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Find video protocols related to scientific articles indexed in Pubmed.
High density micro-pyramids with silicon nanowire array for photovoltaic applications.
Nanotechnology
PUBLISHED: 11-10-2014
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We use a metal assisted chemical etch process to fabricate silicon nanowire arrays (SiNWAs) onto a dense periodic array of pyramids that are formed using an alkaline etch masked with an oxide layer. The hybrid micro-nano structure acts as an anti-reflective coating with experimental reflectivity below 1% over the visible and near-infrared spectral regions. This represents an improvement of up to 11 and 14 times compared to the pyramid array and SiNWAs on bulk, respectively. In addition to the experimental work, we optically simulate the hybrid structure using a commercial finite difference time domain package. The results of the optical simulations support our experimental work, illustrating a reduced reflectivity in the hybrid structure. The nanowire array increases the absorbed carrier density within the pyramid by providing a guided transition of the refractive index along the light path from air into the silicon. Furthermore, electrical simulations which take into account surface and Auger recombination show an efficiency increase for the hybrid structure of 56% over bulk, 11% over pyramid array and 8.5% over SiNWAs.
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Identification and Characterization of Hundreds of Potent and Selective Inhibitors of Trypanosoma brucei Growth from a Kinase-Targeted Library Screening Campaign.
PLoS Negl Trop Dis
PUBLISHED: 10-01-2014
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In the interest of identification of new kinase-targeting chemotypes for target and pathway analysis and drug discovery in Trypanosomal brucei, a high-throughput screen of 42,444 focused inhibitors from the GlaxoSmithKline screening collection was performed against parasite cell cultures and counter-screened against human hepatocarcinoma (HepG2) cells. In this way, we have identified 797 sub-micromolar inhibitors of T. brucei growth that are at least 100-fold selective over HepG2 cells. Importantly, 242 of these hit compounds acted rapidly in inhibiting cellular growth, 137 showed rapid cidality. A variety of in silico and in vitro physicochemical and drug metabolism properties were assessed, and human kinase selectivity data were obtained, and, based on these data, we prioritized three compounds for pharmacokinetic assessment and demonstrated parasitological cure of a murine bloodstream infection of T. brucei rhodesiense with one of these compounds (NEU-1053). This work represents a successful implementation of a unique industrial-academic collaboration model aimed at identification of high quality inhibitors that will provide the parasitology community with chemical matter that can be utilized to develop kinase-targeting tool compounds. Furthermore these results are expected to provide rich starting points for discovery of kinase-targeting tool compounds for T. brucei, and new HAT therapeutics discovery programs.
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MAS and its related G protein-coupled receptors, Mrgprs.
Pharmacol. Rev.
PUBLISHED: 09-24-2014
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The Mas-related G protein-coupled receptors (Mrgprs or Mas-related genes) comprise a subfamily of receptors named after the first discovered member, Mas. For most Mrgprs, pruriception seems to be the major function based on the following observations: 1) they are relatively promiscuous in their ligand specificity with best affinities for itch-inducing substances; 2) they are expressed in sensory neurons and mast cells in the skin, the main cellular components of pruriception; and 3) they appear in evolution first in tetrapods, which have arms and legs necessary for scratching to remove parasites or other noxious substances from the skin before they create harm. Because parasites coevolved with hosts, each species faced different parasitic challenges, which may explain another striking observation, the multiple independent duplication and expansion events of Mrgpr genes in different species as a consequence of parallel adaptive evolution. Their predominant expression in dorsal root ganglia anticipates additional functions of Mrgprs in nociception. Some Mrgprs have endogenous ligands, such as ?-alanine, alamandine, adenine, RF-amide peptides, or salusin-?. However, because the functions of these agonists are still elusive, the physiologic role of the respective Mrgprs needs to be clarified. The best studied Mrgpr is Mas itself. It was shown to be a receptor for angiotensin-1-7 and to exert mainly protective actions in cardiovascular and metabolic diseases. This review summarizes the current knowledge about Mrgprs, their evolution, their ligands, their possible physiologic functions, and their therapeutic potential.
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Melatonin and metabolic regulation: a review.
Food Funct
PUBLISHED: 09-11-2014
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Human life expectancy has increased over the past 50 years due to scientific and medical advances and higher food availability. However, overweight and obesity affect more than 50% of adults and 15% of infants and adolescents. There has also been a marked increase in the prevalence of metabolic syndrome in recent decades, which has been associated with a reduction in nocturnal pineal production of melatonin with aging and an increased risk of coronary diseases, type 2 diabetes mellitus (T2DM) and death. Melatonin is currently under intensive investigation in experimental animal models of diabetes, obesity and MS at pharmacological doses (between 5 and 20 mg kg(-1) body weight), demonstrating its capacity to ameliorate the total metabolic profile and its potential as an alternative to conventional drug therapies for the disorders associated with the MS, i.e. elevated systolic blood pressure, and impairment of glucose homeostasis, plasma lipid profile, inflammation, oxidative stress, and increased body weight. An especially significant finding is the induction by melatonin of white adipose tissue browning, which may be related to its effects against oxidative stress, uncoupling the mitochondrial bioenergetic process by enhancing the expression of uncoupled-protein-1 (UCP-1), which has been related to body weight reduction in experimental animals. Further research is required to improve knowledge of this mechanism. Clinical studies are needed with the administration of pharmacological melatonin doses, because the dose has ranged between 0.050 and 0.16 mg kg(-1) bw in most studies to date. Melatonin is a natural phytochemical, and it is also important to test its beneficial metabolic effects when consumed in functional foods.
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Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen.
PLoS Comput. Biol.
PUBLISHED: 09-01-2014
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Characterizing the activating and inhibiting effect of protein-protein interactions (PPI) is fundamental to gain insight into the complex signaling system of a human cell. A plethora of methods has been suggested to infer PPI from data on a large scale, but none of them is able to characterize the effect of this interaction. Here, we present a novel computational development that employs mitotic phenotypes of a genome-wide RNAi knockdown screen and enables identifying the activating and inhibiting effects of PPIs. Exemplarily, we applied our technique to a knockdown screen of HeLa cells cultivated at standard conditions. Using a machine learning approach, we obtained high accuracy (82% AUC of the receiver operating characteristics) by cross-validation using 6,870 known activating and inhibiting PPIs as gold standard. We predicted de novo unknown activating and inhibiting effects for 1,954 PPIs in HeLa cells covering the ten major signaling pathways of the Kyoto Encyclopedia of Genes and Genomes, and made these predictions publicly available in a database. We finally demonstrate that the predicted effects can be used to cluster knockdown genes of similar biological processes in coherent subgroups. The characterization of the activating or inhibiting effect of individual PPIs opens up new perspectives for the interpretation of large datasets of PPIs and thus considerably increases the value of PPIs as an integrated resource for studying the detailed function of signaling pathways of the cellular system of interest.
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Cross-resistance and baseline susceptibility of spirotetramat in Frankliniella occidentalis (Thysanoptera: Thripidae).
J. Econ. Entomol.
PUBLISHED: 07-17-2014
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Western flower thrips, Frankliniella occidentalis (Pergande), is an economically important pest all over the world. New products against thrips are necessary, as there are few effective compounds exhibiting cross-resistance among them. Lethal effects, cross-resistance, and baseline susceptibility to spirotetramat were evaluated in this study. A new bioassay method for testing thrips against spirotetramat was developed. Spirotetramat showed a significant mortality effect on larvae after 7 d of exposure, but a low effect was observed on adults. Baseline results for larval instars showed LC50 values ranging from 11.59 to 49.81 mg AI/liter, with a low natural variability (3.2-fold). Cross-resistance studies showed overlapping confidence limits of the LC50 values for laboratory-selected (against acrinathrin, methiocarb, formetanate, and spinosad) resistant and susceptible strains, and low resistance factors, from 0.5 to 1.9, suggesting no cross-resistance to conventional insecticides previously used. A slight ovicidal effect (21-40% reduction) was also detected. Despite presenting low effects on adults, spirotetramat showed high but slow efficacy on F. occidentalis larvae. Field populations in southeast Spain showed a consistent susceptibility to spirotetramat. Given the scarcity of effective products and the lack of cross-resistance to other insecticides, spirotetramat can be considered as a good chemical tool to control F. occidentalis.
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Establishment of a structure-activity relationship of 1H-imidazo[4,5-c]quinoline-based kinase inhibitor NVP-BEZ235 as a lead for African sleeping sickness.
J. Med. Chem.
PUBLISHED: 05-21-2014
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Compound NVP-BEZ235 (1) is a potent inhibitor of human phospoinositide-3-kinases and mammalian target of rapamycin (mTOR) that also showed high inhibitory potency against Trypanosoma brucei cultures. With an eye toward using 1 as a starting point for anti-trypanosomal drug discovery, we report efforts to reduce host cell toxicity, to improve the physicochemical properties, and to improve the selectivity profile over human kinases. In this work, we have developed structure-activity relationships for analogues of 1 and have prepared analogues of 1 with improved solubility properties and good predicted central nervous system exposure. In this way, we have identified 4e, 9, 16e, and 16g as the most promising leads to date. We also report cell phenotype and phospholipidomic studies that suggest that these compounds exert their anti-trypanosomal effects, at least in part, by inhibition of lipid kinases.
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Influence of aortic regurgitation after TAVI on left ventricular filling pattern.
Eur. J. Clin. Invest.
PUBLISHED: 05-19-2014
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Paravalvular aortic regurgitation after transcatheter aortic valve implantation is associated with a hemodynamic deterioration and a poor outcome. We aim to determine the early hemodynamic effect of paravalvular aortic regurgitation in relation with the change in the left ventricle filling pattern and to assess their clinical outcome.
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Alkemio: association of chemicals with biomedical topics by text and data mining.
Nucleic Acids Res.
PUBLISHED: 05-16-2014
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The PubMed® database of biomedical citations allows the retrieval of scientific articles studying the function of chemicals in biology and medicine. Mining millions of available citations to search reported associations between chemicals and topics of interest would require substantial human time. We have implemented the Alkemio text mining web tool and SOAP web service to help in this task. The tool uses biomedical articles discussing chemicals (including drugs), predicts their relatedness to the query topic with a naïve Bayesian classifier and ranks all chemicals by P-values computed from random simulations. Benchmarks on seven human pathways showed good retrieval performance (areas under the receiver operating characteristic curves ranged from 73.6 to 94.5%). Comparison with existing tools to retrieve chemicals associated to eight diseases showed the higher precision and recall of Alkemio when considering the top 10 candidate chemicals. Alkemio is a high performing web tool ranking chemicals for any biomedical topics and it is free to non-commercial users.
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Aortic Valve Stenosis Planimetry by Means of Three-Dimensional Transesophageal Echocardiography in the Real Clinical Setting: Feasibility, Reliability and Systematic Deviations.
Echocardiography
PUBLISHED: 05-08-2014
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To assess the feasibility and reliability of aortic valve area (AVA) planimetry by means of three-dimensional transesophageal echocardiography (3DTEE) as compared with the transthoracic echocardiogram (TTE) calculation of AVA, to determine the systematic deviations between measurements, and to describe the distribution of mean systolic in relation with 3DTEE anatomical AVA.
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Similarity in targets with REST points to neural and glioblastoma related miRNAs.
Nucleic Acids Res.
PUBLISHED: 04-11-2014
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There are groups of genes that need coordinated repression in multiple contexts, for example if they code for proteins that work together in a pathway or in a protein complex. Redundancy of biological regulatory networks implies that such coordinated repression might occur at both the pre- and post-transcriptional level, though not necessarily simultaneously or under the same conditions. Here, we propose that such redundancy in the global regulatory network can be detected by the overlap between the putative targets of a transcriptional repressor, as identified by a ChIP-seq experiment, and predicted targets of a microRNA (miRNA). To test this hypothesis, we used publicly available ChIP-seq data of the neural transcriptional repressor RE1 silencing transcription factor (REST) from 15 different cell samples. We found 20 miRNAs, each of which shares a significant amount of predicted targets with REST. The set of predicted associations between these 20 miRNAs and the overlapping REST targets is enriched in known miRNA targets. Many of the detected miRNAs have functions related to neural identity and glioblastoma, which could be expected from their overlap in targets with REST. We propose that the integration of experimentally determined transcription factor binding sites with miRNA-target predictions provides functional information on miRNAs.
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Identification of LRRC8 heteromers as an essential component of the volume-regulated anion channel VRAC.
Science
PUBLISHED: 04-10-2014
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Regulation of cell volume is critical for many cellular and organismal functions, yet the molecular identity of a key player, the volume-regulated anion channel VRAC, has remained unknown. A genome-wide small interfering RNA screen in mammalian cells identified LRRC8A as a VRAC component. LRRC8A formed heteromers with other LRRC8 multispan membrane proteins. Genomic disruption of LRRC8A ablated VRAC currents. Cells with disruption of all five LRRC8 genes required LRRC8A cotransfection with other LRRC8 isoforms to reconstitute VRAC currents. The isoform combination determined VRAC inactivation kinetics. Taurine flux and regulatory volume decrease also depended on LRRC8 proteins. Our work shows that VRAC defines a class of anion channels, suggests that VRAC is identical to the volume-sensitive organic osmolyte/anion channel VSOAC, and explains the heterogeneity of native VRAC currents.
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Differences in cerebrospinal fluid inflammatory cell reaction of patients with leptomeningeal involvement by lymphoma and carcinoma.
Transl Res
PUBLISHED: 03-25-2014
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Dissemination of neoplastic cells into the cerebrospinal fluid (CSF) and leptomeninges is a devastating complication in patients with epithelial cell neoplasia (leptomeningeal carcinomatosis [LC]) and lymphomas (lymphomatous meningitis [LyM]). Information about the surrounding inflammatory cell populations is scarce. In this study, flow cytometry immunophenotyping was used to describe the distribution of the main leukocyte populations in the CSF of 83 patients diagnosed with neoplastic meningitis (LC, n = 65; LyM, n = 18). These data were compared with those obtained in the CSF from 55 patients diagnosed with the same groups of neoplasia without meningeal involvement (solid tumors, n = 36; high-grade lymphoma, n = 19). Median (interquartile) rates of lymphocytes, monocytes, and polymorphonuclear (PMN) cells were 59.7% (range, 35-76.6%), 24% (range, 16-53%), and 1.5% (range, 0-7.6%) in LC, respectively, and 98.5% (range, 70.8-100%), 1.5% (range, 0-29.3%), and 0% in LyM, respectively (P < 0.001). No difference was observed between patients with breast adenocarcinoma (n = 30) and lung adenocarcinoma (n = 21), nor with different rates of malignant CSF involvement. Patients with lymphoma (with or without LyM) had a similar CSF leukocyte distribution, but cancer patients with LC and without LC had a distinctive PMN cell rate (P = 0.002). These data show that CSF samples from patients with LC have a greater number of inflammatory cells and a different leukocyte distribution than seen in the CSF from patients with LyM. Description of PMN cells is a distinctive parameter of patients with LC, compared with the CSF from patients with LyM and patients with cancer but without LC.
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Activity of melatonin against Leishmania infantum promastigotes by mitochondrial dependent pathway.
Chem. Biol. Interact.
PUBLISHED: 02-14-2014
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Visceral leishmaniasis, a potentially fatal disease, remains a major international health problem. Only a limited number of effective antileishmanial agents are available for chemotherapy, and many of them are expensive with severe side effects or have a markedly reduced effectiveness due to the development of drug resistance. Hence, there is a genuine need to develop a novel effective and less toxic antileishmanial drug. Melatonin, a neurohormone found in animals, plants, and microbes, can participate in various biological and physiological functions. Several in vitro or in vivo studies have reported the inhibitory effect of melatonin against many parasites via various mechanisms, including modulation of intracellular concentrations of calcium in the parasite and/or any other suggested mechanism. Importantly, many of available antileishmanial drugs have been reported to exert their effects by disrupting calcium homeostasis in the parasite. The objective of the present study was to test the efficacy of exogenous melatonin against Leishmania infantum promastigotes in vitro. Interestingly, melatonin not only demonstrated a significant antileishmanial activity of against promastigote viability in tested cultures but was also accompanied by an alteration of the calcium homeostasis of parasite mitochondrion, represented by earlier mitochondrial permeability transition pore opening, and by changes in some mitochondrial parameters are critical to parasite survival. These pioneering findings suggest that melatonin may be a candidate for the development of novel effective antileishmanial agents either alone or in associations with other drugs.
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ROMO1 is an essential redox-dependent regulator of mitochondrial dynamics.
Sci Signal
PUBLISHED: 01-30-2014
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The dynamics of mitochondria undergoing fusion and fragmentation govern many mitochondrial functions, including the regulation of cell survival. Although the machinery that catalyzes fusion and fragmentation has been well described, less is known about the signaling components that regulate these phenomena. We performed a genome-wide RNA interference (RNAi) screen and identified reactive oxygen species modulator 1 (ROMO1) as a redox-regulated protein required for mitochondrial fusion and normal cristae morphology. We showed that oxidative stress promoted the formation of high-molecular weight ROMO1 complexes and that knockdown of ROMO1 promoted mitochondrial fission. ROMO1 was essential for the oligomerization of the inner membrane guanosine triphosphatase (GTPase) OPA1, which is required to maintain the integrity of cristae junctions. As a consequence, cells lacking ROMO1 displayed fragmented mitochondria and loss of cristae, causing impaired mitochondrial respiration and increased sensitivity to cell death stimuli. Together, our data identify ROMO1 as a critical molecular switch that couples metabolic stress and mitochondrial morphology, linking mitochondrial fusion to cell survival.
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Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma.
BMC Cancer
PUBLISHED: 01-29-2014
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This study aimed at the identification of prognostic gene expression markers in early primary colorectal carcinomas without metastasis at the time point of surgery by analyzing genome-wide gene expression profiles using oligonucleotide microarrays.
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Serum Zn levels and Cu/Zn ratios worsen in hemodialysis patients, implying increased cardiovascular risk: a 2-year longitudinal study.
Biol Trace Elem Res
PUBLISHED: 01-28-2014
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The objective of this study was to analyze serum Zn and Cu concentrations and Cu/Zn ratios in 116 hemodialysis patients (HPs) over a 2-year longitudinal study at four time points (6-month intervals). The relation exerted on these values by 26 biochemical and nutritional indexes, the age and drug consumption of the patients, and the etiology of their disease were also evaluated. A healthy control group (n?=?50) was also studied. Mean serum Zn concentrations were lower (p?=?0.009) and the Cu/Zn ratios higher (p?=?0.009) in HPs than in controls. Serum Cu levels in HP did not differ to those of controls. At all four sampling times, the mean serum Zn levels and Cu/Zn ratios were lower and higher, respectively, in HPs than in the controls. There was a significant reduction in serum Zn levels and an increase in Cu concentrations and Cu/Zn ratios in HPs from the second to the fourth sampling. Serum Zn levels of the HPs diminish with age older than 50 years. Serum Cu levels were significantly higher in patients consuming antihypercalcemic or anti-infarction drugs, whereas serum Cu levels and Cu/Zn ratios were significantly lower in those treated with diuretics. Diminished Zn levels were negatively correlated with low-density lipoprotein (LDL) cholesterol in HPs; however, enhanced Cu/Zn ratios were positively correlated with total cholesterol and LDL cholesterol. Both findings indicate an increased cardiovascular risk. We conclude that this study contributes the first evidence of a correlation between marked dyslipidemia and worsened Cu/Zn ratios in HPs, implying an increased risk of diseases associated with elevated oxidative stress, inflammation, and depressed immune function, such as cardiovascular diseases.
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Transient neonatal zinc deficiency due to a new autosomal dominant mutation in gene SLC30A2 (ZnT-2).
Pediatr Dermatol
PUBLISHED: 01-23-2014
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Transient neonatal zinc deficiency (TNZD) has a clinical presentation similar to that of acrodermatitis enteropathica but is caused by a low zinc concentration in maternal breast milk. TNZD becomes clinically evident during breastfeeding and is resolved by weaning and the introduction of complementary nutrition. We present a 4-month-old girl with TNZD due to a new autosomal dominant mutation (663delC) in the maternal SLC30A2 gene not previously described in the literature.
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Third-harmonic-upconversion enhancement from a single semiconductor nanoparticle coupled to a plasmonic antenna.
Nat Nanotechnol
PUBLISHED: 01-22-2014
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The ability to convert low-energy quanta into a quantum of higher energy is of great interest for a variety of applications, including bioimaging, drug delivery and photovoltaics. Although high conversion efficiencies can be achieved using macroscopic nonlinear crystals, upconverting light at the nanometre scale remains challenging because the subwavelength scale of materials prevents the exploitation of phase-matching processes. Light-plasmon interactions that occur in nanostructured noble metals have offered alternative opportunities for nonlinear upconversion of infrared light, but conversion efficiency rates remain extremely low due to the weak penetration of the exciting fields into the metal. Here, we show that third-harmonic generation from an individual semiconductor indium tin oxide nanoparticle is significantly enhanced when coupled within a plasmonic gold dimer. The plasmonic dimer acts as a receiving optical antenna, confining the incident far-field radiation into a near field localized at its gap; the indium tin oxide nanoparticle located at the plasmonic dimer gap acts as a localized nonlinear transmitter upconverting three incident photons at frequency ? into a photon at frequency 3?. This hybrid nanodevice provides third-harmonic-generation enhancements of up to 10(6)-fold compared with an isolated indium tin oxide nanoparticle, with an effective third-order susceptibility up to 3.5 × 10(3) nm V(-2) and conversion efficiency of 0.0007%. We also show that the upconverted third-harmonic emission can be exploited to probe the near-field intensity at the plasmonic dimer gap.
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CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.
Bioinformatics
PUBLISHED: 01-21-2014
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The current methods available to detect chromosomal abnormalities from DNA microarray expression data are cumbersome and inflexible. CAFE has been developed to alleviate these issues. It is implemented as an R package that analyzes Affymetrix *.CEL files and comes with flexible plotting functions, easing visualization of chromosomal abnormalities.
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Melatonin administration in diabetes: regulation of plasma Cr, V, and Mg in young male Zucker diabetic fatty rats.
Food Funct
PUBLISHED: 01-21-2014
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The use of melatonin, a neurohormone present in plants, represents an exciting approach for the maintenance of optimum health conditions. Melatonin administration ameliorates glucose homeostasis in Zucker diabetic fatty (ZDF) rats. The objective of this study was to investigate the effects of melatonin in diabetes in relation to the levels and regulation of plasma chromium (Cr), vanadium (V), and magnesium (Mg) in Zucker diabetic fatty (ZDF) and Zucker lean (ZL) rats. At the age of 6 weeks, ZDF (n = 30) and ZL (n = 30) groups were each subdivided into three groups: control (C) (n = 10), vehicle-treated (V') (n = 10) and melatonin-treated (M) (10 mg kg(-1) per day; n = 10) groups for a 6 week period. After treatment, plasma mineral concentrations were measured by flame (Mg) and electrothermal (Cr and V) atomic absorption spectrometry. No significant differences were found between the C and V' groups (p > 0.05). Plasma Mg levels were significantly lower in C-ZDF vs. C-ZL rats, demonstrating the presence of hypomagnesemia in this diabetes mellitus model. Plasma V and Cr levels were significantly higher in M-ZDF vs. C-ZDF rats. Plasma Mg levels in ZDF rats were not affected by melatonin treatment (p > 0.05). Melatonin administration ameliorates the diabetic status of ZDF rats by enhancing plasma Cr and V concentrations. This appears to be the first report of a beneficial effect of melatonin treatment on plasma Cr and V regulation in ZDF rats.
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Glossina palpalis palpalis populations from Equatorial Guinea belong to distinct allopatric clades.
Parasit Vectors
PUBLISHED: 01-14-2014
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Luba is one of the four historical foci of Human African Trypanosomiasis (HAT) on Bioko Island, in Equatorial Guinea. Although no human cases have been detected since 1995, T. b. gambiense was recently observed in the vector Glossina palpalis palpalis. The existence of cryptic species within this vector taxon has been previously suggested, although no data are available regarding the evolutionary history of tsetse flies populations in Bioko.
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Mid-infrared plasmonic inductors: enhancing inductance with meandering lines.
Sci Rep
PUBLISHED: 01-08-2014
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We present a mid-infrared inductor that when applied to an extraordinary transmission hole array produces a strong redshift of the resonant peak accompanied by an unprecedented enlargement of the operation bandwidth. The importance of the result is twofold: from a fundamental viewpoint, the direct applicability of equivalent circuit concepts borrowed from microwaves is demonstrated, in frequencies as high as 17 THz upholding unification of plasmonics and microwave concepts and allowing for a simplification of structure design and analysis; in practical terms, a broadband funnelling of infrared radiation with fractional bandwidth and efficiency as high as 97% and 48%, respectively, is achieved through an area less than one hundredth the squared wavelength, which leads to an impressive accessible strong field localization that may be of great interest in sensing applications.
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CellFinder: a cell data repository.
Nucleic Acids Res.
PUBLISHED: 12-03-2013
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CellFinder (http://www.cellfinder.org) is a comprehensive one-stop resource for molecular data characterizing mammalian cells in different tissues and in different development stages. It is built from carefully selected data sets stemming from other curated databases and the biomedical literature. To date, CellFinder describes 3394 cell types and 50 951 cell lines. The database currently contains 3055 microscopic and anatomical images, 205 whole-genome expression profiles of 194 cell/tissue types from RNA-seq and microarrays and 553 905 protein expressions for 535 cells/tissues. Text mining of a corpus of >2000 publications followed by manual curation confirmed expression information on ?900 proteins and genes. CellFinders data model is capable to seamlessly represent entities from single cells to the organ level, to incorporate mappings between homologous entities in different species and to describe processes of cell development and differentiation. Its ontological backbone currently consists of 204 741 ontology terms incorporated from 10 different ontologies unified under the novel CELDA ontology. CellFinders web portal allows searching, browsing and comparing the stored data, interactive construction of developmental trees and navigating the partonomic hierarchy of cells and tissues through a unique body browser designed for life scientists and clinicians.
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uORFdb--a comprehensive literature database on eukaryotic uORF biology.
Nucleic Acids Res.
PUBLISHED: 10-24-2013
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Approximately half of all human transcripts contain at least one upstream translational initiation site that precedes the main coding sequence (CDS) and gives rise to an upstream open reading frame (uORF). We generated uORFdb, publicly available at http://cbdm.mdc-berlin.de/tools/uorfdb, to serve as a comprehensive literature database on eukaryotic uORF biology. Upstream ORFs affect downstream translation by interfering with the unrestrained progression of ribosomes across the transcript leader sequence. Although the first uORF-related translational activity was observed >30 years ago, and an increasing number of studies link defective uORF-mediated translational control to the development of human diseases, the features that determine uORF-mediated regulation of downstream translation are not well understood. The uORFdb was manually curated from all uORF-related literature listed at the PubMed database. It categorizes individual publications by a variety of denominators including taxon, gene and type of study. Furthermore, the database can be filtered for multiple structural and functional uORF-related properties to allow convenient and targeted access to the complex field of eukaryotic uORF biology.
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Terahertz wave transmission in flexible polystyrene-lined hollow metallic waveguides for the 2.5-5 THz band.
Opt Express
PUBLISHED: 10-10-2013
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A low-loss and low-dispersive optical-fiber-like hybrid HE?? mode is developed within a wide band in metallic hollow waveguides if their inner walls are coated with a thin dielectric layer. We investigate terahertz (THz) transmission losses from 0.5 to 5.5 THz and bending losses at 2.85 THz in a polystyrene-lined silver waveguides with core diameters small enough (1 mm) to minimize the number of undesired modes and to make the waveguide flexible, while keeping the transmission loss of the HE?? mode low. The experimentally measured loss is below 10 dB/m for 2 < ? < 2.85 THz (~4-4.5 dB/m at 2.85 THz) and it is estimated to be below 3 dB/m for 3 < ? < 5 THz according to the numerical calculations. At ~1.25 THz, the waveguide shows an absorption peak of ~75 dB/m related to the transition between the TM??-like mode and the HE?? mode. Numerical modeling reproduces the measured absorption spectrum but underestimates the losses at the absorption peak, suggesting imperfections in the waveguide walls and that the losses can be reduced further.
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Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence.
Genes Dev.
PUBLISHED: 09-10-2013
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Understanding how distinct cell types arise from multipotent progenitor cells is a major quest in stem cell biology. The liver and pancreas share many aspects of their early development and possibly originate from a common progenitor. However, how liver and pancreas cells diverge from a common endoderm progenitor population and adopt specific fates remains elusive. Using RNA sequencing (RNA-seq), we defined the molecular identity of liver and pancreas progenitors that were isolated from the mouse embryo at two time points, spanning the period when the lineage decision is made. The integration of temporal and spatial gene expression profiles unveiled mutually exclusive signaling signatures in hepatic and pancreatic progenitors. Importantly, we identified the noncanonical Wnt pathway as a potential developmental regulator of this fate decision and capable of inducing the pancreas program in endoderm and liver cells. Our study offers an unprecedented view of gene expression programs in liver and pancreas progenitors and forms the basis for formulating lineage-reprogramming strategies to convert adult hepatic cells into pancreatic cells.
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A novel approach for protein subcellular location prediction using amino acid exposure.
BMC Bioinformatics
PUBLISHED: 08-23-2013
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Proteins perform their functions in associated cellular locations. Therefore, the study of protein function can be facilitated by predictions of protein location. Protein location can be predicted either from the sequence of a protein alone by identification of targeting peptide sequences and motifs, or by homology to proteins of known location. A third approach, which is complementary, exploits the differences in amino acid composition of proteins associated to different cellular locations, and can be useful if motif and homology information are missing. Here we expand this approach taking into account amino acid composition at different levels of amino acid exposure.
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Target of rapamycin (TOR) kinase in Trypanosoma brucei: an extended family.
Biochem. Soc. Trans.
PUBLISHED: 07-19-2013
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The complex life cycle of Trypanosoma brucei provides an excellent model system to understand signalling pathways that regulate development. We described previously the classical functions of TOR (target of rapamycin) 1 and TOR2 in T. brucei. In a more recent study, we described a novel TOR kinase, named TOR4, which regulates differentiation from the proliferative infective form to the quiescent form. In contrast with TOR1 loss-of-function, down-regulation of TOR4 triggers an irreversible differentiation process through the development of the insect pre-adapted quiescent form. TOR4 governs a signalling pathway distinct from those controlled by the conventional TOR complexes TORC1 and TORC2. Depletion of TOR4 induces all well-known characteristics of the quiescent developmental stage in trypanosomes, including expression of the PAD (proteins associated with differentiation) surface proteins and transcriptional down-regulation of the VSG (variant surface glycoprotein) gene. TOR4 kinase forms a structurally and functionally distinct complex named TORC4. TOR4 associates with LST8 (lethal with sec-13 protein 8) and other factors including an armadillo-domain-containing protein and the major vault protein, which probably serves as a scaffold for this kinase. Research in T. brucei, a protozoan parasite that diverged from the eukaryotic tree early in evolution, may help to uncover new functions of TOR kinases.
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A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations.
BMC Biotechnol.
PUBLISHED: 05-15-2013
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Gene transcripts specifically expressed in a particular cell type (cell-type specific gene markers) are useful for its detection and isolation from a tissue or other cell mixtures. However, finding informative marker genes can be problematic when working with a poorly characterized cell type, as markers can only be unequivocally determined once the cell type has been isolated. We propose a method that could identify marker genes of an uncharacterized cell type within a mixed cell population, provided that the proportion of the cell type of interest in the mixture can be estimated by some indirect method, such as a functional assay.
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Terahertz epsilon-near-zero graded-index lens.
Opt Express
PUBLISHED: 04-11-2013
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An epsilon-near-zero graded-index converging lens with planar faces is proposed and analyzed. Each perfectly-electric conducting (PEC) waveguide comprising the lens operates slightly above its cut-off frequency and has the same length but different cross-sectional dimensions. This allows controlling individually the propagation constant and the normalized characteristic impedance of each waveguide for the desired phase front at the lens output while Fresnel reflection losses are minimized. A complete theoretical analysis based on the waveguide theory and Fermats principle is provided. This is complemented with numerical simulation results of two-dimensional and three-dimensional lenses, made of PEC and aluminum, respectively, and working in the terahertz regime, which show good agreement with the analytical work.
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PU.1 level-directed chromatin structure remodeling at the Irf8 gene drives dendritic cell commitment.
Cell Rep
PUBLISHED: 04-08-2013
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Dendritic cells (DCs) are essential regulators of immune responses; however, transcriptional mechanisms that establish DC lineage commitment are poorly defined. Here, we report that the PU.1 transcription factor induces specific remodeling of the higher-order chromatin structure at the interferon regulatory factor 8 (Irf8) gene to initiate DC fate choice. An Irf8 reporter mouse enabled us to pinpoint an initial progenitor stage at which DCs separate from other myeloid lineages in the bone marrow. In the absence of Irf8, this progenitor undergoes DC-to-neutrophil reprogramming, indicating that DC commitment requires an active, Irf8-dependent escape from alternative myeloid lineage potential. Mechanistically, myeloid Irf8 expression depends on high PU.1 levels, resulting in local chromosomal looping and activation of a lineage- and developmental-stage-specific cis-enhancer. These data delineate PU.1 as a concentration-dependent rheostat of myeloid lineage selection by controlling long-distance contacts between regulatory elements and suggest that specific higher-order chromatin remodeling at the Irf8 gene determines DC differentiation.
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Using cited references to improve the retrieval of related biomedical documents.
BMC Bioinformatics
PUBLISHED: 03-18-2013
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A popular query from scientists reading a biomedical abstract is to search for topic-related documents in bibliographic databases. Such a query is challenging because the amount of information attached to a single abstract is little, whereas classification-based retrieval algorithms are optimally trained with large sets of relevant documents. As a solution to this problem, we propose a query expansion method that extends the information related to a manuscript using its cited references.
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Aggregation of polyQ-extended proteins is promoted by interaction with their natural coiled-coil partners.
Bioessays
PUBLISHED: 03-11-2013
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Polyglutamine (polyQ) diseases are genetically inherited neurodegenerative disorders. They are caused by mutations that result in polyQ expansions of particular proteins. Mutant proteins form intranuclear aggregates, induce cytotoxicity and cause neuronal cell death. Protein interaction data suggest that polyQ regions modulate interactions between coiled-coil (CC) domains. In the case of the polyQ disease spinocerebellar ataxia type-1 (SCA1), interacting proteins with CC domains further enhance aggregation and toxicity of mutant ataxin-1 (ATXN1). Here, we suggest that CC partners interacting with the polyQ region of a mutant protein, increase its aggregation while partners that interact with a different region reduce the formation of aggregates. Computational analysis of genetic screens revealed that CC-rich proteins are highly enriched among genes that enhance pathogenicity of polyQ proteins, supporting our hypothesis. We therefore suggest that blocking interactions between mutant polyQ proteins and their CC partners might constitute a promising preventive strategy against neurodegeneration.
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Short tandem repeats in the inhibitory domain of the mineralocorticoid receptor: prediction of a ?-solenoid structure.
BMC Struct. Biol.
PUBLISHED: 01-31-2013
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The human mineralocorticoid receptor (MR) is one of the main components of the renin-angiotensin-aldosterone system (RAAS), the system that regulates the body exchange of water and sodium. The evolutionary origins of this protein predate those of renin and the RAAS; accordingly it has other roles, which are being characterized. The MR has two trans-activating ligand independent domains and one inhibitory domain (ID), which modulates the activity of the former. The structure of the ID is currently unknown.
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Antioxidant activity of melatonin in diabetes in relation to the regulation and levels of plasma Cu, Zn, Fe, Mn, and Se in Zucker diabetic fatty rats.
Nutrition
PUBLISHED: 01-24-2013
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To study the antioxidant activity of melatonin in diabetes in relation to the regulation and levels of plasma copper (Cu), zinc (Zn), iron (Fe), manganese (Mn), and selenium (Se) in Zucker diabetic fatty (ZDF) and lean (ZL) rats.
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The effect of social trust on citizens’ health risk perception in the context of a petrochemical industrial complex.
Int J Environ Res Public Health
PUBLISHED: 01-08-2013
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Perceived risk of environmental threats often translates into psychological stress with a wide range of effects on health and well-being. Petrochemical industrial complexes constitute one of the sites that can cause considerable pollution and health problems. The uncertainty around emissions results in a perception of risk for citizens residing in neighboring areas, which translates into anxiety and physiological stress. In this context, social trust is a key factor in managing the perceived risk. In the case of industrial risks, it is essential to distinguish between trust in the companies that make up the industry, and trust in public institutions. In the context of a petrochemical industrial complex located in the port of Castellón (Spain), this paper primarily discusses how trust - both in the companies located in the petrochemical complex and in the public institutions - affects citizens health risk perception. The research findings confirm that while the trust in companies negatively affects citizens health risk perception, trust in public institutions does not exert a direct and significant effect. Analysis also revealed that trust in public institutions and health risk perception are essentially linked indirectly (through trust in companies).
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Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.
PLoS Comput. Biol.
PUBLISHED: 01-03-2013
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Interactions of proteins regulate signaling, catalysis, gene expression and many other cellular functions. Therefore, characterizing the entire human interactome is a key effort in current proteomics research. This challenge is complicated by the dynamic nature of protein-protein interactions (PPIs), which are conditional on the cellular context: both interacting proteins must be expressed in the same cell and localized in the same organelle to meet. Additionally, interactions underlie a delicate control of signaling pathways, e.g. by post-translational modifications of the protein partners - hence, many diseases are caused by the perturbation of these mechanisms. Despite the high degree of cell-state specificity of PPIs, many interactions are measured under artificial conditions (e.g. yeast cells are transfected with human genes in yeast two-hybrid assays) or even if detected in a physiological context, this information is missing from the common PPI databases. To overcome these problems, we developed a method that assigns context information to PPIs inferred from various attributes of the interacting proteins: gene expression, functional and disease annotations, and inferred pathways. We demonstrate that context consistency correlates with the experimental reliability of PPIs, which allows us to generate high-confidence tissue- and function-specific subnetworks. We illustrate how these context-filtered networks are enriched in bona fide pathways and disease proteins to prove the ability of context-filters to highlight meaningful interactions with respect to various biological questions. We use this approach to study the lung-specific pathways used by the influenza virus, pointing to IRAK1, BHLHE40 and TOLLIP as potential regulators of influenza virus pathogenicity, and to study the signalling pathways that play a role in Alzheimers disease, identifying a pathway involving the altered phosphorylation of the Tau protein. Finally, we provide the annotated human PPI network via a web frontend that allows the construction of context-specific networks in several ways.
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Trypanosoma brucei gambiense Adaptation to Different Mammalian Sera Is Associated with VSG Expression Site Plasticity.
PLoS ONE
PUBLISHED: 01-01-2013
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Trypanosoma brucei gambiense infection is widely considered an anthroponosis, although it has also been found in wild and domestic animals. Thus, fauna could act as reservoir, constraining the elimination of the parasite in hypo-endemic foci. To better understand the possible maintenance of T. b. gambiense in local fauna and investigate the molecular mechanisms underlying adaptation, we generated adapted cells lines (ACLs) by in vitro culture of the parasites in different mammalian sera. Using specific antibodies against the Variant Surface Glycoproteins (VSGs) we found that serum ACLs exhibited different VSG variants when maintained in pig, goat or human sera. Although newly detected VSGs were independent of the sera used, the consistent appearance of different VSGs suggested remodelling of the co-transcribed genes at the telomeric Expression Site (VSG-ES). Thus, Expression Site Associated Genes (ESAGs) sequences were analysed to investigate possible polymorphism selection. ESAGs 6 and 7 genotypes, encoding the transferrin receptor (TfR), expressed in different ACLs were characterised. In addition, we quantified the ESAG6/7 mRNA levels and analysed transferrin (Tf) uptake. Interestingly, the best growth occurred in pig and human serum ACLs, which consistently exhibited a predominant ESAG7 genotype and higher Tf uptake than those obtained in calf and goat sera. We also detected an apparent selection of specific ESAG3 genotypes in the pig and human serum ACLs, suggesting that other ESAGs could be involved in the host adaptation processes. Altogether, these results suggest a model whereby VSG-ES remodelling allows the parasite to express a specific set of ESAGs to provide selective advantages in different hosts. Finally, pig serum ACLs display phenotypic adaptation parameters closely related to human serum ACLs but distinct to parasites grown in calf and goat sera. These results suggest a better suitability of swine to maintain T. b. gambiense infection supporting previous epidemiological results.
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Functional and genomic analyses of alpha-solenoid proteins.
PLoS ONE
PUBLISHED: 01-01-2013
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Alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some alpha-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of alpha-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of alpha-solenoids. Unexpectedly, we identified occurrences of alpha-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known alpha-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that alpha-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of alpha-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that alpha-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of alpha-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/.
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Preimplantation development regulatory pathway construction through a text-mining approach.
BMC Genomics
PUBLISHED: 12-22-2011
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The integration of sequencing and gene interaction data and subsequent generation of pathways and networks contained in databases such as KEGG Pathway is essential for the comprehension of complex biological processes. We noticed the absence of a chart or pathway describing the well-studied preimplantation development stages; furthermore, not all genes involved in the process have entries in KEGG Orthology, important information for knowledge application with relation to other organisms.
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Dual-band double-negative-index fishnet metamaterial at millimeter-waves.
Opt Lett
PUBLISHED: 11-04-2011
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An effective negative refractive index (NRI) is demonstrated and experimentally verified for the first two propagation bands of a fishnet-like metamaterial at millimeter-wave frequencies. The dual-band NRI behavior is achieved by engineering the diffraction order (±1, ±1) associated with the internal mode supported between holey layers to correspond with the second propagation band. In addition to the experimental interferometric technique that accounts for the handedness of the propagation, numerical results are given to predict the dual-band effective NRI and to confirm dual-band negative refraction for a prism composed of the proposed metamaterial.
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Role of flow cytometry immunophenotyping in the diagnosis of leptomeningeal carcinomatosis.
Neuro-oncology
PUBLISHED: 10-12-2011
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To explore the contribution of flow cytometry immunophenotyping (FCI) in detecting leptomeningeal disease in patients with solid tumors.
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The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.
BMC Bioinformatics
PUBLISHED: 10-03-2011
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Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional metrics. The BioCreative III Protein-Protein Interaction (PPI) tasks were motivated by such considerations, trying to address aspects including how the end user would oversee the generated output, for instance by providing ranked results, textual evidence for human interpretation or measuring time savings by using automated systems. Detecting articles describing complex biological events like PPIs was addressed in the Article Classification Task (ACT), where participants were asked to implement tools for detecting PPI-describing abstracts. Therefore the BCIII-ACT corpus was provided, which includes a training, development and test set of over 12,000 PPI relevant and non-relevant PubMed abstracts labeled manually by domain experts and recording also the human classification times. The Interaction Method Task (IMT) went beyond abstracts and required mining for associations between more than 3,500 full text articles and interaction detection method ontology concepts that had been applied to detect the PPIs reported in them.
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Cardiac alpha-myosin (MYH6) is the predominant sarcomeric disease gene for familial atrial septal defects.
PLoS ONE
PUBLISHED: 09-23-2011
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Secundum-type atrial septal defects (ASDII) account for approximately 10% of all congenital heart defects (CHD) and are associated with a familial risk. Mutations in transcription factors represent a genetic source for ASDII. Yet, little is known about the role of mutations in sarcomeric genes in ASDII etiology. To assess the role of sarcomeric genes in patients with inherited ASDII, we analyzed 13 sarcomeric genes (MYH7, MYBPC3, TNNT2, TCAP, TNNI3, MYH6, TPM1, MYL2, CSRP3, ACTC1, MYL3, TNNC1, and TTN kinase region) in 31 patients with familial ASDII using array-based resequencing. Genotyping of family relatives and control subjects as well as structural and homology analyses were used to evaluate the pathogenic impact of novel non-synonymous gene variants. Three novel missense mutations were found in the MYH6 gene encoding alpha-myosin heavy chain (R17H, C539R, and K543R). These mutations co-segregated with CHD in the families and were absent in 370 control alleles. Interestingly, all three MYH6 mutations are located in a highly conserved region of the alpha-myosin motor domain, which is involved in myosin-actin interaction. In addition, the cardiomyopathy related MYH6-A1004S and the MYBPC3-A833T mutations were also found in one and two unrelated subjects with ASDII, respectively. No mutations were found in the 11 other sarcomeric genes analyzed. The study indicates that sarcomeric gene mutations may represent a so far underestimated genetic source for familial recurrence of ASDII. In particular, perturbations in the MYH6 head domain seem to play a major role in the genetic origin of familial ASDII.
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Diamine and aminoalcohol derivatives active against Trypanosoma brucei.
Bioorg. Med. Chem. Lett.
PUBLISHED: 09-22-2011
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Twenty compounds selected as representative members of three series of long-chain 1,2-diamines, 2-amino-1-alkanols and 1-amino-2-alkanols structurally related to dihydrosphingosin, were synthesized and tested in vitro for their ability to inhibit the sleeping sickness parasites Trypanosoma bruceirhodesiense and Trypanosoma brucei gambiense. Eight compounds showed EC(50) values in the submicromolar range, with selectivity indexes up to 39 related to the respective cytotoxicity values for Vero cells. The parasite phenotype detected after treatment with the most potent compounds showed irreversible cell morphology alterations of the flagellar pocket that lead to inhibition of cell growth and parasite death.
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A directed protein interaction network for investigating intracellular signal transduction.
Sci Signal
PUBLISHED: 09-09-2011
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Cellular signal transduction is a complex process involving protein-protein interactions (PPIs) that transmit information. For example, signals from the plasma membrane may be transduced to transcription factors to regulate gene expression. To obtain a global view of cellular signaling and to predict potential signal modulators, we searched for protein interaction partners of more than 450 signaling-related proteins by means of automated yeast two-hybrid interaction mating. The resulting PPI network connected 1126 proteins through 2626 PPIs. After expansion of this interaction map with publicly available PPI data, we generated a directed network resembling the signal transduction flow between proteins with a naïve Bayesian classifier. We exploited information on the shortest PPI paths from membrane receptors to transcription factors to predict input and output relationships between interacting proteins. Integration of directed PPI with time-resolved protein phosphorylation data revealed network structures that dynamically conveyed information from the activated epidermal growth factor and extracellular signal-regulated kinase (EGF/ERK) signaling cascade to directly associated proteins and more distant proteins in the network. From the model network, we predicted 18 previously unknown modulators of EGF/ERK signaling, which we validated in mammalian cell-based assays. This generic experimental and computational approach provides a framework for elucidating causal connections between signaling proteins and facilitates the identification of proteins that modulate the flow of information in signaling networks.
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Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases.
Bioinformatics
PUBLISHED: 07-28-2011
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Protein-protein interaction (PPI) databases are widely used tools to study cellular pathways and networks; however, there are several databases available that still do not account for cell type-specific differences. Here, we evaluated the characteristics of six interaction databases, incorporated tissue-specific gene expression information and finally, investigated if the most popular proteins of scientific literature are involved in good quality interactions.
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Prediction of protein secondary structure from circular dichroism using theoretically derived spectra.
Proteins
PUBLISHED: 07-20-2011
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Circular dichroism (CD) is a spectroscopic technique commonly used to investigate the structure of proteins. Major secondary structure types, alpha-helices and beta-strands, produce distinctive CD spectra. Thus, by comparing the CD spectrum of a protein of interest to a reference set consisting of CD spectra of proteins of known structure, predictive methods can estimate the secondary structure of the protein. Currently available methods, including K2D2, use such experimental CD reference sets, which are very small in size when compared to the number of tertiary structures available in the Protein Data Bank (PDB). Conversely, given a PDB structure, it is possible to predict a theoretical CD spectrum from it. The methodological framework for this calculation was established long ago but only recently a convenient implementation called DichroCalc has been developed. In this study, we set to determine whether theoretically derived spectra could be used as reference set for accurate CD based predictions of secondary structure. We used DichroCalc to calculate the theoretical CD spectra of a nonredundant set of structures representing most proteins in the PDB, and applied a straightforward approach for predicting protein secondary structure content using these theoretical CD spectra as reference set. We show that this method improves the predictions, particularly for the wavelength interval between 200 and 240 nm and for beta-strand content. We have implemented this method, called K2D3, in a publicly accessible web server at http://www. ogic.ca/projects/k2d3. Proteins 2011. © 2011 Wiley Periodicals, Inc.
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PDBpaint, a visualization webservice to tag protein structures with sequence annotations.
Bioinformatics
PUBLISHED: 07-14-2011
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Protein features are often displayed along the linear sequence of amino acids that make up that protein, but in reality these features occupy a position in the folded proteins 3D space. Mapping sequence features to known or predicted protein structures is useful when trying to deduce the function of those features and when evaluating sequence or structural predictions. To facilitate this goal, we developed PDBpaint, a simple tool that displays protein sequence features gathered from bioinformatics resources on top of protein structures, which are displayed in an interactive window (using the Jmol Java viewer). PDBpaint can be used either with existing protein structures or with novel structures provided by the user. The current version of PDBpaint allows the visualization of annotations from Pfam, ARD (detection of HEAT-repeats), UniProt, TMHMM2.0 and SignalP. Users can also add other annotations manually.
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Altered serum selenium and uric acid levels and dyslipidemia in hemodialysis patients could be associated with enhanced cardiovascular risk.
Biol Trace Elem Res
PUBLISHED: 07-08-2011
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In the present study, the first objective was to follow up serum selenium (Se) concentrations in 117 hemodialysis patients (HPs) during a 2-year longitudinal study, relating concentrations to biochemical indexes (n?=?6; namely lipoprotein profile, uric acid, and total protein levels). It was also evaluated whether the disease is associated with an enhanced cardiovascular risk. A healthy control group (n?=?50) was also studied. Mean serum Se levels were significantly lower in HPs than in the controls (p?=?0.002); mean levels significantly increased from the first to third blood sampling (p?
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Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory network.
PLoS ONE
PUBLISHED: 06-16-2011
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Somatic cells can be reprogrammed to induced pluripotent stem cells by over-expression of OCT4, SOX2, KLF4 and c-MYC (OSKM). With the aim of unveiling the early mechanisms underlying the induction of pluripotency, we have analyzed transcriptional profiles at 24, 48 and 72 hours post-transduction of OSKM into human foreskin fibroblasts. Experiments confirmed that upon viral transduction, the immediate response is innate immunity, which induces free radical generation, oxidative DNA damage, p53 activation, senescence, and apoptosis, ultimately leading to a reduction in the reprogramming efficiency. Conversely, nucleofection of OSKM plasmids does not elicit the same cellular stress, suggesting viral response as an early reprogramming roadblock. Additional initiation events include the activation of surface markers associated with pluripotency and the suppression of epithelial-to-mesenchymal transition. Furthermore, reconstruction of an OSKM interaction network highlights intermediate path nodes as candidates for improvement intervention. Overall, the results suggest three strategies to improve reprogramming efficiency employing: 1) anti-inflammatory modulation of innate immune response, 2) pre-selection of cells expressing pluripotency-associated surface antigens, 3) activation of specific interaction paths that amplify the pluripotency signal.
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Génie: literature-based gene prioritization at multi genomic scale.
Nucleic Acids Res.
PUBLISHED: 05-23-2011
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Biomedical literature is traditionally used as a way to inform scientists of the relevance of genes in relation to a research topic. However many genes, especially from poorly studied organisms, are not discussed in the literature. Moreover, a manual and comprehensive summarization of the literature attached to the genes of an organism is in general impossible due to the high number of genes and abstracts involved. We introduce the novel Génie algorithm that overcomes these problems by evaluating the literature attached to all genes in a genome and to their orthologs according to a selected topic. Génie showed high precision (up to 100%) and the best performance in comparison to other algorithms in most of the benchmarks, especially when high sensitivity was required. Moreover, the prioritization of zebrafish genes involved in heart development, using human and mouse orthologs, showed high enrichment in differentially expressed genes from microarray experiments. The Génie web server supports hundreds of species, millions of genes and offers novel functionalities. Common run times below a minute, even when analyzing the human genome with hundreds of thousands of literature records, allows the use of Génie in routine lab work. Availability: http://cbdm.mdc-berlin.de/tools/genie/.
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PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.
BMC Bioinformatics
PUBLISHED: 04-19-2011
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Biological function is greatly dependent on the interactions of proteins with other proteins and genes. Abstracts from the biomedical literature stored in the NCBIs PubMed database can be used for the derivation of interactions between genes and proteins by identifying the co-occurrences of their terms. Often, the amount of interactions obtained through such an approach is large and may mix processes occurring in different contexts. Current tools do not allow studying these data with a focus on concepts of relevance to a user, for example, interactions related to a disease or to a biological mechanism such as protein aggregation.
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Functional evidence of post-transcriptional regulation by pseudogenes.
Biochimie
PUBLISHED: 04-14-2011
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Pseudogenes have been mainly considered as functionless evolutionary relics since their discovery in 1977. However, multiple mechanisms of pseudogene functionality have been proposed both at the transcriptional and post-transcriptional level. This review focuses on the role of pseudogenes as post-transcriptional regulators. Two lines of research have recently presented strong evidence of their potential function as post-transcriptional regulators of the corresponding parental genes from which they originate. First, pseudogene genomic sequences can encode siRNAs. Second, pseudogene transcripts can act as indirect post-transcriptional regulators decoying ncRNA, in particular miRNAs that target the parental gene. This has been demonstrated for PTEN and KRAS, two genes involved in tumorigenesis. The role of pseudogenes in disease has not been proven and seems to be the next research landmark. In this review, we chronicle the events following the initial discovery of the useless pseudogene to its breakthrough as a functional molecule with hitherto unbeknownst potential to influence human disease.
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The susceptibility of trypanosomatid pathogens to PI3/mTOR kinase inhibitors affords a new opportunity for drug repurposing.
PLoS Negl Trop Dis
PUBLISHED: 03-26-2011
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Target repurposing utilizes knowledge of "druggable" targets obtained in one organism and exploits this information to pursue new potential drug targets in other organisms. Here we describe such studies to evaluate whether inhibitors targeting the kinase domain of the mammalian Target of Rapamycin (mTOR) and human phosphoinositide-3-kinases (PI3Ks) show promise against the kinetoplastid parasites Trypanosoma brucei, T. cruzi, Leishmania major, and L. donovani. The genomes of trypanosomatids encode at least 12 proteins belonging to the PI3K protein superfamily, some of which are unique to parasites. Moreover, the shared PI3Ks differ greatly in sequence from those of the human host, thereby providing opportunities for selective inhibition.
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QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards.
BMC Res Notes
PUBLISHED: 03-09-2011
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High-throughput biological experiments can produce a large amount of data showing little overlap with current knowledge. This may be a problem when evaluating alternative scoring mechanisms for such data according to a gold standard dataset because standard statistical tests may not be appropriate.
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Loss of Lrp2 in zebrafish disrupts pronephric tubular clearance but not forebrain development.
Dev. Dyn.
PUBLISHED: 03-08-2011
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Low-density lipoprotein receptor-related protein 2 (LRP2) is a multifunctional cell surface receptor conserved from nematodes to humans. In mammals, it acts as regulator of sonic hedgehog and bone morphogenetic protein pathways in patterning of the embryonic forebrain and as a clearance receptor in the adult kidney. Little is known about activities of this LRP in other phyla. Here, we extend the functional elucidation of LRP2 to zebrafish as a model organism of receptor (dys)function. We demonstrate that expression of Lrp2 in embryonic and larval fish recapitulates the patterns seen in mammalian brain and kidney. Furthermore, we studied the consequence of receptor deficiencies in lrp2 and in lrp2b, a homologue unique to fish, using ENU mutagenesis or morpholino knockdown. While receptor-deficient zebrafish suffer from overt renal resorption deficiency, their brain development proceeds normally, suggesting evolutionary conservation of receptor functions in pronephric duct clearance but not in patterning of the teleost forebrain.
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Integration of expressed sequence tag data flanking predicted RNA secondary structures facilitates novel non-coding RNA discovery.
PLoS ONE
PUBLISHED: 02-14-2011
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Many computational methods have been used to predict novel non-coding RNAs (ncRNAs), but none, to our knowledge, have explicitly investigated the impact of integrating existing cDNA-based Expressed Sequence Tag (EST) data that flank structural RNA predictions. To determine whether flanking EST data can assist in microRNA (miRNA) prediction, we identified genomic sites encoding putative miRNAs by combining functional RNA predictions with flanking ESTs data in a model consistent with miRNAs undergoing cleavage during maturation. In both human and mouse genomes, we observed that the inclusion of flanking ESTs adjacent to and not overlapping predicted miRNAs significantly improved the performance of various methods of miRNA prediction, including direct high-throughput sequencing of small RNA libraries. We analyzed the expression of hundreds of miRNAs predicted to be expressed during myogenic differentiation using a customized microarray and identified several known and predicted myogenic miRNA hairpins. Our results indicate that integrating ESTs flanking structural RNA predictions improves the quality of cleaved miRNA predictions and suggest that this strategy can be used to predict other non-coding RNAs undergoing cleavage during maturation.
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[Preoperative mood disorders in patients undergoing cardiac surgery: risk factors and postoperative morbidity in the intensive care unit].
Rev Esp Cardiol
PUBLISHED: 02-07-2011
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To estimate the preoperative levels of anxiety and depression in patients awaiting heart surgery and to identify the risk factors associated with the development of these mood disorders. To evaluate the relationship between preoperative anxiety and depression and postoperative morbidity.
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Autophagy in protists.
Autophagy
PUBLISHED: 02-01-2011
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Autophagy is the degradative process by which eukaryotic cells digest their own components using acid hydrolases within the lysosome. Originally thought to function almost exclusively in providing starving cells with nutrients taken from their own cellular constituents, autophagy is in fact involved in numerous cellular events including differentiation, turnover of macromolecules and organelles, and defense against parasitic invaders. During the last 10-20 years, molecular components of the autophagic machinery have been discovered, revealing a complex interactome of proteins and lipids, which, in a concerted way, induce membrane formation to engulf cellular material and target it for lysosomal degradation. Here, our emphasis is autophagy in protists. We discuss experimental and genomic data indicating that the canonical autophagy machinery characterized in animals and fungi appeared prior to the radiation of major eukaryotic lineages. Moreover, we describe how comparative bioinformatics revealed that this canonical machinery has been subject to moderation, outright loss or elaboration on multiple occasions in protist lineages, most probably as a consequence of diverse lifestyle adaptations. We also review experimental studies illustrating how several pathogenic protists either utilize autophagy mechanisms or manipulate host-cell autophagy in order to establish or maintain infection within a host. The essentiality of autophagy for the pathogenicity of many parasites, and the unique features of some of the autophagy-related proteins involved, suggest possible new targets for drug discovery. Further studies of the molecular details of autophagy in protists will undoubtedly enhance our understanding of the diversity and complexity of this cellular phenomenon and the opportunities it offers as a drug target.
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Recognition of 2-O-methylated 3-end of piRNA by the PAZ domain of a Piwi protein.
Structure
PUBLISHED: 01-20-2011
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Piwi proteins are germline-specific Argonautes that associate with small RNAs called Piwi-interacting RNAs (piRNAs), and together with these RNAs are implicated in transposon silencing. The PAZ domain of Argonaute proteins recognizes the 3-end of the RNA, which in the case of piRNAs is invariably modified with a 2-O-methyl group. Here, we present the solution structure of the PAZ domain from the mouse Piwi protein, MIWI, in complex with an 8-mer piRNA mimic. The methyl group is positioned in a hydrophobic cavity made of conserved amino acids from strand ?7 and helix ?3, where it is contacted by the side chain of methionine-382. Our structure is similar to that of Ago-PAZ, but subtle differences illustrate how the PAZ domain has evolved to accommodate distinct 3 ends from a variety of RNA substrates.
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Millimeter-wave phase resonances in compound re?ection gratings with subwavelength grooves.
Opt Express
PUBLISHED: 12-18-2010
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Experimental evidence of phase resonances in a dual-period re?ection structure comprising three subwavelength grooves in each period is provided in the millimeter-wave regime. We have analyzed and measured the response of these structures and show that phase resonances are characterized by a minimum in the re?ected response, as predicted by numerical calculations. It is also shown that under oblique incidence these structures exhibit additional phase resonances not present for normal illumination because of the potentially permitted odd ?eld distribution. A satisfactory agreement between the experimental and numerical re?ectance curves is obtained. These results con?rm the recent theoretical predictions of phase resonances in re?ection gratings in the millimeter-wave regime, and encourage research in this subject due to the multiple potential applications, such as frequency selective surfaces, backscattering reduction and complex-surface-wave-based sensing. In addition, it is underlined here that the response becomes much more complex than the mere in?nite analysis when one considers ?nite periodic structures as in the real experiment.
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Beneficial effects of melatonin on obesity and lipid profile in young Zucker diabetic fatty rats.
J. Pineal Res.
PUBLISHED: 11-19-2010
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The study objective was to investigate the effects of melatonin on obesity and obesity-associated systolic hypertension and dyslipidemia in young male Zucker diabetic fatty (ZDF) rats, an experimental model of the metabolic syndrome. ZDF rats (n=30) and lean littermates (ZL) (n=30) were used. At 6wk of age, both lean and fatty animals were subdivided into three groups (n=10): naive (N), vehicle-treated (V), and melatonin-treated (M) (10mg/kg/day) for 6wk. Vehicle and melatonin were added to the drinking water. Melatonin reduced mean weight gain (51±2/100g BW) versus N-ZDF group (58±3, P<0.05) without food intake differences. M-ZDF rats showed an apparent reduction in systolic hypertension that proved not to be statistically significant, and a significant improvement in dyslipidemia, with a reduction in hypertriglyceridemia from 580±40 to 420.6±40.9mg/dL (P<0.01). Melatonin raised high-density-lipoprotein (HDL) cholesterol in ZDF (from 81.6±4.9 to 103.1±4.5mg/dL, P<0.01) and ZL rats (from 62.8±4.8 to 73.5±4.8mg/dL, P<0.05) and significantly reduced low-density-lipoprotein (LDL) cholesterol in ZDF rats from 5.20±0.4 to 4.14±0.3?mg/dL (P<0.05) but had no effect on total cholesterol levels. To our knowledge, this is the first evidence of a positive effect of melatonin on overweight and lipid pattern of obese Zucker diabetic rats, supporting the proposition that melatonin administration may ameliorate overweight and lipid metabolism in humans. Because these benefits occurred in youth, before advanced metabolic and vascular complications, melatonin might help to prevent cardiovascular disease associated with obesity and dyslipidemia.
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The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons.
Nucleic Acids Res.
PUBLISHED: 11-04-2010
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Almost 50 years following the discovery of the prokaryotic operon, the functional relevance of gene order within operons remains unclear. In this work, we take advantage of the eroded genome of Mycobacterium leprae to add evidence supporting the notion that functionally less important genes have a tendency to be located at the end of its operons. M. lepraes genome includes 1133 pseudogenes and 1614 protein-coding genes and can be compared with the close genome of M. tuberculosis. Assuming M. lepraes pseudogenes to represent dispensable genes, we have studied the position of these pseudogenes in the operons of M. leprae and of their orthologs in M. tuberculosis. We observed that both tend to be located in the 3 (downstream) half of the operon (P-values of 0.03 and 0.18, respectively). Analysis of pseudogenes in all available prokaryotic genomes confirms this trend (P-value of 7.1?×?10(-7)). In a complementary analysis, we found a significant tendency for essential genes to be located at the 5 (upstream) half of the operon (P-value of 0.006). Our work provides an indication that, in prokarya, functionally less important genes have a tendency to be located at the end of operons, while more relevant genes tend to be located toward operon starts.
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Serum selenium levels in cirrhotic patients are not influenced by the disease severity index.
Nutr Res
PUBLISHED: 06-09-2010
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Selenium (Se) is an antioxidant element that protects against cellular damage by reactive oxygen species. Therefore, total serum Se concentration may reflect protection during the development of cirrhosis, an oxidative stress-related disease. We hypothesized that serum Se levels are diminished in cirrhotic patients due to their enhanced oxidative stress, and serum Se levels are reduced the most in patients with the highest severity of cirrhosis. A case-control study was performed to determine whether cirrhosis is associated with changes in serum Se levels. Blood samples from 30 healthy controls and 93 cirrhotic patients were analyzed for total serum Se by hydride generation atomic absorption spectrometry. The Child-Pugh index score was used to evaluate the severity of liver disease. The mean serum Se concentration was significantly lower in patients vs controls (0.721 ± 0.239 vs 0.926 ± 0.241 ?mol/L; P = .001). Mean serum Se levels were not significantly lower in patients with higher severity of cirrhosis (0.691 ± 0.229 vs 0.755 ± 0.255 ?mol/L; P = .144). A positive and significant correlation was found between age and serum Se levels in patients (r = 0.277, P = .007). Patients showed significant sex differences in serum Se level (higher in male) and severity index (higher in female). The significantly decreased serum Se level in patients indicates that the Se component of the antioxidant system is severely impaired in cirrhosis. However, serum Se levels were not influenced by the severity of the disease.
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The soluble intracellular domain of megalin does not affect renal proximal tubular function in vivo.
Kidney Int.
PUBLISHED: 06-09-2010
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Megalin-mediated endocytic uptake constitutes the main pathway for clearance of plasma proteins from the glomerular filtrate in proximal tubules. Little is known, however, about mechanisms that control megalin expression and activity in the kidney. A widely discussed hypothesis states that upon ligand binding a regulated intramembrane proteolysis releases the cytosolic domain of megalin and this fragment subsequently modulates megalin gene transcription. Here, we tested this by generating a mouse model that co-expressed both the soluble intracellular domain and full-length megalin. Despite pronounced synthesis in the proximal tubules, the soluble intracellular domain failed to exert distinct effects on renal proximal tubular function, including megalin expression, endocytic retrieval of proteins, or global renal gene transcription. Hence, our study argues that the soluble intracellular domain does not have a role in regulating the activity of megalin in the kidney.
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Target of rapamycin (TOR)-like 1 kinase is involved in the control of polyphosphate levels and acidocalcisome maintenance in Trypanosoma brucei.
J. Biol. Chem.
PUBLISHED: 05-21-2010
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Target of rapamycin (TOR) kinases are highly conserved protein kinases that integrate signals from nutrients and growth factors to coordinate cell growth and cell cycle progression. It has been previously described that two TOR kinases control cell growth in the protozoan parasite Trypanosoma brucei, the causative agent of African trypanosomiasis. Here we studied an unusual TOR-like protein named TbTOR-like 1 containing a PDZ domain and found exclusively in kinetoplastids. TbTOR-like 1 localizes to unique cytosolic granules. After hyperosmotic stress, the localization of the protein shifts to the cell periphery, different from other organelle markers. Ablation of TbTOR-like 1 causes a progressive inhibition of cell proliferation, producing parasites accumulating in the S/G(2) phase of the cell cycle. TbTOR-like 1 knocked down cells have an increased area occupied by acidic vacuoles, known as acidocalcisomes, and are enriched in polyphosphate and pyrophosphate. These results suggest that TbTOR-like 1 might be involved in the control of acidocalcisome and polyphosphate metabolism in T. brucei.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.