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Find video protocols related to scientific articles indexed in Pubmed.
Preventive sublingual immunotherapy in preschool children: first evidence for safety and pro-tolerogenic effects.
Pediatr Allergy Immunol
PUBLISHED: 11-20-2014
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Prevention of new IgE-sensitizations has been described during allergen-specific immunotherapy. However, prospective data using a preventive approach in very young children who would benefit most is missing. We initiated a prospective pilot study investigating the safety, immunomodulatory and sensitization-preventive effect of sublingual immunotherapy (SLIT) in mono/oligoclonally sensitized, clinically asymptomatic children 2-5 years of age.
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Hemorheology in experimental research: is it necessary to consider blood fluidity differences in the laboratory rat?
Lab. Anim.
PUBLISHED: 10-17-2014
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This study was designed to identify whether blood fluidity differs between commercially available laboratory rat strains. The hemorheological profiles of seven clinically healthy wild-type rat strains were analyzed to determine whether any diversity in blood fluidity might affect the outcome of cardiovascular studies. Study 1: 65 healthy adult rats (Lewis, Long-Evans, Hairless, Wistar and Fisher; mixed gender and comparable ages) were compared. In order to determine the greatest possible difference, the two strains with the greatest hematocrit (HCT) differences were selected for more detailed evaluation. Red blood cell (RBC) deformability (maximum elongation index, shear stress for half-maximal deformation of RBC; both P?
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Cytotoxicity of post and core composites as a function of environmental conditions.
Dent Mater
PUBLISHED: 08-30-2014
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In the revised version of ISO 7405 there are so far no detailed recommendations concerning temperature and humidity during specimen production for light curing and chemically setting dental materials. The main objective of the present study was to observe if different environmental conditions during specimen production influence cytotoxicity and degree of conversion of four post and core composite materials and to investigate if cytotoxicity of post and core materials is influenced by their corresponding bonding substances.
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Adaptive designs for subpopulation analysis optimizing utility functions.
Biom J
PUBLISHED: 08-19-2014
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If the response to treatment depends on genetic biomarkers, it is important to identify predictive biomarkers that define (sub-)populations where the treatment has a positive benefit risk balance. One approach to determine relevant subpopulations are subgroup analyses where the treatment effect is estimated in biomarker positive and biomarker negative groups. Subgroup analyses are challenging because several types of risks are associated with inference on subgroups. On the one hand, by disregarding a relevant subpopulation a treatment option may be missed due to a dilution of the treatment effect in the full population. Furthermore, even if the diluted treatment effect can be demonstrated in an overall population, it is not ethical to treat patients that do not benefit from the treatment when they can be identified in advance. On the other hand, selecting a spurious subpopulation increases the risk to restrict an efficacious treatment to a too narrow fraction of a potential benefiting population. We propose to quantify these risks with utility functions and investigate nonadaptive study designs that allow for inference on subgroups using multiple testing procedures as well as adaptive designs, where subgroups may be selected in an interim analysis. The characteristics of such adaptive and nonadaptive designs are compared for a range of scenarios.
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CEA Change After Neoadjuvant Chemotherapy Including Bevacizumab and Clinical Outcome in Patients Undergoing Liver Resection for Colorectal Liver Metastases.
Ann. Surg. Oncol.
PUBLISHED: 05-27-2014
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Liver resection after neoadjuvant chemotherapy offers the chance of cure and long-term survival in patients with resectable colorectal liver metastases (CLM). Currently, there are no established biomarkers that could help identify patients with low risk of recurrence who may benefit most from liver resection in curative intent. To address this issue, the value of carcinoembryonic antigen (CEA) change after neoadjuvant chemotherapy was investigated to predict clinical outcome in this study.
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Elite level rhythmic gymnasts have significantly more and stronger pain than peers of similar age: a prospective study.
Wien. Klin. Wochenschr.
PUBLISHED: 05-11-2014
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Rhythmic gymnastics (RG) unites aesthetic, ballet-like motion, and all aspects of gymnastics. To reach elite level, girls begin at early age the intensive training. To date it is unclear if such demanding training influences the incidence and intensity of painful overuse injuries. The purpose of this study is to analyze anatomical painful regions and pain intensity in elite level rhythmic gymnasts (elRG) and compare results with an age-matched control group (CG).
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One-year evaluation of two hybrid composites placed in a randomized-controlled clinical trial.
Dent Mater
PUBLISHED: 04-29-2014
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The aim of this prospective randomized-controlled clinical trial is to assess the long-term performance of two direct composite resins in posterior teeth. This study provides a survey of the one-year results.
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Identification of microRNAs specific for high producer CHO cell lines using steady-state cultivation.
Appl. Microbiol. Biotechnol.
PUBLISHED: 04-11-2014
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MicroRNAs are short non-coding RNAs that play an important role in the regulation of gene expression. Hence, microRNAs are considered as potential targets for engineering of Chinese hamster ovary (CHO) cells to improve recombinant protein production. Here, we analyzed and compared the microRNA expression patterns of high, low, and non-producing recombinant CHO cell lines expressing two structurally different model proteins in order to identify microRNAs that are involved in heterologous protein synthesis and secretion and thus might be promising targets for cell engineering to increase productivity. To generate reproducible and comparable data, the cells were cultivated in a bioreactor under steady-state conditions. Global microRNA expression analysis showed that mature microRNAs were predominantly upregulated in the producing cell lines compared to the non-producer. Several microRNAs were significantly differentially expressed between high and low producers, but none of them commonly for both model proteins. The identification of target messenger RNAs (mRNAs) is essential to understand the biological function of microRNAs. Therefore, we negatively correlated microRNA and global mRNA expression data and combined them with computationally predicted and experimentally validated targets. However, statistical analysis of the identified microRNA-mRNA interactions indicated a considerable false positive rate. Our results and the comparison to published data suggest that the reaction of CHO cells to the heterologous protein expression is strongly product- and/or clone-specific. In addition, this study highlights the urgent need for reliable CHO-specific microRNA target prediction tools and experimentally validated target databases in order to facilitate functional analysis of high-throughput microRNA expression data in CHO cells.
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Maximum type 1 error rate inflation in multiarmed clinical trials with adaptive interim sample size modifications.
Biom J
PUBLISHED: 01-20-2014
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Sample size modifications in the interim analyses of an adaptive design can inflate the type 1 error rate, if test statistics and critical boundaries are used in the final analysis as if no modification had been made. While this is already true for designs with an overall change of the sample size in a balanced treatment-control comparison, the inflation can be much larger if in addition a modification of allocation ratios is allowed as well. In this paper, we investigate adaptive designs with several treatment arms compared to a single common control group. Regarding modifications, we consider treatment arm selection as well as modifications of overall sample size and allocation ratios. The inflation is quantified for two approaches: a naive procedure that ignores not only all modifications, but also the multiplicity issue arising from the many-to-one comparison, and a Dunnett procedure that ignores modifications, but adjusts for the initially started multiple treatments. The maximum inflation of the type 1 error rate for such types of design can be calculated by searching for the "worst case" scenarios, that are sample size adaptation rules in the interim analysis that lead to the largest conditional type 1 error rate in any point of the sample space. To show the most extreme inflation, we initially assume unconstrained second stage sample size modifications leading to a large inflation of the type 1 error rate. Furthermore, we investigate the inflation when putting constraints on the second stage sample sizes. It turns out that, for example fixing the sample size of the control group, leads to designs controlling the type 1 error rate.
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Cardiac magnetic resonance postcontrast t1 time is associated with outcome in patients with heart failure and preserved ejection fraction.
Circ Cardiovasc Imaging
PUBLISHED: 09-13-2013
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Background- The underlying pathophysiology of heart failure with preserved ejection fraction (HFPEF) is incompletely understood, but myocardial extracellular matrix accumulation is thought to play a major role. Our aims were to estimate myocardial extracellular matrix using cardiac magnetic resonance T1 mapping and to assess the relationship between pathobiology/pathophysiology and prognosis. Methods and Results- Patients with suspected HFPEF (n=100) were enrolled in this prospective, observational study. Confirmatory diagnostic tests, cardiac magnetic resonance imaging including T1 mapping, and invasive hemodynamic assessments were performed at baseline. Sixty-one patients with confirmed HFPEF entered a longitudinal outcome-monitoring phase (mean, 22.9±5.0 months), during which 16 had a cardiac event. Cardiac magnetic resonance T1 time (hazard ratio, 0.99; 95% confidence interval, 0.98-0.99; P=0.046), left atrial area (hazard ratio, 1.08; 95% confidence interval, 1.03-1.13; P<0.01), and pulmonary vascular resistance (hazard ratio, 1.01; 95% confidence interval, 1.00-1.01; P=0.03) were significantly associated with cardiac events. Patients with T1 times below the median (<388.3 ms) were at greater risk of cardiac events than the rest of the group (P<0.01). Extracellular matrix of left ventricular biopsies (n=9), quantified by TissueFAXS technology correlated with T1 time (R=0.98; P<0.01). T1 time also correlated with right ventricular-pulmonary arterial coupling (pulmonary vascular resistance: R=-0.36; P<0.01; right ventricular ejection fraction: R=0.28; P=0.01). Conclusions- In the present preliminary study, cardiac magnetic resonance postcontrast T1 time is associated with prognosis in HFPEF, suggesting postcontrast T1 as possible biomarker for HFPEF.
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Size matters! Impact of age, sex, height, and weight on the normal heart size.
Circ Cardiovasc Imaging
PUBLISHED: 09-06-2013
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Background- Therapeutic decisions in cardiology are determined frequently by cardiac chamber size. To decide whether cardiac dimensions are still in the normal range, reliable reference values are needed. However, published reference values mostly refer to historical cohorts using motion-mode measurements and have not been adjusted for sex or age. The impact of body size was only vaguely addressed. The importance of such adjustments is illustrated by studies, which show that smaller individuals and women are at risk of delayed treatment and impaired outcome when currently used reference values are applied. The aim of the present study was to assess the impact of body size, sex, and age on the normal heart size. Methods and Results- We prospectively studied 622 individuals (52.7% women; 17-91 years; 143-200 cm; 32-240 kg) without cardiac disease by standard transthoracic echocardiography. Multivariable linear regression analyses of the impact of sex, age, height, and weight on cardiac chamber size were performed. By multivariable regression analysis (n=500), all 4 variables independently influenced cardiac chamber size. The validity of cardiac dimensions predicted by the regression model was tested prospectively in a validation cohort (n=122). A calculator is proposed that estimates cardiac dimensions on the basis of the regression analysis. Conclusions- Sex, height, weight, and age significantly affect the normal heart size. These parameters need to be considered when cutoff values indicating the need for treatment or even surgery are established.
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The effect of a bolus dose of intravenous lidocaine on the minimum alveolar concentration of sevoflurane: a prospective, randomized, double-blinded, placebo-controlled trial.
Anesth. Analg.
PUBLISHED: 06-06-2013
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The anesthetic effect of volatile anesthetics can be quantified by the minimum alveolar concentration (MAC) of the drug that prevents movement in response to a noxious stimulus in 50% of patients. The underlying mechanism regarding how immobilization is achieved by volatile anesthetics is not thoroughly understood, but several drugs affect MAC. In this study, we investigated the effect of a single IV bolus dose of lidocaine on the MAC of sevoflurane in humans.
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Intra-articular versus periarticular acromioclavicular joint injection: a multicenter, prospective, randomized, controlled trial.
Arthroscopy
PUBLISHED: 04-17-2013
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The purpose of this randomized study was to compare the clinical efficacy of intra-articular versus periarticular acromioclavicular joint injections.
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Prediction of transcribed PIWI-interacting RNAs from CHO RNAseq data.
J. Biotechnol.
PUBLISHED: 02-27-2013
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Chinese hamster ovary (CHO) cells are currently the most important mammalian host for the manufacture of biopharmaceuticals. To enhance our understanding of cellular processes, pathways, and the genetic setup of CHO cell lines, we predicted PIWI interacting RNAs (piRNAs) from small RNA sequencing data. Although piRNAs are the least understood class of small non-coding RNAs that mediate RNA silencing, it is believed that they play a pivotal role in protecting genome integrity by repressing transposable elements. Since genomic integrity is the key to prolonged stability of recombinant CHO cell lines, we characterized piRNA sequences and expression in six CHO cell lines by computational analysis of an existing small RNA sequencing dataset using proTRAC and the published CHO genome as reference. Here we present the result of this analysis consisting of 25,626 piRNAs and 540 piRNA clusters. Moreover we provide first evidence for differential piRNA expression in adherent and suspension-adapted CHO-K1 and DUKXB11 host cell lines as well as their recombinant derivatives, indicating that piRNAs might be tools for cell line development and engineering.
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The secretory pathway: exploring yeast diversity.
FEMS Microbiol. Rev.
PUBLISHED: 02-14-2013
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Protein secretion is an essential process for living organisms. In eukaryotes, this encompasses numerous steps mediated by several hundred cellular proteins. The core functions of translocation through the endoplasmic reticulum membrane, primary glycosylation, folding and quality control, and vesicle-mediated secretion are similar from yeasts to higher eukaryotes. However, recent research has revealed significant functional differences between yeasts and mammalian cells, and even among diverse yeast species. This review provides a current overview of the canonical protein secretion pathway in the model yeast Saccharomyces cerevisiae, highlighting differences to mammalian cells as well as currently unresolved questions, and provides a genomic comparison of the S. cerevisiae pathway to seven other yeast species where secretion has been investigated due to their attraction as protein production platforms, or for their relevance as pathogens. The analysis of Candida albicans, Candida glabrata, Kluyveromyces lactis, Pichia pastoris, Hansenula polymorpha, Yarrowia lipolytica, and Schizosaccharomyces pombe reveals that many - but not all - secretion steps are more redundant in S. cerevisiae due to duplicated genes, while some processes are even absent in this model yeast. Recent research obviates that even where homologous genes are present, small differences in protein sequence and/or differences in the regulation of gene expression may lead to quite different protein secretion phenotypes.
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Association between ultrasound measurements of muscle thickness, pennation angle, echogenicity and skeletal muscle strength in the elderly.
Age (Dordr)
PUBLISHED: 02-10-2013
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The increase of elderly in our society requires simple tools for quantification of sarcopenia in inpatient and outpatient settings. The aim of this study was to compare parameters determined with musculoskeletal ultrasound (M-US) with muscle strength in young and elderly patients. In this prospective, randomised and observer blind study, 26 young (24.2 ± 3.7 years) and 26 old (age 67.8 ± 4.8 years) patients were included. Muscle thickness, pennation angle and echogenicity of all muscles of musculus quadriceps were measured by M-US and correlated with isometric maximum voluntary contraction force (MVC) of musculus quadriceps. Reproducibility of M-US measurements as well as simple and multiple regression models were calculated. Of all measured M-US variables the highest reproducibility was found for measurements of thickness (intraclass correlation coefficients, 85-97%). Simple regression analysis showed a highly significant correlation of thickness measurements of all muscles of musculus quadriceps with MVC in the elderly and in the young. Multiple regression analysis revealed that thickness of musculus vastus medialis had the best correlation with MVC in the elderly. This study showed that measurement of muscle thickness, especially of musculus vastus medialis, by M-US is a reliable, bedside method for monitoring the extent of sarcopenia.
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Factors determining patient-prosthesis mismatch after aortic valve replacement - a prospective cohort study.
PLoS ONE
PUBLISHED: 01-01-2013
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"Patient-prosthesis mismatch" (PPM) after aortic valve replacement (AVR) has been reported to increase morbidity and mortality. Although algorithms have been developed to avoid PPM, factors favouring its occurrence have not been well defined.
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Combined medial and lateral anatomic ligament reconstruction for chronic rotational instability of the ankle.
Foot Ankle Int
PUBLISHED: 10-27-2011
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This study aimed to extend knowledge on the arthroscopic evaluation of the unstable ankle joint and the outcome of ligament reconstruction on rotational instability. In contrast to previous studies, we investigated the combined repair of lateral and medial ligaments.
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Genome sequence of the ruminal bacterium Megasphaera elsdenii.
J. Bacteriol.
PUBLISHED: 09-15-2011
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Megasphaera elsdenii is a Gram-negative ruminal bacterium. It is being investigated as a probiotic supplement for ruminants as it may provide benefits for energy balance and animal productivity. Furthermore, it is of biotechnological interest due to its capability of producing various volatile fatty acids. Here we report the complete genome sequence of M. elsdenii DSM 20460, the type strain for the species.
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How many spots with missing values can be tolerated in quantitative two-dimensional gel electrophoresis when applying univariate statistics?
J Proteomics
PUBLISHED: 08-02-2011
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Quantitative proteomic comparisons require a sufficient number of samples to reach an acceptable level of significance. But 2D gel electrophoresis commonly results in incomplete data sets due to spots with missing values reducing thereby the number of parallel measurements for individual proteins. Here we investigated how many missing values per spot can be tolerated. The number of spots in common between all gels was found to decrease with the number of parallel gels in a non-linear fashion. Increasing numbers of missing values were associated with a moderate increase in the quantitative variation of spot volumes. Based on the missing value pattern in 20 gels we performed an analysis of the multiple testing power for the hypothetical scenario of a comparative 2DE study with six or twelve parallel gels. The calculation considered the statistical power of the individual spot as well as the number of spots included in the analysis. The power increased with inclusion of spots with higher number of missing values and showed an optimum at a specific minimum number of spot replicates. The results suggest that proteins with missing values can be included in a univariate analysis as long as a sufficient number of parallel gels are made.
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Modeling and measuring intracellular fluxes of secreted recombinant protein in Pichia pastoris with a novel 34S labeling procedure.
Microb. Cell Fact.
PUBLISHED: 05-16-2011
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The budding yeast Pichia pastoris is widely used for protein production. To determine the best suitable strategy for strain improvement, especially for high secretion, quantitative data of intracellular fluxes of recombinant protein are very important. Especially the balance between intracellular protein formation, degradation and secretion defines the major bottleneck of the production system. Because these parameters are different for unlimited growth (shake flask) and carbon-limited growth (bioreactor) conditions, they should be determined under "production like" conditions. Thus labeling procedures must be compatible with minimal production media and the usage of bioreactors. The inorganic and non-radioactive 34S labeled sodium sulfate meets both demands.
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The impact of oxygen on the transcriptome of recombinant S. cerevisiae and P. pastoris - a comparative analysis.
BMC Genomics
PUBLISHED: 05-09-2011
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Saccharomyces cerevisiae and Pichia pastoris are two of the most relevant microbial eukaryotic platforms for the production of recombinant proteins. Their known genome sequences enabled several transcriptomic profiling studies under many different environmental conditions, thus mimicking not only perturbations and adaptations which occur in their natural surroundings, but also in industrial processes. Notably, the majority of such transcriptome analyses were performed using non-engineered strains.In this comparative study, the gene expression profiles of S. cerevisiae and P. pastoris, a Crabtree positive and Crabtree negative yeast, respectively, were analyzed for three different oxygenation conditions (normoxic, oxygen-limited and hypoxic) under recombinant protein producing conditions in chemostat cultivations.
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Extracorporeal shockwave therapy in calcifying tendinitis of the shoulder.
Knee Surg Sports Traumatol Arthrosc
PUBLISHED: 03-03-2011
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Strategies for extracorporeal shockwave therapy in calcifying tendinitis of the rotator cuff vary concerning quantity of sessions and doses. The purpose of this prospective pilot study was to determine the difference between the outcome of a single high-dosage extracorporeal shockwave therapy and two sessions of low-dosage extracorporeal shockwave therapy.
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Reproducibility and comparison of retinal thickness and volume measurements in normal eyes determined with two different Cirrus OCT scanning protocols.
Retina (Philadelphia, Pa.)
PUBLISHED: 03-03-2011
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To assess reproducibility and compare raster scanning protocols of Cirrus high-definition optical coherence tomography (Carl Zeiss Meditec, Dublin, CA).
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Microleakage after thermocycling of cemented crowns--a meta-analysis.
Dent Mater
PUBLISHED: 03-01-2011
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Microleakage testing of dental materials is a commonly accepted evaluation technique of margin integrity. Thermocycling has been utilized by many researchers to study the influence of temperature extremes on the marginal gap of cemented restorations. The aim of this investigation was to analyze microleakage data on cemented crowns, published in the dental literature until Dec 2009, to identify methodological factors that might potentially affect the results of in vitro microleakage tests and to compare the results.
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Treatment of peroneal tendon dislocation and coexisting medial and lateral ligamentous laxity in the ankle joint.
Knee Surg Sports Traumatol Arthrosc
PUBLISHED: 02-24-2011
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Acute dislocation of the peroneal tendon is caused by massive combined flexion-torsion trauma supported by preexisting ligamentous laxity of the ankle joint. This study aimed to investigate the clinical outcome of combined treatment of peroneal tendon dislocation and lateral and medial ligamentous laxity.
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Maximum inflation of the type 1 error rate when sample size and allocation rate are adapted in a pre-planned interim look.
Stat Med
PUBLISHED: 02-15-2011
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We calculate the maximum type 1 error rate of the pre-planned conventional fixed sample size test for comparing the means of independent normal distributions (with common known variance) which can be yielded when sample size and allocation rate to the treatment arms can be modified in an interim analysis. Thereby it is assumed that the experimenter fully exploits knowledge of the unblinded interim estimates of the treatment effects in order to maximize the conditional type 1 error rate. The worst-case strategies require knowledge of the unknown common treatment effect under the null hypothesis. Although this is a rather hypothetical scenario it may be approached in practice when using a standard control treatment for which precise estimates are available from historical data. The maximum inflation of the type 1 error rate is substantially larger than derived by Proschan and Hunsberger (Biometrics 1995; 51:1315-1324) for design modifications applying balanced samples before and after the interim analysis. Corresponding upper limits for the maximum type 1 error rate are calculated for a number of situations arising from practical considerations (e.g. restricting the maximum sample size, not allowing sample size to decrease, allowing only increase in the sample size in the experimental treatment). The application is discussed for a motivating example.
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Setting kinetics and shrinkage of self-adhesive resin cements depend on cure-mode and temperature.
Dent Mater
PUBLISHED: 02-10-2011
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To investigate the influence of curing mode and temperature on the shrinkage kinetics of self-adhesive resin cements in comparison to a conventional multi-step resin cement.
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Trends in primary retinal detachment surgery: results of a Bicenter study.
Retina (Philadelphia, Pa.)
PUBLISHED: 01-19-2011
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To assess trends and outcomes in retinal detachment (RD) surgery based on a retrospective, interventional, bicenter study.
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Outcome after silicone oil removal and simultaneous 360° endolaser treatment.
Acta Ophthalmol
PUBLISHED: 12-14-2010
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To evaluate the outcome after silicone oil removal combined with a 360° endolaser treatment in complex retinal detachment (RD) cases and to assess prognostic factors.
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Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production.
Biotechnol J
PUBLISHED: 05-27-2010
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The methylotrophic yeast Pichia pastoris has gained much attention during the last decade as a platform for producing heterologous recombinant proteins of pharmaceutical importance, due to its ability to reproduce post-translational modification similar to higher eukaryotes. With the recent release of the full genome sequence for P. pastoris, in-depth study of its functions has become feasible. Here we present the first reconstruction of the genome-scale metabolic model of the eukaryote P. pastoris type strain DSMZ 70382, PpaMBEL1254, consisting of 1254 metabolic reactions and 1147 metabolites compartmentalized into eight different regions to represent organelles. Additionally, equations describing the production of two heterologous proteins, human serum albumin and human superoxide dismutase, were incorporated. The protein-producing model versions of PpaMBEL1254 were then analyzed to examine the impact on oxygen limitation on protein production.
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A multi-level study of recombinant Pichia pastoris in different oxygen conditions.
BMC Syst Biol
PUBLISHED: 05-05-2010
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Yeasts are attractive expression platforms for many recombinant proteins, and there is evidence for an important interrelation between the protein secretion machinery and environmental stresses. While adaptive responses to such stresses are extensively studied in Saccharomyces cerevisiae, little is known about their impact on the physiology of Pichia pastoris. We have recently reported a beneficial effect of hypoxia on recombinant Fab secretion in P. pastoris chemostat cultivations. As a consequence, a systems biology approach was used to comprehensively identify cellular adaptations to low oxygen availability and the additional burden of protein production. Gene expression profiling was combined with proteomic analyses and the 13C isotope labelling based experimental determination of metabolic fluxes in the central carbon metabolism.
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The response to unfolded protein is involved in osmotolerance of Pichia pastoris.
BMC Genomics
PUBLISHED: 03-26-2010
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The effect of osmolarity on cellular physiology has been subject of investigation in many different species. High osmolarity is of importance for biotechnological production processes, where high cell densities and product titers are aspired. Several studies indicated that increased osmolarity of the growth medium can have a beneficial effect on recombinant protein production in different host organisms. Thus, the effect of osmolarity on the cellular physiology of Pichia pastoris, a prominent host for recombinant protein production, was studied in carbon limited chemostat cultures at different osmolarities. Transcriptome and proteome analyses were applied to assess differences upon growth at different osmolarities in both, a wild type strain and an antibody fragment expressing strain. While our main intention was to analyze the effect of different osmolarities on P. pastoris in general, this was complemented by studying it in context with recombinant protein production.
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Changes in interleukin-10 mRNA expression are predictive for 9-day survival of pigs in an emergency preservation and resuscitation model.
Resuscitation
PUBLISHED: 01-19-2010
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This study aimed at evaluating (I) the impact of different intra-arrest hypothermia levels on the expression of selected cytokines and (II) their prognostic value for 9-day survival.
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Open access to sequence: browsing the Pichia pastoris genome.
Microb. Cell Fact.
PUBLISHED: 10-16-2009
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The first genome sequences of the important yeast protein production host Pichia pastoris have been released into the public domain this spring. In order to provide the scientific community easy and versatile access to the sequence, two web-sites have been installed as a resource for genomic sequence, gene and protein information for P. pastoris: A GBrowse based genome browser was set up at http://www.pichiagenome.org and a genome portal with gene annotation and browsing functionality at http://bioinformatics.psb.ugent.be/webtools/bogas. Both websites are offering information on gene annotation and function, regulation and structure. In addition, a WiKi based platform allows all users to create additional information on genes, proteins, physiology and other items of P. pastoris research, so that the Pichia community can benefit from exchange of knowledge, data and materials.
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Model selection based on FDR-thresholding optimizing the area under the ROC-curve.
Stat Appl Genet Mol Biol
PUBLISHED: 06-25-2009
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We evaluate variable selection by multiple tests controlling the false discovery rate (FDR) to build a linear score for prediction of clinical outcome in high-dimensional data. Quality of prediction is assessed by the receiver operating characteristic curve (ROC) for prediction in independent patients. Thus we try to combine both goals: prediction and controlled structure estimation. We show that the FDR-threshold which provides the ROC-curve with the largest area under the curve (AUC) varies largely over the different parameter constellations not known in advance. Hence, we investigated a new cross validation procedure based on the maximum rank correlation estimator to determine the optimal selection threshold. This procedure (i) allows choosing an appropriate selection criterion, (ii) provides an estimate of the FDR close to the true FDR and (iii) is simple and computationally feasible for rather moderate to small sample sizes. Low estimates of the cross validated AUC (the estimates generally being positively biased) and large estimates of the cross validated FDR may indicate a lack of sufficiently prognostic variables and/or too small sample sizes. The method is applied to an oncology dataset.
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Genome, secretome and glucose transport highlight unique features of the protein production host Pichia pastoris.
Microb. Cell Fact.
PUBLISHED: 05-13-2009
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Pichia pastoris is widely used as a production platform for heterologous proteins and model organism for organelle proliferation. Without a published genome sequence available, strain and process development relied mainly on analogies to other, well studied yeasts like Saccharomyces cerevisiae.
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Yeast systems biotechnology for the production of heterologous proteins.
FEMS Yeast Res.
PUBLISHED: 04-01-2009
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Systems biotechnology has been established as a highly potent tool for bioprocess development in recent years. The applicability to complex metabolic processes such as protein synthesis and secretion, however, is still in its infancy. While yeasts are frequently applied for heterologous protein production, more progress in this field has been achieved for bacterial and mammalian cell culture systems than for yeasts. A critical comparison between different protein production systems, as provided in this review, can aid in assessing the potentials and pitfalls of applying systems biotechnology concepts to heterologous protein producing yeasts. Apart from modelling, the methodological basis of systems biology strongly relies on postgenomic methods. However, this methodology is rapidly moving so that more global data with much higher sensitivity will be achieved in near future. The development of next generation sequencing technology enables an unexpected revival of genomic approaches, providing new potential for evolutionary engineering and inverse metabolic engineering.
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The bi-objective stochastic covering tour problem.
Comput Oper Res
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We formulate a bi-objective covering tour model with stochastic demand where the two objectives are given by (i) cost (opening cost for distribution centers plus routing cost for a fleet of vehicles) and (ii) expected uncovered demand. In the model, it is assumed that depending on the distance, a certain percentage of clients go from their homes to the nearest distribution center. An application in humanitarian logistics is envisaged. For the computational solution of the resulting bi-objective two-stage stochastic program with recourse, a branch-and-cut technique, applied to a sample-average version of the problem obtained from a fixed random sample of demand vectors, is used within an epsilon-constraint algorithm. Computational results on real-world data for rural communities in Senegal show the viability of the approach.
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The role of the peroneal tendons in passive stabilisation of the ankle joint: an in vitro study.
Knee Surg Sports Traumatol Arthrosc
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Peroneal tendons are known as active stabilizer in acute ankle sprain while an intact ankle mortise and intact lateral ligaments are required for passive stability of the ankle joint. The goal of this study is to determine the peroneal tendons as passive stabilizer in case of lateral ligament instability.
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Pathomorphologic findings of wrist arthroscopy in children and adolescents with chronic wrist pain.
Arthroscopy
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The purposes of this diagnostic study were to show pathomorphologic findings of children and adolescents with persistent wrist pain and to compare these arthroscopic findings with preoperative magnetic resonance imaging (MRI).
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Lung transplantation in children and young adults: a 20-year single-centre experience.
Eur. Respir. J.
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Lung transplantation in adults is an accepted therapeutic option, whereas there is ongoing debate on its positive impact on survival in children. We report our experience of the first 20 yrs of paediatric lung transplantation at a single centre in Austria. Patient survival, organ survival and freedom from bronchiolitis obliterans were estimated by Kaplan-Meier curves. Pre- and post-transplant parameters were assessed and their influence on patient and organ survival evaluated by univariate tests and stepwise multivariate analyses. A total of 55 transplantations were performed in 43 patients. 1- and 5-yr patient survival rates were 72.1% and 60.6%, respectively, and 52.6% of patients were found to be free from bronchiolitis obliterans syndrome at 5 yrs post-transplant. Analysing different eras of transplantation suggests an improvement over the years with a 5-yr survival rate of 70.6% in the second decade. A positive effect of pre-transplant diabetes mellitus and immunosuppression was found with the newer drug tacrolimus, and a negative effect of pre-transplant in-hospital admission was reported. A high rate of successful re-transplantation prolonged total patient survival.
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Study design in DIGE-based biomarker discovery.
Methods Mol. Biol.
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The DIGE technology allows the detection of small differences in the expression level of abundant proteins. Many diseases are associated with quantitative deviations of proteins which might represent useful biomarkers for diagnosis or prognosis. DIGE is therefore a highly convenient method for the characterization of disease-related expression changes. This chapter focuses on the study design in DIGE-based biomarker discovery. It introduces the statistical implications of testing thousands of proteins in parallel and discusses the solutions proposed by the literature. The outline provided in the method section tries to guide the researcher through the different statistical considerations, which have to be taken into account in biomarker detection. Special emphasis is given to the use of sample sizes of sufficient statistical power and to the statistical evaluation of the results.
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Pichia pastoris growth rate regulates protein synthesis and secretion, mating, and stress response.
Biotechnol J
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Protein production in yeasts is related to the specific growth rate ?. To elucidate on this correlation, we studied the transcriptome of Pichia pastoris at different specific growth rates by cultivating a strain secreting human serum albumin at ? = 0.015 h(-1) to 0.15 h(-1) in glucose-limited chemostats. Genome-wide regulation revealed that translation-related as well as mitochondrial genes were upregulated with increasing ?, while autophagy and other proteolytic processes, carbon source-responsive genes and other targets of the TOR pathway as well as many transcriptional regulators were downregulated at higher ?. Mating and sporulation genes were most active at intermediate ? of 0.05 h(-1) and 0.075 h(-1) . At very slow growth (? = 0.015 h(-1) ) gene regulation differs significantly, affecting many transporters and glucose sensing. Analysis of a subset of genes related to protein folding and secretion reveals that unfolded protein response targets such as translocation, endoplasmic reticulum genes and cytosolic chaperones are upregulated with increasing growth rate while proteolytic degradation of secretory proteins is downregulated. We conclude that a high ? positively affects specific protein secretion rates by acting on multiple cellular processes.
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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.

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

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