimized by controlling the compaction of the fill.