An overview of the use of neural networks for data mining tasks

In the recent years, the area of data mining has been experiencing considerable demand for technologies that extract knowledge from large and complex data sources. There has been substantial commercial interest as well as active research in the area that aim to develop new and improved approaches for extracting information, relationships, and patterns from large datasets. Artificial neural networks (NNs) are popular biologically-inspired intelligent methodologies, whose classification, prediction, and pattern recognition capabilities have been utilized successfully in many areas, including science, engineering, medicine, business, banking, telecommunication, and many other fields. This paper highlights from a data mining perspective the implementation of NN, using supervised and unsupervised learning, for pattern recognition, classification, prediction, and cluster analysis, and focuses the discussion on their usage in bioinformatics and financial data analysis tasks. © 2012 Wiley Periodicals, Inc.

Platelet protein disulfide isomerase is required for thrombus formation but not essential for hemostasis in mice

Protein disulfide isomerase (PDI) derived from intravascular cells is required for thrombus formation. However, it remains unclear whether platelet PDI contributes to the process. Using platelet-specific PDI-deficient mice, we demonstrate that PDI-null platelets have defects in aggregation and ATP secretion induced by thrombin, collagen, and ADP. Such defects were rescued by exogenously-added wild-type but not mutant PDI, indicating that the isomerase activity of platelet surface PDI is critical for the regulatory effect. PDI-deficient platelets expressed increased levels of intracellular ERp57 and ERp72. Platelet PDI regulated αIIbβ3 integrin activation but not P-selectin exposure, Ca2+ mobilization, β3-talin interaction, and platelet spreading on immobilized fibrinogen. Inhibition of ERp57 further diminished αIIbβ3 integrin activation, aggregation and ATP secretion of activated PDI-deficient platelets, suggesting distinct roles of PDI and ERp57 in platelet functions. We found that platelet PDI is important for thrombus formation on collagen-coated surfaces under arteriolar shear. Intravital microscopy demonstrates that platelet PDI is important for platelet accumulation but not initial adhesion and fibrin generation following laser-induced arteriolar injury. Tail bleeding time and blood loss in platelet-specific PDI-deficient mice were not significantly increased. Our results provide important evidence that platelet PDI is essential for thrombus formation but not for hemostasis in mice.

Sustainable agricultural intensification or Jevons paradox? The role of public governance in tropical South America

The process of global deforestation calls for urgent attention, particularly in South America where deforestation rates have failed to decline over the past 20 years. The main direct cause of deforestation is land conversion to agriculture. We combine data from the FAO and the World Bank for six tropical Southern American countries over the period 1970–2006, estimate a panel data model accounting for various determinants of agricultural land expansion and derive elasticities to quantify the effect of the different independent variables. We investigate whether agricultural intensification, in conjunction with governance factors, has been promoting agricultural expansion, leading to a ‘‘Jevons paradox’’. The paradox occurs if an increase in the productivity of one factor (here agricultural land) leads to its increased, rather than decreased, utilization. We find that for high values of our governance indicators a Jevons paradox exists even for moderate levels of agricultural productivity, leading to an overall expansion of agricultural area. Agricultural expansion is also positively related to the level of service on external debt and population growth, while its association with agricultural exports is only moderate. Finally, we find no evidence of an environmental Kuznets curve, as agricultural area is ultimately positively correlated to per-capita income levels.

Ionospheric Signatures of Pulsed Magnetopause Reconnection

The concept of zero-flow equilibria of the magnetosphere-ionosphere system leads to a large number of predictions concerning the ionospheric signatures of pulsed magnetopause reconnection. These include: poleward-moving F-region electron temperature enhancements and associated transient 630nm emission; associated poleward plasma flow which, compared to the pulsed variation of the reconnection rate, is highly smoothed by induction effects; oscillatory latitudinal motion of the open/closed field line boundary; phase lag of plasma flow enhancements after equatorward motions of the boundary; azimuthal plasma flow bursts, coincident in time and space with the 630nm-dominant auroral transients, only when the magnitude of the By component of the interplanetary magnetic field (IMF) is large; azimuthal-then-poleward motion of 630nm-dominant transients at a velocity which at all times equals the internal plasma flow velocity; 557.7nm-dominant transients on one edge of the 630nm-dominant transient (initially, and for large |By|, on the poleward or equatorward edge depending on the polarity of IMF By); tailward expansion of the flow response at several km s-1; and discrete steps in the cusp ion dispersion signature between the polewardmoving structures. This paper discusses these predictions and how all have recently been confirmed by combinations of observations by optical instruments on the Svalbard Islands, the EISCAT radars and the DMSP and DE satellites.

Population structure of the migratory fish Prochilodus lineatus (Characiformes) from rio Grande basin (Brazil), an area fragmented by dams

1. Prochilodus lineatus (Prochilodontidae, Characiformes) is a migratory species of great economic importance both in fisheries and aquaculture that is found throughout the Jacui, Paraiba do Sul, Parana, Paraguay and Uruguay river basins in South America. Earlier population studies of P. lineatus in the rio Grande basin (Parana basin) indicated the existence of a single population; however, the range of this species has been fragmented by the construction of several dams. Such dams modified the environmental conditions and could have constrained the reproductive migration of P. lineatus, possibly leading to changes in the population genetic structure. 2. In order to evaluate how genetic diversity is allocated in the rio Grande basin, 141 specimens of P. lineatus from eight collection sites were analysed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) with 15 restriction enzymes. 3. Forty-six haplotypes were detected, and 70% of them are restricted. The mean genetic variability indexes (h = 0.7721 and pi = 1.6%) were similar to those found in natural populations with a large effective size. Fst and Exact Test values indicated a lack of structuring among the samples, and the model of isolation by distance was tested and rejected. 4. The haplotype network indicated that this population of P. lineatus has been maintained as a single variable stock with some differences in the genetic composition (haplotypes) between samples. Indications of population expansion were detected, and this finding was supported by neutrality tests and mismatch distribution analyses. 5. The present study focused on regions between dams to serve as a parameter for further evaluations of genetic variability and the putative impact of dams and repopulation programmes in natural populations of P. lineatus. Copyright (C) 2011 John Wiley & Sons, Ltd.

Evaluation of Quantitative RT-PCR Using Nonamplified and Amplified RNA

Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) is a standard assay in molecular medicine for gene expression analysis. Samples from incisional/needle biopsies, laser-microdissected tumor cells and other biologic sources, normally available in clinical cancer studies, generate very small amounts of RNA that are restrictive for expression analysis. As a consequence, an RNA amplification procedure is required to assess the gene expression levels of such sample types. The reproducibility and accuracy of relative gene expression data produced by sensitive methodology as qRT-PCR when cDNA converted from amplified (A) RNA is used as template has not yet been properly addressed. In this study, to properly evaluate this issue, we performed 1 round of linear RNA amplification in 2 breast cell lines (C5.2 and HB4a) and assessed the relative expression of 34 genes using cDNA converted from both nonamplified (NA) and A RNA. Relative gene expression was obtained from beta actin or glyceraldehyde 3-phosphate dehydrogenase normalized data using different dilutions of cDNA, wherein the variability and fold-change differences in the expression of the 2 methods were compared. Our data showed that 1 round of linear RNA amplification, even with suboptimal-quality RNA, is appropriate to generate reproducible and high-fidelity qRT-PCR relative expression data that have similar confidence levels as those from NA samples. The use of cDNA that is converted from both A and NA RNA in a single qRT-PCR experiment clearly creates bias in relative gene expression data.

Effects of hyperbaric oxygen therapy on facial nerve regeneration

Conclusion. Hyperbaric oxygen treatment (HBOT) promoted an increase of the mean axonal diameter in the group evaluated 2 weeks after lesion induction, which suggests a more advanced regeneration process. However, the number of myelin nerve fibers of the facial nerve of the rabbits was similar when compared to the control and treatment groups, in both evaluation periods. Objective. To evaluate the effect of HBOT on the histological pattern of the facial nerve in rabbits exposed to a nerve crush injury. Materials and methods. Twenty rabbits were exposed to facial nerve crush injury. Ten rabbits received HBOT, 10 rabbits comprised the control group. The rabbits were sacrificed 2 and 4 weeks after the trauma. Qualitative morphological analysis, measurement of the external axonal diameters and myelin fiber count were carried out in an area of 185 000 mu m(2). Results. There was an increase in the area of the axons and thicker myelin in the 2 weeks treatment group in comparison with the control group. The mean diameter of the axons was of 2.34 mu m in the control group and of 2.81 mu m in the HBOT group, with statistically significant differences. The 2 week control group had a mean number of myelin fibers of 186 +/- 5.2664, and the HBOT group had a mean number of 2026.3 +/- 302; this was not statistically significant. The 4 week control group presented a mean of 2495.1 +/- 479 fibers and the HBOT group presented a mean of 2359.9 +/- 473; this was not statistically significant.

Effects of Micelles and Vesicles on the Oximolysis of p-Nitrophenyl Diphenyl Phosphate: A Model System for Surfactant-Based Skin-defensive Formulations against Organophosphates

The rates of oximolysis of p-nitrophenyl diphenyl phosphate (PNPDPP) by Acetophenoxime; 10-phenyl-10-hydi-oxyiminodecanoic acid; 4-(9-carboxynonanyl)-1-(9-carboxy-1-hydroyiminononanyl) benzene; 1-dodecyl-2-[(hydroxyimino)methyl]-pyridinium chloride (IV) and N-methylpyridinium-2-aldoxime chloride were determined in micelles of N-hexadecyl-N,N,N-trimethylammonium chloride (CTAC), N-hexadecyl-N,N-dimethylammonium propanesulfonate and dioctadecyldimethylammonium chloride (DODAC) vesicles. The effects of CTAC micelles and DODAC vesicles on the rates of oxymolysis of O,O-Diethyl O-(4-nitrophenyl) phosphate (paraoxon) by oxime IV were also determined. Analysis of micellar and vesicular effects on oximolysis of PNPDPP, using pseudophase or pseudophase with explicit consideration of ion exchange models, required the determination of the aggregate`s effects on the pK(a), of oximes and on the rates of PNPDPP hydrolysis. All aggregates increased the rate of oximolysis of PNPDPP and the results were analyzed quantitatively. In particular, DODAC vesicles catalyzed the reaction and increased the rate of oximolysis of PNPDPP by IV several million fold at pH`s compatible with pharmaceutical formulations. The rate increase produced by DODAC vesicles on the rate of oximolysis paraoxon by IV demonstrates the pharmaceutical potential of this system, since the substrate is used as an agricultural defensive agent and the surfactant is extensively employed in cosmetic formulations. (C) 2008 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 98:1040-1052, 2009

Levine Family Reunion Members, interviewed by Wendy Miller in September 2009: Transcript

The Levine family held an extensive reunion during the Summer of 2009 during which 29 DVDs of raw material were recorded for use in the creation of a Levine family mini-documentary. Many of these DVDs contain oral history interviews conducted by Wendy Miller, one of the organizers of the reunion. Although these interviews were not designed for historical research, they contain valuable historical information. Some of the family members interviewed include: Ben Arnon (4/5), Marjorie, Stephen, and Michael Kaplan (8), Glenyce Miller Kaplan (starts in 15, continues in 9; separate interview in 13), Burt, Phyllis, and Louis Shiro (9) [Burt Shiro also in 26/27], Myrt and Gordon Wolman (9), Ted and Billy Alfond (10), Barbara and Joan Alfond (10), Susan and Peter Alfond (10), Alice Emory [caregiver for Bibby] (11), Eric Bloom and Stu Cushner (11), Saralee Kaplan Bloom (11), Sarah Miller Arnon (12), Kayla and Jenna Cushner (12), Josh Soros and Eliana Miller-Kaplan (12), Sarah, Wendy, and Julie Miller (starts in 12, continues in 14), Bill Shutzer (13), Maschia and Glicka Kaplan, Sharon Kushner, Dan Hood (13), Gene, Alex, Kate Cohen (14), Ben, Jeremy, Joselyn Arnon (14), Wendy and Julie Miller at the store (15), and Eric Bloom (15).

Sculptural abstraction of landscape

The purpose of my Senior Scholar project was to create a series of sculptures that are based on the interaction of natural forms within a selected landscape setting. I hope to convey a sense of how I view and interpret the landscape and to create works that stimulate a sense of wonder in the mind of the viewer. This fascination, perhaps even obsession, with the power of the landscape has kept me going throughout the year. As a source of ideas and imagery, the landscape can never be depleted. There will always be new combinations of landscape elements, different light conditions, and changing seasons to provide me with fresh ideas. Research for the project took me to many different places, be it my trip to Monhegan Island or driving to New York City to study the cityscape. I began the year working in steel and plaster, combining the two in works that explore the interaction between living tree roots and inanimate rocks. This led to a series entitled Landscape Recollections, comprised of welded steel forms housed in protective wooden boxes and lit from inside. After visiting New York City, architecture began to playa role in my work, as seen in the two Roadcut pieces and the Cathedral Woods series. Roadcut #1 and Roadcut #2 explore the relationship between a man-made road and the landscape that lies beneath and around it. The Cathedral Woods pieces incorporate architecture in a more abstract manner, using imagery derived from Gothic cathedrals to convey a sense of quiet peacefulness. The soaring verticality of Gothic architecture integrates with the tall tree forms in each piece, enabling me to intertwine these two elements into one another and create a harmonious relationship between architecture and nature. Throughout the year I have kept a sketchbook in which I draw from life, jot down ideas, and take notes on how the project is progressing. I have also completed several large charcoal drawings of my sculptures in which I explore different ways of viewing the steel forms. I am grateful to have had the opportunity to undertake this project, as it has been a very difficult but rewarding process of observing, interpreting, and manifesting the landscape according to my personal vision and experiences.