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Find video protocols related to scientific articles indexed in Pubmed.
Polymeric Microbubbles as Delivery Vehicles for Sensitisers in Sonodynamic Therapy.
Langmuir
PUBLISHED: 11-20-2014
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Microbubbles (MBs) have recently emerged as promising delivery vehicles for sensitiser drugs in sonodynamic therapy (SDT). The ability to selectively destroy the MB and activate the sensitizer using an external ultrasound trigger could provide a minimally invasive and highly targeted therapy. While lipid MBs have been approved for use as contrast agents in diagnostic ultrasound, the attachment of sensitiser drugs to their surface results in a significant reduction in particle stability. In this manuscript, we prepare both lipid and polymer (PLGA) MBs with rose bengal attached to their surface and demonstrate that PLGA MB conjugates are significantly more stable than their lipid counterparts. In addition, the improved stability offered by the PLGA shell does not hinder their selective destruction using therapeutically acceptable ultrasound intensities. Furthermore, we demonstrate that treatment of ectopic human tumours (BxPC-3) in mice with the PLGA MB-rose bengal conjugate and ultrasound reduced tumour volume by 34% 4 days after treatment while tumours treated with the conjugate alone increased in volume by 48% over the same time period. Therefore, PLGA MBs may offer a more stable alternative to lipid MBs for the site specific delivery of sensitisers in SDT.
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Did Hospital Engagement Networks Actually Improve Care?
N. Engl. J. Med.
PUBLISHED: 11-20-2014
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To the Editor: The Partnership for Patients model test (PfP), discussed in a Perspective article by Pronovost and Jha (Aug. 21 issue),(1) is a large-scale quality-improvement program designed to make hospital care safer, more reliable, and less costly by engaging the nation's hospitals in work to reduce 30-day all-cause readmissions and preventable all-cause harm. We are writing to respond to several points made in the article. First, the test model, like all models from the Centers for Medicare and Medicaid Services (CMS) Innovation Center, does have an independent evaluation. The first evaluation report is posted publicly.(2),(3) Second, the evaluation . . .
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Long-term incidence of symptomatic urolithiasis post-bariatric surgery.
Can Urol Assoc J
PUBLISHED: 11-20-2014
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The risk of urolithiasis post-Roux-en-Y gastric bypass (RYGB) surgery is higher when compared to the general population. Calcium and vitamin D supplementation is routinely prescribed to these patients, yet compliance with these supplements is unknown. The aim of this study was to assess the incidence of symptomatic de novo urolithiasis post-RYGB and compliance with calcium and vitamin D supplementation.
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Intermittent PTH administration and mechanical loading are anabolic for periprosthetic cancellous bone.
J. Orthop. Res.
PUBLISHED: 11-20-2014
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The purpose of this study was to determine the individual and combined effects on periprosthetic cancellous bone of intermittent parathyroid hormone administration (iPTH) and mechanical loading at the cellular, molecular, and tissue levels. Porous titanium implants were inserted bilaterally on the cancellous bone of adult rabbits beneath a loading device attached to the distal lateral femur. The left femur received a sham loading device. The right femur was loaded daily, and half of the rabbits received daily PTH. Periprosthetic bone was evaluated up to 28 days for gene expression, histology, and µCT analysis. Loading and iPTH increased bone mass by a combination of two mechanisms: (1) Altering cell populations in a pro-osteoblastic/anti-adipocytic direction, and (2) controlling bone turnover by modulating the RANKL-OPG ratio. At the tissue level, BV/TV increased with both loading (+53%, p??0.05). This study suggests that iPTH and loading are potential therapies for enhancing periprosthetic bone formation. The elucidation of the cellular and molecular response may help further enhance the combined therapy and related targeted treatment strategies. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res.
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PyFDAP: Automated analysis of Fluorescence Decay After Photoconversion (FDAP) experiments.
Bioinformatics
PUBLISHED: 11-09-2014
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We developed the graphical user interface PyFDAP for the fitting of linear and non-linear decay functions to data obtained by Fluorescence Decay After Photoconversion (FDAP) experiments. PyFDAP structures and analyzes large FDAP data sets and features multiple fitting and plotting options. Availability and Implementation: PyFDAP was written in Python and runs on Ubuntu Linux, Mac OS X, and Microsoft Windows operating systems. The software, a user guide, and a test FDAP data set are freely available for download from http://people.tuebingen.mpg.de/mueller-lab.
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Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates.
Biol Open
PUBLISHED: 11-02-2014
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In order to gain insight into the impact of yolk increase on endoderm development, we have analyzed the mechanisms of endoderm formation in the catshark S. canicula, a species exhibiting telolecithal eggs and a distinct yolk sac. We show that in this species, endoderm markers are expressed in two distinct tissues, the deep mesenchyme, a mesenchymal population of deep blastomeres lying beneath the epithelial-like superficial layer, already specified at early blastula stages, and the involuting mesendoderm layer, which appears at the blastoderm posterior margin at the onset of gastrulation. Formation of the deep mesenchyme involves cell internalizations from the superficial layer prior to gastrulation, by a movement suggestive of ingressions. These cell movements were observed not only at the posterior margin, where massive internalizations take place prior to the start of involution, but also in the center of the blastoderm, where internalizations of single cells prevail. Like the adjacent involuting mesendoderm, the posterior deep mesenchyme expresses anterior mesendoderm markers under the control of Nodal/activin signaling. Comparisons across vertebrates support the conclusion that endoderm is specified in two distinct temporal phases in the catshark as in all major osteichthyan lineages, in line with an ancient origin of a biphasic mode of endoderm specification in gnathostomes. They also highlight unexpected similarities with amniotes, such as the occurrence of cell ingressions from the superficial layer prior to gastrulation. These similarities may correspond to homoplastic traits fixed separately in amniotes and chondrichthyans and related to the increase in egg yolk mass.
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Patient and Partner Experiences With Obstructive Sleep Apnea and CPAP Treatment: A Qualitative Analysis.
Behav Sleep Med
PUBLISHED: 09-10-2014
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Few studies have investigated factors associated with continuous positive airway pressure (CPAP) treatment for sleep apnea from the patients' and their partners' perspective. This qualitative research study explored patients' and partners' experiences of CPAP and facilitators and barriers to CPAP use, and elicited suggestions for a first-time CPAP user program. Data from 27 participants were collected via four sleep apnea patient and four partner focus groups. Qualitative content analysis identified five themes: knowledge of sleep apnea, effects of sleep apnea, effects of CPAP, barriers and facilitators of CPAP, and ideas for a new user support program. Patients and partners emphasized the importance of partner involvement in the early CPAP treatment period. These data suggest consideration of a couple-oriented approach to improving CPAP adherence.
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Randomized Controlled Withdrawal Study of Upper Airway Stimulation on OSA: Short- and Long-term Effect.
Otolaryngol Head Neck Surg
PUBLISHED: 09-09-2014
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To assess the efficacy and durability of upper airway stimulation via the hypoglossal nerve on obstructive sleep apnea (OSA) severity including objective and subjective clinical outcome measures.
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The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.
Science
PUBLISHED: 09-04-2014
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Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.
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Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
Science
PUBLISHED: 08-21-2014
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Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
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Pain patients and who they live with: a correlational study of coresidence patterns and pain interference.
Pain Res Manag
PUBLISHED: 08-09-2014
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Mixed associations have been observed between various aspects of 'social support' and patient pain experiences.
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The effect of oral contraceptive pills and the natural menstrual cYCLe on arterial stiffness and hemodynamICs (CYCLIC).
J. Hypertens.
PUBLISHED: 08-02-2014
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Over 100 million women currently use oral contraceptive pills (OCPs) worldwide. However, little is known about the effects of OCPs on arterial stiffness and hemodynamics. Furthermore, whether arterial stiffness and hemodynamics vary throughout the natural menstrual cycle remains controversial. Herein, we estimated the effect of the natural menstrual cycle and OCP use on arterial stiffness and hemodynamics.
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Upper Airway Stimulation for Obstructive Sleep Apnea: Past, Present, and Future.
Sleep
PUBLISHED: 07-30-2014
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Obstructive sleep apnea (OSA) is an increasingly prevalent clinical problem with significant effects on both personal and public health. Continuous positive airway pressure (CPAP) has demonstrated excellent efficacy and low morbidity; long-term adherence rates approach 50%. Although traditional upper airway surgical procedures target the anatomic component of obstruction, upper airway stimulation tackles the twin goals of improving anatomic and neuromuscular pathology. After decades of trials demonstrating proof of concept of hypoglossal nerve stimulation in animal and human subjects, the results of a large multicenter, prospective trial were recently published. The trial demonstrated that hypoglossal nerve stimulation led to significant improvements in objective and subjective measurements of the severity of OSA. This novel approach is the first to combine sleep surgery techniques with a titratable medical device for the treatment of OSA. Further research is required to define optimal patient selection and device performance and to demonstrate long-term effectiveness.
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Structural and functional partitioning of bread wheat chromosome 3B.
Science
PUBLISHED: 07-19-2014
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We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.
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TE-Tracker: systematic identification of transposition events through whole-genome resequencing.
BMC Bioinformatics
PUBLISHED: 07-09-2014
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BackgroundTransposable elements (TEs) are DNA sequences that are able to move from their location in the genome by cutting or copying themselves to another locus. As such, they are increasingly recognized as impacting all aspects of genome function. With the dramatic reduction in cost of DNA sequencing, it is now possible to resequence whole genomes in order to systematically characterize novel TE mobilization in a particular individual. However, this task is made difficult by the inherently repetitive nature of TE sequences, which in some eukaryotes compose over half of the genome sequence. Currently, only a few software tools dedicated to the detection of TE mobilization using next-generation-sequencing are described in the literature. They often target specific TEs for which annotation is available, and are only able to identify families of closely related TEs, rather than individual elements.ResultsWe present TE-Tracker, a general and accurate computational method for the de-novo detection of germ line TE mobilization from re-sequenced genomes, as well as the identification of both their source and destination sequences. We compare our method with the two classes of existing software: specialized TE-detection tools and generic structural variant (SV) detection tools. We show that TE-Tracker, while working independently of any prior annotation, bridges the gap between these two approaches in terms of detection power. Indeed, its positive predictive value (PPV) is comparable to that of dedicated TE software while its sensitivity is typical of a generic SV detection tool. TE-Tracker demonstrates the benefit of adopting an annotation-independent, de novo approach for the detection of TE mobilization events. We use TE-Tracker to provide a comprehensive view of transposition events induced by loss of DNA methylation in Arabidopsis. TE-Tracker is freely available at http://www.genoscope.cns.fr/TE-Tracker.ConclusionsWe show that TE-Tracker accurately detects both the source and destination of novel transposition events in re-sequenced genomes. Moreover, TE-Tracker is able to detect all potential donor sequences for a given insertion, and can identify the correct one among them. Furthermore, TE-Tracker produces significantly fewer false positives than common SV detection programs, thus greatly facilitating the detection and analysis of TE mobilization events.
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Relation of Obstructive Sleep Apnea to Coronary Artery Calcium in Non-Obese Versus Obese Men and Women Aged 45 - 75 Years.
Am. J. Cardiol.
PUBLISHED: 07-01-2014
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Sleep apnea and obesity are strongly associated, and both increase the risk for coronary artery disease. Several cross-sectional studies have reported discrepant results regarding the role obesity plays in the relation between sleep apnea and coronary artery calcium (CAC), a marker of subclinical coronary disease. The aim of the present study was to investigate the association between sleep apnea and the presence of CAC in a community cohort of middle-aged men and women without preexisting cardiovascular disease, stratified by body mass index (<30 vs ?30 kg/m(2)). Participants underwent electron-beam computed tomography to measure CAC and underwent home sleep testing for sleep apnea. The presence of CAC was defined as an Agatston score >0. Sleep apnea was analyzed categorically using the apnea-hypopnea index. The sample was composed of primarily men (61%) and Caucasians (56%), with a mean age of 61 years. The prevalence of CAC was 76%. In participants with body mass indexes <30 kg/m(2) (n = 139), apnea-hypopnea index ?15 (vs <5) was associated with 2.7-fold odds of having CAC, but the effect only approached significance. Conversely, in participants with body mass indexes ?30 kg/m(2), sleep apnea was not independently associated with CAC. In conclusion, sleep apnea is independently associated with early atherosclerotic plaque burden in nonobese patients.
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[Electrical storm in the emergency room: clinical pathways].
Herzschrittmacherther Elektrophysiol
PUBLISHED: 06-06-2014
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In patients with structural heart disease, occurrence of an electrical storm (ES) is associated with increased mortality acutely and during medium term follow-up. Depending on the underlying heart disease and baseline type of arrhythmia, different clinical pathways have to be followed to reach sustained freedom from ventricular arrhythmia recurrences. Trigger elimination, sympathetic blockade (initially using betablockers and sedation), antiarrhythmic therapy with amiodarone and catheter ablation, treatment of heart failure and invasive hemodynamic support are cornerstones of the treatment. We present an algorithm which may help to organize an optimized treatment for each ES patient, implementing invasive treatment options like coronary angioplasty, catheter ablation and invasive circulatory support. Further studies are necessary to evaluate medium term outcome of such a structured therapy.
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In situ oxidation study of Pd-Rh nanoparticles on MgAl?O?(001).
Phys Chem Chem Phys
PUBLISHED: 06-04-2014
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Alloy nanoparticles on oxide supports are widely used as heterogeneous catalysts in reactions involving oxygen. Here we discuss the oxidation behavior of Pd-Rh alloy nanoparticles on MgAl2O4(001) supports with a particle diameter from 6-11 nm. As an In situ tool, we employed high energy grazing incidence X-ray diffraction at a photon energy of 85 keV. We find that physical vapor deposited Pd-Rh nanoparticles grow epitaxially on MgAl2O4(001) with a truncated octahedral shape over the whole concentration range. During our systematic oxidation experiments performed at 670 K in the pressure range from 10(-3) to 0.1 mbar, we observe for Rh containing nanoparticles the formation of two different Rh oxide phases, namely RhO2 and a spinel-like Rh3O4 phase. PdO formation is only observed for pure Pd nanoparticles. This oxidation induced segregation behavior is also reflected in the oxidation induced enlargement of the average nanoparticle lattice parameter towards to value for pure Pd. Our results have ramifications for the phase separation behavior of alloy nanocatalysts under varying reducing and oxidizing environments.
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Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data.
BMC Genomics
PUBLISHED: 05-22-2014
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Metatranscriptomics is rapidly expanding our knowledge of gene expression patterns and pathway dynamics in natural microbial communities. However, to cope with the challenges of environmental sampling, various rRNA removal and cDNA synthesis methods have been applied in published microbial metatranscriptomic studies, making comparisons arduous. Whereas efficiency and biases introduced by rRNA removal methods have been relatively well explored, the impact of cDNA synthesis and library preparation on transcript abundance remains poorly characterized. The evaluation of potential biases introduced at this step is challenging for metatranscriptomic samples, where data analyses are complex, for example because of the lack of reference genomes.
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Catheter ablation in patients with electrical storm: benefit of a network of cooperating clinics.
Herzschrittmacherther Elektrophysiol
PUBLISHED: 05-21-2014
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Catheter ablation has been shown to be an effective treatment for rhythm stabilization in patients with multiple ventricular arrhythmia episodes called electrical storm (ES). These procedures may be complex and are usually only performed in highly specialized and experienced centers. Still the optimum timing for catheter ablation in ES remains unclear.Early access to perform acute ablation should be considered in patients who are not rhythm stabilized with antiarrhythmic medical treatment. Also patients with hemodynamic compromise (cardiogenic shock) are candidates for an early interventional strategy. In specialized centers it is consensus to perform catheter ablation in these patients as early as eligible especially when considering a high early and late mortality without interventional management. Establishing a structured protocol for treatment and admission to EP centers has helped to further reduce pre-ablation mortality and may optimize treatment of ES. Large scale networking to optimize and structure access to experienced electrophysiology centers is of importance to create a basis for optimizing treatment strategies.
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Long-Term Cost-Effectiveness of Upper Airway Stimulation for the Treatment of Obstructive Sleep Apnea: A Model-Based Projection Based on the STAR Trial.
Sleep
PUBLISHED: 05-16-2014
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Upper airway stimulation (UAS) is a new approach to treat moderate-to-severe obstructive sleep apnea. Recently, 12-month data from the Stimulation Treatment for Apnea Reduction (STAR) trial were reported, evaluating the effectiveness of UAS in patients intolerant or non-adherent to continuous positive airway pressure therapy. Our objective was to assess the cost-effectiveness of UAS from a U.S. payer perspective.
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Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication.
Nat. Biotechnol.
PUBLISHED: 04-14-2014
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Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.
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Traditional and nontraditional cardiovascular risk factors in comorbid insomnia and sleep apnea.
Sleep
PUBLISHED: 03-04-2014
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Insomnia and sleep apnea frequently co-occur and are independently associated with an increased risk of cardiovascular disease, but little is known about cardiovascular disease risk among individuals with comorbid insomnia and sleep apnea. The current study examined traditional risk factors and a physiologic biomarker of cardiovascular risk in comorbid insomnia and sleep apnea.
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Substituent effects on the binding of natural product anthocyanidin inhibitors to influenza neuraminidase with mass spectrometry.
Anal. Chim. Acta
PUBLISHED: 02-24-2014
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The binding of three closely related anthocyanins within the 430-cavity of influenza neuraminidase is studied using a combination of mass spectrometry and molecular docking. Despite their similar structures, which differ only in the number and position of the hydroxyl substituents on the phenyl group attached to the chromenylium ring, subtle differences in their binding characteristics are revealed by mass spectrometry and molecular docking that are in accord with their inhibitory properties by neuraminidase inhibition assays. The cyanidin and delphinidin, with the greatest number of hydroxyl groups, bind more strongly and are better inhibitors than pelargonidin that contains a lone hydroxyl group at the 4' position. The study demonstrates, for the first time, the sensitivity of the mass spectrometry based approach for investigating the molecular basis and relative affinity of antiviral inhibitors, with subtly different structures, to their target protein. It has broader application for the screening of other protein interactions more generally with reasonable high-throughput.
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Maintaining two mating types: structure of the mating type locus and its role in heterokaryosis in Podospora anserina.
Genetics
PUBLISHED: 02-20-2014
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Pseudo-homothallism is a reproductive strategy elected by some fungi producing heterokaryotic sexual spores containing genetically different but sexually compatible nuclei. This lifestyle appears as a compromise between true homothallism (self-fertility with predominant inbreeding) and complete heterothallism (with exclusive outcrossing). However, pseudohomothallic species face the problem of maintaining heterokaryotic mycelia to fully benefit from this lifestyle, as homokaryons are self-sterile. Here, we report on the structure of chromosome 1 in mat+ and mat- isolates of strain S of the pseudohomothallic fungus Podospora anserina. Chromosome 1 contains either one of the mat+ and mat- mating types of P. anserina, which is mostly found in nature as a mat+/mat- heterokaryotic mycelium harboring sexually compatible nuclei. We identified a "mat" region ?0.8 Mb long, devoid of meiotic recombination and containing the mating-type idiomorphs, which is a candidate to be involved in the maintenance of the heterokaryotic state, since the S mat+ and S mat- strains have different physiology that may enable hybrid-vigor-like phenomena in the heterokaryons. The mat region contains 229 coding sequences. A total of 687 polymorphisms were detected between the S mat+ and S mat- chromosomes. Importantly, the mat region is colinear between both chromosomes, which calls for an original mechanism of recombination inhibition. Microarray analyses revealed that 10% of the P. anserina genes have different transcriptional profiles in S mat+ and S mat-, in line with their different phenotypes. Finally, we show that the heterokaryotic state is faithfully maintained during mycelium growth of P. anserina, yet mat+/mat+ and mat-/mat- heterokaryons are as stable as mat+/mat- ones, evidencing a maintenance of heterokaryosis that does not rely on fitness-enhancing complementation between the S mat+ and S mat- strains.
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Fifty thousand years of Arctic vegetation and megafaunal diet.
Nature
PUBLISHED: 02-07-2014
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Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr bp (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25-15 kyr bp), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr bp, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.
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Mapping the epigenetic basis of complex traits.
Science
PUBLISHED: 02-06-2014
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Quantifying the impact of heritable epigenetic variation on complex traits is an emerging challenge in population genetics. Here, we analyze a population of isogenic Arabidopsis lines that segregate experimentally induced DNA methylation changes at hundreds of regions across the genome. We demonstrate that several of these differentially methylated regions (DMRs) act as bona fide epigenetic quantitative trait loci (QTL(epi)), accounting for 60 to 90% of the heritability for two complex traits, flowering time and primary root length. These QTL(epi) are reproducible and can be subjected to artificial selection. Many of the experimentally induced DMRs are also variable in natural populations of this species and may thus provide an epigenetic basis for Darwinian evolution independently of DNA sequence changes.
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Sleep, Health-Related Quality of Life, and Functional Outcomes in Adults With Diabetes.
Appl Nurs Res
PUBLISHED: 02-04-2014
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This study explored the association of sleep quality with physical and mental health-related quality of life (HRQoL) and functional outcomes in 116 participants with type 2 diabetes.
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The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants.
PLoS Genet.
PUBLISHED: 02-01-2014
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Members of the family Trypanosomatidae infect many organisms, including animals, plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While some Phytomonas spp. multiply in the latex of plants, or in fruit or seeds without apparent pathogenicity, others colonize the phloem sap and afflict plants of substantial economic value, including the coffee tree, coconut and oil palms. Plant trypanosomes have not been studied extensively at the genome level, a major gap in understanding and controlling pathogenesis. We describe the genome sequences of two plant trypanosomatids, one pathogenic isolate from a Guianan coconut and one non-symptomatic isolate from Euphorbia collected in France. Although these parasites have extremely distinct pathogenic impacts, very few genes are unique to either, with the vast majority of genes shared by both isolates. Significantly, both Phytomonas spp. genomes consist essentially of single copy genes for the bulk of their metabolic enzymes, whereas other trypanosomatids e.g. Leishmania and Trypanosoma possess multiple paralogous genes or families. Indeed, comparison with other trypanosomatid genomes revealed a highly streamlined genome, encoding for a minimized metabolic system while conserving the major pathways, and with retention of a full complement of endomembrane organelles, but with no evidence for functional complexity. Identification of the metabolic genes of Phytomonas provides opportunities for establishing in vitro culturing of these fastidious parasites and new tools for the control of agricultural plant disease.
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The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome.
Genome Biol.
PUBLISHED: 01-31-2014
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BackgroundLegume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking.ResultsIn the model legume Medicago truncatula, we analyze the small RNA transcriptome of roots submitted to symbiotic and pathogenic interactions. Genome mapping and a computational pipeline identify 416 miRNA candidates, including known and novel variants of 78 miRNA families present in miRBase. Stringent criteria of pre-miRNA prediction yield 52 new mtr-miRNAs, including 27 miRtrons. Analyzing miRNA precursor polymorphisms in 26 M. truncatula ecotypes identifies higher sequence polymorphism in conserved rather than Medicago-specific miRNA precursors. An average of 19 targets, mainly involved in environmental responses and signalling, is predicted per novel miRNA. We identify miRNAs responsive to bacterial and fungal pathogens or symbionts as well as their related Nod and Myc-LCO symbiotic signals. Network analyses reveal modules of new and conserved co-expressed miRNAs that regulate distinct sets of targets, highlighting potential miRNA-regulated biological pathways relevant to pathogenic and symbiotic interactions.ConclusionsWe identify 52 novel genuine miRNAs and large plasticity of the root miRNAome in response to the environment, and also in response to purified Myc/Nod signaling molecules. The new miRNAs identified and their sequence variation across M. truncatula ecotypes may be crucial to understand the adaptation of root growth to the soil environment, notably in the agriculturally important legume crops.
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Patterns of rare and abundant marine microbial eukaryotes.
Curr. Biol.
PUBLISHED: 01-27-2014
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Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions.
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Spatial distribution and structural arrangement of a murine cytomegalovirus glycoprotein detected by SPDM localization microscopy.
Histochem. Cell Biol.
PUBLISHED: 01-20-2014
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Novel approaches of localization microscopy have opened new insights into the molecular nano-cosmos of cells. We applied a special embodiment called spectral position determination microscopy (SPDM) that has the advantage to run with standard fluorescent dyes or proteins under standard preparation conditions. Pointillist images with a resolution in the order of 10 nm can be obtained by SPDM. Therefore, vector pEYFP-m164, encoding the murine cytomegalovirus glycoprotein gp36.5/m164 fused to enhanced yellow fluorescent protein, was transiently transfected into COS-7 cells. This protein shows exceptional intracellular trafficking dynamics, moving within the endoplasmic reticulum (ER) and outer nuclear membrane. The molecular positions of gp36.5/m164 were visualized and determined by SPDM imaging. From the position point patterns of the protein molecules, their arrangements were quantified by next neighbour distance analyses. Three different structural arrangements were discriminated: (a) a linear distribution along the membrane, (b) a highly structured distribution in the ER, and (c) a homogenous distribution in the cellular cytoplasm. The results indicate that the analysis of next neighbour distances on the nano-scale allows the identification and discrimination of different structural arrangements of molecules within their natural cellular environment.
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Development of a targeted metagenomic approach to study a genomic region involved in light harvesting in marine Synechococcus.
FEMS Microbiol. Ecol.
PUBLISHED: 01-12-2014
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Synechococcus, one of the most abundant cyanobacteria in marine ecosystems, displays a broad pigment diversity. However, the in situ distribution of pigment types remains largely unknown. In this study, we combined flow cytometry cell sorting, whole-genome amplification, and fosmid library construction to target a genomic region involved in light-harvesting complex (phycobilisome) biosynthesis and regulation. Synechococcus community composition and relative contamination by heterotrophic bacteria were assessed at each step of the pipeline using terminal restriction fragment length polymorphism targeting the petB and 16S rRNA genes, respectively. This approach allowed us to control biases inherent to each method and select reliable WGA products to construct a fosmid library from a natural sample collected off Roscoff (France). Sequencing of 25 fosmids containing the targeted region led to the assembly of whole or partial phycobilisome regions. Most contigs were assigned to clades I and IV consistent with the known dominance of these clades in temperate coastal waters. However, one of the fosmids contained genes distantly related to their orthologs in reference genomes, suggesting that it belonged to a novel phylogenetic clade. Altogether, this study provides novel insights into Synechococcus community structure and pigment type diversity at a representative coastal station of the English Channel.
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Upper-airway stimulation for obstructive sleep apnea.
N. Engl. J. Med.
PUBLISHED: 01-10-2014
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Obstructive sleep apnea is associated with considerable health risks. Although continuous positive airway pressure (CPAP) can mitigate these risks, effectiveness can be reduced by inadequate adherence to treatment. We evaluated the clinical safety and effectiveness of upper-airway stimulation at 12 months for the treatment of moderate-to-severe obstructive sleep apnea.
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The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.
Nat Commun
PUBLISHED: 01-09-2014
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Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions.
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Characterization of AlgMsp, an Alginate Lyase from Microbulbifer sp. 6532A.
PLoS ONE
PUBLISHED: 01-01-2014
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Alginate is a polysaccharide produced by certain seaweeds and bacteria that consists of mannuronic acid and guluronic acid residues. Seaweed alginate is used in food and industrial chemical processes, while the biosynthesis of bacterial alginate is associated with pathogenic Pseudomonas aeruginosa. Alginate lyases cleave this polysaccharide into short oligo-uronates and thus have the potential to be utilized for both industrial and medicinal applications. An alginate lyase gene, algMsp, from Microbulbifer sp. 6532A, was synthesized as an E.coli codon-optimized clone. The resulting 37 kDa recombinant protein, AlgMsp, was expressed, purified and characterized. The alginate lyase displayed highest activity at pH 8 and 0.2 M NaCl. Activity of the alginate lyase was greatest at 50°C; however the enzyme was not stable over time when incubated at 50°C. The alginate lyase was still highly active at 25°C and displayed little or no loss of activity after 24 hours at 25°C. The activity of AlgMsp was not dependent on the presence of divalent cations. Comparing activity of the lyase against polymannuronic acid and polyguluronic acid substrates showed a higher turnover rate for polymannuronic acid. However, AlgMSP exhibited greater catalytic efficiency with the polyguluronic acid substrate. Prolonged AlgMsp-mediated degradation of alginate produced dimer, trimer, tetramer, and pentamer oligo-uronates.
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Alterations in the Expression of the NF-?B Family Member RelB as a Novel Marker of Cardiovascular Outcomes during Acute Exacerbations of Chronic Obstructive Pulmonary Disease.
PLoS ONE
PUBLISHED: 01-01-2014
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Chronic obstructive pulmonary disease (COPD) exacerbations are acute events of worsened respiratory symptoms and enhanced inflammation partly mediated by NF-?B activation. RelB, an NF-?B family member, suppresses cigarette smoke-induced inflammation but its expression in COPD is unknown. Moreover, there is no information on its association with clinical features of COPD. The objectives of this study were to assess RelB expression relative to markers of inflammation as well as its association with cardiovascular and pulmonary features of COPD patients at stable-state and exacerbation.
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Localized Epidermal Cysts as a Radiation Recall Phenomenon in a Melanoma Patient Treated with Radiotherapy and the BRAF Inhibitor Vemurafenib.
Case Rep Dermatol
PUBLISHED: 01-01-2014
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BRAF inhibitors are broadly used for metastatic melanoma with BRAF mutations. Their use results in various cutaneous side effects, such as the development of keratoacanthomas and squamous cell carcinomas. We report a patient with metastatic melanoma treated with vemurafenib who developed dozens of histologically confirmed epidermal cysts within 2 months after initiation of vemurafenib administration. The cystic lesions were observed only in the localized area where a large exophytic melanoma tumor mass had been previously irradiated. Localized epidermal cysts may constitute an unusual radiation recall reaction in patients treated with BRAF inhibitors.
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Exchanging Catheters Over a Single Transseptal Sheath During Left Atrial Ablation is Associated with a Higher Risk for Silent Cerebral Events.
Indian Pacing Electrophysiol J
PUBLISHED: 01-01-2014
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Silent cerebral events (SCE) have been identified on magnetic resonance imaging (MRI) in asymptomatic patients after atrial fibrillation (AF) ablation. Procedural determinants influencing the risk for SCE still remain unclear.
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Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina).
Genome Biol Evol
PUBLISHED: 12-10-2013
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The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present here the complete sequence of the nuclear genome of the haploid-type strain of Kuraishia capsulata (CBS1993(T)), a nitrate-assimilating Saccharomycetales of uncertain taxonomy, isolated from tunnels of insect larvae underneath coniferous barks and characterized by its copious production of extracellular polysaccharides. The sequence is composed of seven scaffolds, one per chromosome, totaling 11.4 Mb and containing 6,029 protein-coding genes, ?13.5% of which being interrupted by introns. This GC-rich yeast genome (45.7%) appears phylogenetically related with the few other nitrate-assimilating yeasts sequenced so far, Ogataea polymorpha, O. parapolymorpha, and Dekkera bruxellensis, with which it shares a very reduced number of tRNA genes, a novel tRNA sparing strategy, and a common nitrate assimilation cluster, three specific features to this group of yeasts. Centromeres were recognized in GC-poor troughs of each scaffold. The strain bears MAT alpha genes at a single MAT locus and presents a significant degree of conservation with Saccharomyces cerevisiae genes, suggesting that it can perform sexual cycles in nature, although genes involved in meiosis were not all recognized. The complete absence of conservation of synteny between K. capsulata and any other yeast genome described so far, including the three other nitrate-assimilating species, validates the interest of this species for long-range evolutionary genomic studies among Saccharomycotina yeasts.
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An official American Thoracic Society statement: continuous positive airway pressure adherence tracking systems. The optimal monitoring strategies and outcome measures in adults.
Am. J. Respir. Crit. Care Med.
PUBLISHED: 09-03-2013
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Continuous positive airway pressure (CPAP) is considered the treatment of choice for obstructive sleep apnea (OSA), and studies have shown that there is a correlation between patient adherence and treatment outcomes. Newer CPAP machines can track adherence, hours of use, mask leak, and residual apnea-hypopnea index (AHI). Such data provide a strong platform to examine OSA outcomes in a chronic disease management model. However, there are no standards for capturing CPAP adherence data, scoring flow signals, or measuring mask leak, or for how clinicians should use these data.
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Acute Safety and Efficacy of a Novel Multipolar Irrigated Radiofrequency Ablation Catheter for Pulmonary Vein Isolation.
J. Cardiovasc. Electrophysiol.
PUBLISHED: 08-22-2013
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"Single shot" ablation devices to treat symptomatic atrial fibrillation have been engineered over the last years. Safety and efficacy also includes subclinical complications only detected with esophageal endoscopy or cerebral MRI in asymptomatic patients. We studied the acute efficacy and safety profile of a novel multipolar irrigated RF ablation catheter (nMARQ™).
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Improving Activity in Adults With Diabetes and Coexisting Obstructive Sleep Apnea.
West J Nurs Res
PUBLISHED: 08-22-2013
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This study in participants with type 2 diabetes and obstructive sleep apnea evaluated changes in activity, sleep quality, and daytime sleepiness after 4 weeks of continuous positive airway pressure (CPAP). This pilot study was a double-blind, randomized, placebo-controlled trial. Sleep apnea was quantified with an overnight sleep study. Sleep quality was measured by the Pittsburgh Sleep Quality Index, daytime sleepiness by the Epworth Sleepiness Scale, vigor and fatigue with the Profiles of Mood States, subjective activity with the Functional Outcomes of Sleep Questionnaire, and objective activity with the Bodymedia SenseWear Armband™. Subjects were randomized to either CPAP (n = 12) or sham-devices (n = 11). The intervention group had reduced apneas and hypopneas, daytime sleepiness, and fatigue; they also had improved sleep quality and increased objective activity and vigor. The study suggested that treatment of obstructive sleep apnea results in a modest improvement of activity in persons with type 2 diabetes.
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Total Atrial Conduction Time Assessed by Tissue Doppler Imaging (PA-TDI Interval) to Predict Early Recurrence of Persistent Atrial Fibrillation After Successful Electrical Cardioversion.
J. Cardiovasc. Electrophysiol.
PUBLISHED: 08-18-2013
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The aim of this study was to investigate whether total atrial conduction time (TACT) assessed via tissue Doppler imaging (PA-TDI interval) can identify patients with early recurrent atrial fibrillation (ERAF) after successful direct-current electrical cardioversion (CV) of persistent atrial fibrillation (persPAF).
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Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.
Environ. Microbiol.
PUBLISHED: 07-26-2013
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Sequencing of 16S rDNA polymerase chain reaction (PCR) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during PCR. Here we show that 16S rDNA fragments derived from Illumina-sequenced environmental metagenomes (mi tags) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the Tara?Oceans global expedition, marine plankton was sampled in three locations, resulting in 29 subsamples for which metagenomes were produced by shotgun Illumina sequencing (ca. 700?Gb). For comparative analyses, a subset of samples was also selected for Roche-454 sequencing using both shotgun (m454 tags; 13 metagenomes, ca. 2.4?Gb) and 16S rDNA amplicon (454 tags; ca. 0.075?Gb) approaches. Our results indicate that by overcoming PCR biases related to amplification and primer mismatch, mi tags may provide more realistic estimates of community richness and evenness than amplicon 454 tags. In addition, mi tags can capture expected beta diversity patterns. Using mi tags is now economically feasible given the dramatic reduction in high-throughput sequencing costs, having the advantage of retrieving simultaneously both taxonomic (Bacteria, Archaea and Eukarya) and functional information from the same microbial community.
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Correlation of breast cancer axillary lymph node metastases with stem cell mutations.
JAMA Surg
PUBLISHED: 07-26-2013
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Mutations in oncogenes AKT1, HRAS, and PIK3CA in breast cancers result in abnormal PI3K/Akt signaling and tumor proliferation. They occur in ductal carcinoma in situ, in breast cancers, and in breast cancer stem and progenitor cells (BCSCs).
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Inhibition of influenza hemagglutinin with the antiviral inhibitor arbidol using a proteomics based approach and mass spectrometry.
Antiviral Res.
PUBLISHED: 07-23-2013
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A proteomics gel electrophoresis based approach has been applied to study the effect of arbidol on the proliferation of influenza virus in vitro through quantitation of hemagglutinin levels. An arbidol concentration of 20?g/ml was required to achieve a 50% reduction in virus proliferation and hemagglutinin levels. The use of a MALDI mass spectrometry approach to study the binding of arbidol to influenza hemagglutinin revealed it bound solely to residues 104-120 of the HA2 subunit, a region known to contain an arbidol resistance mutation. Parallel molecular docking results revealed that this binding site was favoured in which the arbidol molecule binds in two possible orientations approximately 180° to one another at HA2 residues 118-123. The combined studies support the recognized potential of arbidol as an effective and targeted antiviral agent against the influenza virus.
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Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.
Nature
PUBLISHED: 05-30-2013
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Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873), and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.
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Obesity accentuates circadian variability in breathing during sleep in mice but does not predispose to apnea.
J. Appl. Physiol.
PUBLISHED: 05-30-2013
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Obesity is a primary risk factor for the development of obstructive sleep apnea in humans, but the impact of obesity on central sleep apnea is less clear. Given the comorbidities associated with obesity in humans, we developed techniques for long-term recording of diaphragmatic EMG activity and polysomnography in obese mice to assess breathing patterns during sleep and to determine the effect of obesity on apnea generation. We hypothesized that genetically obese ob/ob mice would exhibit less variability in breathing across the 24-h circadian cycle, be more prone to central apneas, and be more likely to exhibit patterns of increased diaphragm muscle activity consistent with obstructive apneas compared with lean mice. Unexpectedly, we found that obese mice exhibited a greater circadian impact on respiratory rate and diaphragmatic burst amplitude than lean mice, particularly during rapid eye movement (REM) sleep. Central apneas were more common in REM sleep (42 ± 17 h(-1)) than non-REM (NREM) sleep (14 ± 5 h(-1)) in obese mice (P < 0.05), but rates were not different between lean and obese mice in either sleep state. Even after experimentally enhancing central apnea generation by acute withdrawal of hypoxic chemoreceptor activation during sleep, central apnea rates remained comparable between lean and obese mice. Last, we were unable to detect patterns of diaphragmatic burst activity suggestive of obstructive apnea events in obese mice. In summary, obesity does not predispose mice to increased occurrence of central or obstructive apneas during sleep, but does lead to a more pronounced circadian variability in respiration.
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Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes.
Environ. Microbiol.
PUBLISHED: 04-12-2013
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Heavy metals are pollutants which affect all organisms. Since a small number of eukaryotes have been investigated with respect to metal resistance, we hypothesize that many genes that control this phenomenon remain to be identified. This was tested by screening soil eukaryotic metatranscriptomes which encompass RNA from organisms belonging to the main eukaryotic phyla. Soil-extracted polyadenylated mRNAs were converted into cDNAs and 35 of them were selected for their ability to rescue the metal (Cd or Zn) sensitive phenotype of yeast mutants. Few of the genes belonged to families known to confer metal resistance when overexpressed in yeast. Several of them were homologous to genes that had not been studied in the context of metal resistance. For instance, the BOLA ones, which conferred cross metal (Zn, Co, Cd, Mn) resistance may act by interfering with Fe homeostasis. Other genes, such as those encoding 110- to 130-amino-acid-long, cysteine-rich polypeptides, had no homologues in databases. This study confirms that functional metatranscriptomics represents a powerful approach to address basic biological processes in eukaryotes. The selected genes can be used to probe new pathways involved in metal homeostasis and to manipulate the resistance level of selected organisms.
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Comparative genomics of emerging pathogens in the Candida glabrata clade.
BMC Genomics
PUBLISHED: 04-08-2013
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Candida glabrata follows C. albicans as the second or third most prevalent cause of candidemia worldwide. These two pathogenic yeasts are distantly related, C. glabrata being part of the Nakaseomyces, a group more closely related to Saccharomyces cerevisiae. Although C. glabrata was thought to be the only pathogenic Nakaseomyces, two new pathogens have recently been described within this group: C. nivariensis and C. bracarensis. To gain insight into the genomic changes underlying the emergence of virulence, we sequenced the genomes of these two, and three other non-pathogenic Nakaseomyces, and compared them to other sequenced yeasts.
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Morphogen transport.
Development
PUBLISHED: 03-28-2013
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The graded distribution of morphogens underlies many of the tissue patterns that form during development. How morphogens disperse from a localized source and how gradients in the target tissue form has been under debate for decades. Recent imaging studies and biophysical measurements have provided evidence for various morphogen transport models ranging from passive mechanisms, such as free or hindered extracellular diffusion, to cell-based dispersal by transcytosis or cytonemes. Here, we analyze these transport models using the morphogens Nodal, fibroblast growth factor and Decapentaplegic as case studies. We propose that most of the available data support the idea that morphogen gradients form by diffusion that is hindered by tortuosity and binding to extracellular molecules.
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Increased Preoperative Serum Apoptosis Marker Fas Ligand Correlates With Histopathology and New-Onset of Atrial Fibrillation in Patients After Cardiac Surgery.
J. Cardiovasc. Electrophysiol.
PUBLISHED: 03-22-2013
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We evaluated if preoperative serum apoptosis markers correlate with atrial histological remodeling and postoperative atrial fibrillation (POAF) after cardiac surgery.
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Correlation between total atrial conduction time estimated via tissue Doppler imaging (PA-TDI Interval), structural atrial remodeling and new-onset of atrial fibrillation after cardiac surgery.
J. Cardiovasc. Electrophysiol.
PUBLISHED: 02-11-2013
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Recent studies identified total atrial conduction time (TACT) as an independent and powerful predictor of new-onset atrial fibrillation (AF). The purpose of this study was to assess the association between the degree of atrial fibrosis, TACT, and frequency of postoperative atrial fibrillation (POAF) among patients undergoing cardiac surgery.
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Sequencing platform and library preparation choices impact viral metagenomes.
BMC Genomics
PUBLISHED: 02-04-2013
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Microbes drive the biogeochemistry that fuels the planet. Microbial viruses modulate their hosts directly through mortality and horizontal gene transfer, and indirectly by re-programming host metabolisms during infection. However, our ability to study these virus-host interactions is limited by methods that are low-throughput and heavily reliant upon the subset of organisms that are in culture. One way forward are culture-independent metagenomic approaches, but these novel methods are rarely rigorously tested, especially for studies of environmental viruses, air microbiomes, extreme environment microbiology and other areas with constrained sample amounts. Here we perform replicated experiments to evaluate Roche 454, Illumina HiSeq, and Ion Torrent PGM sequencing and library preparation protocols on virus metagenomes generated from as little as 10 pg of DNA.
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Synergism between Medihoney and rifampicin against methicillin-resistant Staphylococcus aureus (MRSA).
PLoS ONE
PUBLISHED: 01-24-2013
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Skin and chronic wound infections caused by highly antibiotic resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) are an increasing and urgent health problem worldwide, particularly with sharp increases in obesity and diabetes. New Zealand manuka honey has potent broad-spectrum antimicrobial activity, has been shown to inhibit the growth of MRSA strains, and bacteria resistant to this honey have not been obtainable in the laboratory. Combinational treatment of chronic wounds with manuka honey and common antibiotics may offer a wide range of advantages including synergistic enhancement of the antibacterial activity, reduction of the effective dose of the antibiotic, and reduction of the risk of antibiotic resistance. The aim of this study was to investigate the effect of Medihoney in combination with the widely used antibiotic rifampicin on S. aureus. Using checkerboard microdilution assays, time-kill curve experiments and agar diffusion assays, we show a synergism between Medihoney and rifampicin against MRSA and clinical isolates of S. aureus. Furthermore, the Medihoney/rifampicin combination stopped the appearance of rifampicin-resistant S. aureus in vitro. Methylglyoxal (MGO), believed to be the major antibacterial compound in manuka honey, did not act synergistically with rifampicin and is therefore not the sole factor responsible for the synergistic effect of manuka honey with rifampicin. Our findings support the idea that a combination of honey and antibiotics may be an effective new antimicrobial therapy for chronic wound infections.
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Targeting the giant cell tumor stromal cell: functional characterization and a novel therapeutic strategy.
PLoS ONE
PUBLISHED: 01-01-2013
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Giant cell tumor of bone (GCTB) is a benign, locally destructive neoplasm, with tumors comprised of mesenchymal fibroblast-like stromal cells; monocytic, mononuclear cells of myeloid lineage; and the characteristic osteoclast-like, multinucleated giant cells. Hampering the study of the complex interaction of its constituent cell types is the propensity of longstanding, repeatedly passaged cell cultures to undergo phenotypic alteration and loss of osteoclast-inducing capacities. In this study, we employed a novel, single-step technique to purify freshly harvested stromal cells using a CD14-negative selection column. Using 9 freshly harvested GCTB specimens and the purified stromal cell component, we performed analyses for markers of osteoblast lineage and analyzed the capacity of the stromal cells to undergo osteoblastic differentiation and induce osteoclastogenesis in co-cultures with monocytic cells. Successful purification of the CD14-negative stromal cells was confirmed via flow cytometric analysis and immunocytochemistry. Osteogenic media upregulated the expression of osteocalcin, suggesting an osteoblastic lineage of the GCTB stromal cells. The effects of the Wnt pathway agonist, SB415286, and recombinant human bone morphogenetic protein (BMP)-2 on osteoblastogenesis varied among samples. Notably, osteogenic media and SB415286 reversed the receptor activator of NF-?B ligand (RANKL)/osteoprotegerin (OPG) expression ratio resulting in diminished osteoclastogenic capacity. Recombinant human BMP2 had the opposite effect, resulting in enhanced and sustained support of osteoclastogenesis. Targeting the giant cell tumor stromal cell may be an effective adjunct to existing anti-resorptive strategies.
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Purification and Characterization of Biofilm-Associated EPS Exopolysaccharides from ESKAPE Organisms and Other Pathogens.
PLoS ONE
PUBLISHED: 01-01-2013
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In bacterial biofilms, high molecular weight, secreted exopolysaccharides can serve as a scaffold to which additional carbohydrates, proteins, lipids, and nucleic acids adhere, forming the matrix of the developing biofilm. Here we report methods to extract and purify high molecular weight (>15 kDa) exopolysaccharides from biofilms of eight human pathogens, including species of Staphylcococcus, Klebsiella, Acinetobacter, Pseudomonas, and a toxigenic strain of Escherichia coli O157:H7. Glycosyl composition analysis indicated a high total mannose content across all strains with P. aeruginosa and A. baumannii exopolysaccharides comprised of 80-90% mannose, K. pneumoniae and S. epidermidis strains containing 40-50% mannose, and E. coli with ?10% mannose. Galactose and glucose were also present in all eight strains, usually as the second and third most abundant carbohydrates. N-acetyl-glucosamine and galacturonic acid were found in 6 of 8 strains, while arabinose, fucose, rhamnose, and xylose were found in 5 of 8 strains. For linkage analysis, 33 distinct residue-linkage combinations were detected with the most abundant being mannose-linked moieties, in line with the composition analysis. The exopolysaccharides of two P. aeruginosa strains analyzed were consistent with the Psl carbohydrate, but not Pel or alginate. The S. epidermidis strain had a composition rich in mannose and glucose, which is consistent with the previously described slime associated antigen (SAA) and the extracellular slime substance (ESS), respectively, but no polysaccharide intracellular adhesion (PIA) was detected. The high molecular weight exopolysaccharides from E. coli, K. pneumoniae, and A. baumannii appear to be novel, based on composition and/or ratio analysis of carbohydrates.
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Rac deletion in osteoclasts causes severe osteopetrosis.
J. Cell. Sci.
PUBLISHED: 11-23-2011
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Cdc42 mediates bone resorption principally by stimulating osteoclastogenesis. Whether its sister GTPase, Rac, meaningfully impacts upon the osteoclast and, if so, by what means, is unclear. We find that whereas deletion of Rac1 or Rac2 alone has no effect, variable reduction of Rac1 in osteoclastic cells of Rac2(-/-) mice causes severe osteopetrosis. Osteoclasts lacking Rac1 and Rac2 in combination (Rac double-knockout, RacDKO), fail to effectively resorb bone. By contrast, osteoclasts are abundant in RacDKO osteopetrotic mice and, unlike those deficient in Cdc42, express the maturation markers of the cells normally. Hence, the osteopetrotic lesion of RacDKO mice largely reflects impaired function, and not arrested differentiation, of the resorptive polykaryon. The dysfunction of RacDKO osteoclasts represents failed cytoskeleton organization as evidenced by reduced motility of the cells and their inability to spread or generate the key resorptive organelles (i.e. actin rings and ruffled borders), which is accompanied by abnormal Arp3 distribution. The cytoskeleton-organizing capacity of Rac1 is mediated through its 20-amino-acid effector domain. Thus, Rac1 and Rac2 are mutually compensatory. Unlike Cdc42 deficiency, their combined absence does not impact upon differentiation but promotes severe osteopetrosis by dysregulating the osteoclast cytoskeleton.
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Endothelial nitric oxide synthase of the bone marrow regulates myocardial hypertrophy, fibrosis, and angiogenesis.
Cardiovasc. Res.
PUBLISHED: 11-21-2011
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The endothelial nitric oxide synthase (eNOS) regulates the mobilization and function of endothelial progenitor cells (EPC). We hypothesized that eNOS of the bone marrow (BM) affects cardiac remodelling during myocardial hypertrophy via the regulation of BM-derived vascular progenitor cells.
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RAS mutations are associated with the development of cutaneous squamous cell tumors in patients treated with RAF inhibitors.
J. Clin. Oncol.
PUBLISHED: 11-07-2011
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RAF inhibitors are effective against melanomas with BRAF V600E mutations but may induce keratoacanthomas (KAs) and cutaneous squamous cell carcinomas (cSCCs). The potential of these agents to promote secondary malignancies is concerning. We analyzed cSCC and KA lesions for genetic mutations in an attempt to identify an underlying mechanism for their formation.
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A holistic approach to marine eco-systems biology.
PLoS Biol.
PUBLISHED: 10-18-2011
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The structure, robustness, and dynamics of ocean plankton ecosystems remain poorly understood due to sampling, analysis, and computational limitations. The Tara Oceans consortium organizes expeditions to help fill this gap at the global level.
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Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure.
Microb Biotechnol
PUBLISHED: 10-12-2011
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Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15,000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.
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Superresolution imaging of biological nanostructures by spectral precision distance microscopy.
Biotechnol J
PUBLISHED: 09-13-2011
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For the improved understanding of biological systems on the nanoscale, it is necessary to enhance the resolution of light microscopy in the visible wavelength range beyond the limits of conventional epifluorescence microscopy (optical resolution of about 200 nm laterally, 600 nm axially). Recently, various far-field methods have been developed allowing a substantial increase of resolution ("superresolution microscopy", or "lightoptical nanoscopy"). This opens an avenue to nano-image intact and even living cells, as well as other biostructures like viruses, down to the molecular detail. Thus, it is possible to combine light optical spatial nanoscale information with ultrastructure analyses and the molecular interaction information provided by molecular cell biology. In this review, we describe the principles of spectrally assigned localization microscopy (SALM) of biological nanostructures, focusing on a special SALM approach, spectral precision distance/position determination microscopy (SPDM) with physically modified fluorochromes (SPDM(Phymod) . Generally, this SPDM method is based on high-precision localization of fluorescent molecules, which can be discriminated using reversibly bleached states of the fluorophores for their optical isolation. A variety of application examples is presented, ranging from superresolution microscopy of membrane and cytoplasmic protein distribution to dual-color SPDM of nuclear proteins. At present, we can achieve an optical resolution of cellular structures down to the 20-nm range, with best values around 5 nm (?1/100 of the exciting wavelength).
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Evaluation of a single-channel portable monitor for the diagnosis of obstructive sleep apnea.
J Clin Sleep Med
PUBLISHED: 09-08-2011
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To validate the ApneaLINK (AL) as an accurate tool for determining the presence of obstructive sleep apnea (OSA) in an at-risk sleep clinic population in a home test environment.
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Characterization of the DNA copy-number genome in the blood of cutaneous T-cell lymphoma patients.
J. Invest. Dermatol.
PUBLISHED: 09-01-2011
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Cutaneous T-cell lymphoma (CTCL) is a heterogeneous non-Hodgkins lymphoma that may variably involve the skin, lymph nodes, and peripheral blood. Malignant burden ranges from cutaneous patches and plaques with little evidence of blood involvement to erythroderma often in association with frank leukemia, as in Sézary syndrome. Toward a better understanding of the pathogenesis of this CD4+ T-cell malignancy, we conducted a high-resolution genomic analysis combining DNA (23 samples) and mRNA (12 samples) data of peripheral blood isolates from CTCL patients across a spectrum of stages. Strikingly, even patients with limited involvement, e.g., normal CD4 counts, contained significant copy-number alterations. Defining genomic characteristics of CTCL blood involvement included gains on 8q and 17q, and deletions on 17p and chromosome 10. A consensus analysis of 108 leukemic CTCL samples demonstrated global similarities among patients with varied blood involvement, narrowing 38 of 62 loci. Toward an annotated framework for in vitro testing, we also characterized genomic alterations in five CTCL cell lines (HH, HUT78, PNO, SeAx, and Sez4), revealing intact core features of leukemic CTCL. Together, these studies produce the most comprehensive view of the leukemic CTCL genome to date, with implications for pathogenesis, molecular classification, and potential future therapeutic developments.
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Sleep quality and asthma control and quality of life in non-severe and severe asthma.
Sleep Breath
PUBLISHED: 08-15-2011
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The effect of sleep quality on asthma control independent from common comorbidities like gastroesophageal reflux disease (GERD) and obstructive sleep apnea (OSA) is unknown. This study examined the association between sleep quality and asthma control and quality of life after accounting for OSA and GERD in non-severe (NSA) and severe (SA) asthma.
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Aldosterone promotes atrial fibrillation.
Eur. Heart J.
PUBLISHED: 08-04-2011
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Hyperaldosteronism is associated with an increased prevalence of atrial fibrillation (AF). However, it is unclear whether this is the consequence of altered haemodynamics or a direct aldosterone effect. It was the aim of the study to demonstrate load-independent effects of aldosterone on atrial structure and electrophysiology.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

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.