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Find video protocols related to scientific articles indexed in Pubmed.
Experimental reconstruction of work distribution and study of fluctuation relations in a closed quantum system.
Phys. Rev. Lett.
PUBLISHED: 10-03-2014
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We report the experimental reconstruction of the nonequilibrium work probability distribution in a closed quantum system, and the study of the corresponding quantum fluctuation relations. The experiment uses a liquid-state nuclear magnetic resonance platform that offers full control on the preparation and dynamics of the system. Our endeavors enable the characterization of the out-of-equilibrium dynamics of a quantum spin from a finite-time thermodynamics viewpoint.
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Molecular Characterization of Toxigenic Clostridium difficile in a Northern Italian Hospital.
Curr. Microbiol.
PUBLISHED: 06-18-2014
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Clostridium difficile is responsible for more than 90 % of cases of antibiotic-associated diarrhea and pseudomembranous colitis. The most important virulence factors are two toxins called enterotoxin A and cytotoxin B; some C. difficile strains contain the C. difficile binary toxin (CDT). The aim of our study was to prospectively analyze C. difficile clinical isolates in a single center to determine the molecular features of collected strains. Among the 252 isolates, 217 were A + B + (86.1 %), 33 were A + B + cdt + (13.1 %) and 2 were A - B + (0.8 %). There were 15 different ribotypes with a predominance of 018.
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Surveillance of healthcare-associated infections in Piemonte, Italy: results from a second regional prevalence study.
BMC Public Health
PUBLISHED: 05-30-2014
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A prevalence survey of healthcare-associated infections (HAIs) was previously performed in the Piemonte region in 2000. In the decade following the survey, many studies were performed at both the regional and hospital levels, and training courses were developed to address issues highlighted by the survey. In 2010, a second regional prevalence study was performed. The aim of this paper is to present the results of the second prevalence study and discuss them within the context of the HAI prevention and control programmes that have been implemented in the decade since the original survey was conducted.
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Exercise training induces mitochondrial biogenesis and glucose uptake in subcutaneous adipose tissue through eNOS-dependent mechanisms.
Diabetes
PUBLISHED: 03-12-2014
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Insulin resistance and obesity are associated with a reduction of mitochondrial content in various tissues of mammals. Moreover, a reduced nitric oxide (NO) bioavailability impairs several cellular functions, including mitochondrial biogenesis and insulin-stimulated glucose uptake, two important mechanisms of body adaptation in response to physical exercise. Although these mechanisms have been thoroughly investigated in skeletal muscle and heart, few studies have focused on the effects of exercise on mitochondria and glucose metabolism in adipose tissue. In this study, we compared the in vivo effects of chronic exercise in subcutaneous adipose tissue of wild-type (WT) and endothelial NO synthase (eNOS) knockout (eNOS(-/-)) mice after a swim training period. We then investigated the in vitro effects of NO on mouse 3T3-L1 and human subcutaneous adipose tissue-derived adipocytes after a chronic treatment with an NO donor: diethylenetriamine-NO (DETA-NO). We observed that swim training increases mitochondrial biogenesis, mitochondrial DNA content, and glucose uptake in subcutaneous adipose tissue of WT but not eNOS(-/-) mice. Furthermore, we observed that DETA-NO promotes mitochondrial biogenesis and elongation, glucose uptake, and GLUT4 translocation in cultured murine and human adipocytes. These results point to the crucial role of the eNOS-derived NO in the metabolic adaptation of subcutaneous adipose tissue to exercise training.
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Exercise training boosts eNOS-dependent mitochondrial biogenesis in mouse heart: role in adaptation of glucose metabolism.
Am. J. Physiol. Endocrinol. Metab.
PUBLISHED: 01-02-2014
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Endurance exercise training increases cardiac energy metabolism through poorly understood mechanisms. Nitric oxide (NO) produced by endothelial NO synthase (eNOS) in cardiomyocytes contributes to cardiac adaptation. Here we demonstrate that the NO donor diethylenetriamine-NO (DETA-NO) activated mitochondrial biogenesis and function, as assessed by upregulated peroxisome proliferator-activated receptor-? coactivator-1? (PGC-1?), nuclear respiratory factor 1, and mitochondrial transcription factor A (Tfam) expression, and by increased mitochondrial DNA content and citrate synthase activity in primary mouse cardiomyocytes. DETA-NO also induced mitochondrial biogenesis and function and enhanced both basal and insulin-stimulated glucose uptake in HL-1 cardiomyocytes. The DETA-NO-mediated effects were suppressed by either PGC-1? or Tfam small-interference RNA in HL-1 cardiomyocytes. Wild-type and eNOS(-/-) mice were subjected to 6 wk graduated swim training. We found that eNOS expression, mitochondrial biogenesis, mitochondrial volume density and number, and both basal and insulin-stimulated glucose uptake were increased in left ventricles of swim-trained wild-type mice. On the contrary, the genetic deletion of eNOS prevented all these adaptive phenomena. Our findings demonstrate that exercise training promotes eNOS-dependent mitochondrial biogenesis in heart, which behaves as an essential step in cardiac glucose transport.
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Association between molecular lesions and specific B-cell receptor subsets in chronic lymphocytic leukemia.
Blood
PUBLISHED: 05-01-2013
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Genetic lesions and B-cell receptor (BCR) signaling are both oncogenic drivers in chronic lymphocytic leukemia (CLL). However, scant data are available on preferential associations between specific genetic alterations and stereotyped BCR subsets. By analyzing 1419 cases, 2 CLL subsets (2 and 8) harboring stereotyped BCR are enriched in specific molecular alterations influencing disease course. SF3B1 mutations are the genetic hallmark of IGHV3-21-CLL belonging to subset 2 (52%) but are evenly represented in nonstereotyped IGHV3-21-CLL. Trisomy 12 (87%) and NOTCH1 mutations (62%) characterize IGHV4-39-CLL belonging to subset 8 but occur with the expected frequency in IGHV4-39-CLL with heterogeneous BCR. Clinically, co-occurrence of SF3B1 mutations and subset 2 BCR configuration prompts disease progression in IGHV3-21-CLL, whereas cooperation between NOTCH1 mutations, +12, and subset 8 BCR configuration invariably primes CLL transformation into Richter syndrome. These findings provide a proof of concept that specific stereotyped BCR may promote or select molecular lesions influencing outcome.
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Mechanism for the formation of density gradients through semipermeable membranes.
Phys Rev E Stat Nonlin Soft Matter Phys
PUBLISHED: 02-13-2013
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We describe and theoretically analyze here a phenomenon which can take place in a system with two different compartments, each containing the same chemicals, which undergo reactions on the surface of both sides of the membrane which separates the two compartments, in the case where the membrane permeabilities to the various chemicals are different and diffusion is fast. There are two main reasons of interest for this kind of system. First, if the overall system is isolated, starting from the case where the initial concentrations of the chemicals are the same in the two phases, one observes the formation of a transient concentration difference. This difference eventually vanishes, although it might last for a long time, depending upon the value of the relevant parameters. The second reason of interest is that, in the case of an open system, one can achieve a steady-state value of the concentration of some chemicals in the smaller compartment which is higher than that in the external one. These results may prove important, inter alia, to understand the behavior of lipid vesicles in water, a topic which is important for studies on the origin of life as well as for possible future applications.
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On the dynamical properties of a model of cell differentiation.
EURASIP J Bioinform Syst Biol
PUBLISHED: 01-23-2013
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One of the major challenges in complex systems biology is that of providing a general theoretical framework to describe the phenomena involved in cell differentiation, i.e., the process whereby stem cells, which can develop into different types, become progressively more specialized. The aim of this study is to briefly review a dynamical model of cell differentiation which is able to cover a broad spectrum of experimentally observed phenomena and to present some novel results.
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A stochastic model of autocatalytic reaction networks.
Theory Biosci.
PUBLISHED: 04-08-2011
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Autocatalytic cycles are rather widespread in nature and in several theoretical models of catalytic reaction networks their emergence is hypothesized to be inevitable when the network is or becomes sufficiently complex. Nevertheless, the emergence of autocatalytic cycles has been never observed in wet laboratory experiments. Here, we present a novel model of catalytic reaction networks with the explicit goal of filling the gap between theoretical predictions and experimental findings. The model is based on previous study of Kauffman, with new features in the introduction of a stochastic algorithm to describe the dynamics and in the possibility to increase the number of elements and reactions according to the dynamical evolution of the system. Furthermore, the introduction of a temporal threshold allows the detection of cycles even in our context of a stochastic model with asynchronous update. In this study, we describe the model and present results concerning the effect on the overall dynamics of varying (a) the average residence time of the elements in the reactor, (b) both the composition of the firing disk and the concentration of the molecules belonging to it, (c) the composition of the incoming flux.
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A dynamical model of genetic networks for cell differentiation.
PLoS ONE
PUBLISHED: 02-08-2011
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A mathematical model is proposed which is able to describe the most important features of cell differentiation, without requiring specific detailed assumptions concerning the interactions which drive the phenomenon. On the contrary, cell differentiation is described here as an emergent property of a generic model of the underlying gene regulatory network, and it can therefore be applied to a variety of different organisms. The model points to a peculiar role of cellular noise in differentiation and leads to non trivial predictions which could be subject to experimental testing. Moreover, a single model proves able to describe several different phenomena observed in various differentiation processes.
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Surgical debridement with VERSAJET: an analysis of bacteria load of the wound bed pre- and post-treatment and skin graft taken. A preliminary pilot study.
Int Wound J
PUBLISHED: 01-25-2011
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Surgical debridement, which is used for the removal of necrotic tissue from a wound, is becoming more and more important in the treatment of skin injuries. VERSAJET (VERSAJET™, Versajet Hydrosurgery System, Smith and Nephew, Hull, UK) is one of the techniques used for wound debridement. Medical literature does not present either analytical or comparative data correlating the bacterial load with the VERSAJET treatment. For this reason, we have decided to carry out a study to evaluate the level of bacterial contamination before and after the surgical debridement treatment with VERSAJET and, in connection with this, the correlation between the bacterial load and the successful healing of the skin graft. We took a total of 100 bacteriological swabs, 50 before and 50 from 27 selected patients after the treatment with VERSAJET, with which the wound bed was prepared to receive the skin graft or Integra graft in order to acquire data about the level of bacterial contamination. After analysing all those data we can assume that reducing the bacterial load is not the only variable which the successful healing of the skin graft depends on. In conclusion, there is still many data to analyse and study in order to better understand the qualitative and quantitative presence of bacteria and the success of this future surgical procedure. We remind that the performance of this study was not sponsored by any company.
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Dynamical properties of a boolean model of gene regulatory network with memory.
J. Comput. Biol.
PUBLISHED: 01-07-2011
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Classical random Boolean networks (RBN) are not well suited to describe experimental data from time-course microarray, mainly because of the strict assumptions about the synchronicity of the regulatory mechanisms. In order to overcome this setback, a generalization of the RBN model is described and analyzed. Gene products (e.g., regulatory proteins) are introduced, with each one characterized by a specific decay time, thereby introducing a form of memory in the system. The dynamics of these networks is analyzed, and it is shown that the distribution of the decay times has a strong effect that can be adequately described and understood. The implications for the dynamical criticality of the networks are also discussed.
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Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia.
Blood
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The identification of new genetic lesions in chronic lymphocytic leukemia (CLL) prompts a comprehensive and dynamic prognostic algorithm including gene mutations and chromosomal abnormalities and their changes during clonal evolution. By integrating mutational and cytogenetic analysis in 1274 CLL samples and using both a training-validation and a time-dependent design, 4 CLL subgroups were hierarchically classified: (1) high-risk, harboring TP53 and/or BIRC3 abnormalities (10-year survival: 29%); (2) intermediate-risk, harboring NOTCH1 and/or SF3B1 mutations and/or del11q22-q23 (10-year survival: 37%); (3) low-risk, harboring +12 or a normal genetics (10-year survival: 57%); and (4) very low-risk, harboring del13q14 only, whose 10-year survival (69.3%) did not significantly differ from a matched general population. This integrated mutational and cytogenetic model independently predicted survival, improved CLL prognostication accuracy compared with FISH karyotype (P < .0001), and was externally validated in an independent CLL cohort. Clonal evolution from lower to higher risk implicated the emergence of NOTCH1, SF3B1, and BIRC3 abnormalities in addition to TP53 and 11q22-q23 lesions. By taking into account clonal evolution through time-dependent analysis, the genetic model maintained its prognostic relevance at any time from diagnosis. These findings may have relevant implications for the design of clinical trials aimed at assessing the use of mutational profiling to inform therapeutic decisions.
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Mortality in patients with early- or late-onset candidaemia.
J. Antimicrob. Chemother.
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Although candidaemia is a well-known complication of hospital stay and has a crude mortality of ?40%, few data are available for episodes diagnosed within 10 days after hospital admission. In this paper, we compared the risk factors for mortality according to the onset of candidaemia.
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Nontoxigenic Vibrio parahaemolyticus strains causing acute gastroenteritis.
J. Clin. Microbiol.
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We investigated the virulence properties of four Vibrio parahaemolyticus strains causing acute gastroenteritis following consumption of indigenous mussels in Italy. The isolated strains were cytotoxic and adhesive but, surprisingly, lacked tdh, trh, and type three secretion system 2 (T3SS2) genes. We emphasize that nontoxigenic V. parahaemolyticus can induce acute gastroenteritis, highlighting the need for more investigation of the pathogenicity of this microorganism.
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Presence of anti-ADAMTS13 antibodies in obesity.
Eur. J. Clin. Invest.
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The low-grade chronic inflammation present in obesity has been recognized as a risk factor for thrombosis, atherosclerosis and cardiovascular complications. In this context, production by adipose organ of a number of inflammatory adipokines could play a crucial role. It has been reported that obesity represents a risk factor for acquired thrombotic thrombocytopenic purpura (TTP), a disease caused by ADAMTS13 deficiency because of anti-ADAMTS13 antibodies, but the pathophysiological link between obesity and TTP is still unknown. We aimed to investigate mechanisms linking obesity to risk of TTP.
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The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development.
J. Exp. Med.
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Splenic marginal zone lymphoma (SMZL) is a B cell malignancy of unknown pathogenesis, and thus an orphan of targeted therapies. By integrating whole-exome sequencing and copy-number analysis, we show that the SMZL exome carries at least 30 nonsilent gene alterations. Mutations in NOTCH2, a gene required for marginal-zone (MZ) B cell development, represent the most frequent lesion in SMZL, accounting for ?20% of cases. All NOTCH2 mutations are predicted to cause impaired degradation of the NOTCH2 protein by eliminating the C-terminal PEST domain, which is required for proteasomal recruitment. Among indolent B cell lymphoproliferative disorders, NOTCH2 mutations are restricted to SMZL, thus representing a potential diagnostic marker for this lymphoma type. In addition to NOTCH2, other modulators or members of the NOTCH pathway are recurrently targeted by genetic lesions in SMZL; these include NOTCH1, SPEN, and DTX1. We also noted mutations in other signaling pathways normally involved in MZ B cell development, suggesting that deregulation of MZ B cell development pathways plays a role in the pathogenesis of ?60% SMZL. These findings have direct implications for the treatment of SMZL patients, given the availability of drugs that can target NOTCH, NF-?B, and other pathways deregulated in this disease.
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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.