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Find video protocols related to scientific articles indexed in Pubmed.
Remote conformational control of a molecular switch via methylation and deprotonation.
Org. Biomol. Chem.
PUBLISHED: 10-15-2014
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Exacting control over conformation in response to an external stimulus is the central focus of molecular switching. Here we describe the synthesis of a series of diphenylacetylene-based molecular switches, and examine their response to covalent modification and deprotonation at remote phenolic positions. A complex interplay between multiple intramolecular hydrogen bond donors and acceptors determines the global conformation.
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A Lewis acid-mediated conformational switch.
Org. Biomol. Chem.
PUBLISHED: 09-04-2014
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Molecules that change conformation in response to a stimulus have numerous uses, such as artificial chemoreceptors, novel drug delivery strategies and liquid crystal technology. Here we describe the design, synthesis and conformational behaviour of an isonicotinamide-substituted diphenylacetylene upon recognition of Lewis acids, including metalloporphyrins. Binding of these at a remote site - the pyridyl nitrogen - increases hydrogen-bond donor ability of the proximal amide NH, causing an increased preference for the alkyne rotamer in which this hydrogen bond is maintained.
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Effects of aging on genioglossus motor units in humans.
PLoS ONE
PUBLISHED: 08-11-2014
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The genioglossus is a major upper airway dilator muscle thought to be important in obstructive sleep apnea pathogenesis. Aging is a risk factor for obstructive sleep apnea although the mechanisms are unclear and the effects of aging on motor unit remodeled in the genioglossus remains unknown. To assess possible changes associated with aging we compared quantitative parameters related to motor unit potential morphology derived from EMG signals in a sample of older (n?=?11; >55 years) versus younger (n?=?29; <55 years) adults. All data were recorded during quiet breathing with the subjects awake. Diagnostic sleep studies (Apnea Hypopnea Index) confirmed the presence or absence of obstructive sleep apnea. Genioglossus EMG signals were analyzed offline by automated software (DQEMG), which estimated a MUP template from each extracted motor unit potential train (MUPT) for both the selective concentric needle and concentric needle macro (CNMACRO) recorded EMG signals. 2074 MUPTs from 40 subjects (mean±95% CI; older AHI 19.6±9.9 events/hr versus younger AHI 30.1±6.1 events/hr) were extracted. MUPs detected in older adults were 32% longer in duration (14.7±0.5 ms versus 11.1±0.2 ms; P ?=? 0.05), with similar amplitudes (395.2±25.1 µV versus 394.6±13.7 µV). Amplitudes of CNMACRO MUPs detected in older adults were larger by 22% (62.7±6.5 µV versus 51.3±3.0 µV; P<0.05), with areas 24% larger (160.6±18.6 µV.ms versus 130.0±7.4 µV.ms; P<0.05) than those detected in younger adults. These results confirm that remodeled motor units are present in the genioglossus muscle of individuals above 55 years, which may have implications for OSA pathogenesis and aging related upper airway collapsibility.
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Diversity and abundance of leafhoppers in Canadian vineyards.
J. Insect Sci.
PUBLISHED: 05-29-2014
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Leafhoppers (Hemiptera: Cicadellidae) are pests of many temperate crops, including grapevines (Vitis species). Uncontrolled populations can induce direct and indirect damage to crops due to feeding that results in significant yield losses and increased mortality in infected vineyards due to virus, bacteria, or phytoplasmas vectored by leafhoppers. The main objective of this work was to determine the diversity of leafhoppers found in vineyards of the three main Canadian production provinces, i.e., in British Columbia, Ontario, and Quebec. Approximately 18,000 specimens were collected in 80 commercial vineyards from 2006 to 2008. We identified 54 genera and at least 110 different species associated with vineyards, among which 22 were predominant and represented more than 91% of all the leafhoppers. Species richness and diversity were estimated by both Shannon's and Pielou's indices. For each province, results indicated a temporal variation in species composition. Color photographs provide a tool to quickly identify 72 leafhoppers commonly associated with vineyards.
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CAPriCORN: Chicago Area Patient-Centered Outcomes Research Network.
J Am Med Inform Assoc
PUBLISHED: 05-12-2014
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The Chicago Area Patient-Centered Outcomes Research Network (CAPriCORN) represents an unprecedented collaboration across diverse healthcare institutions including private, county, and state hospitals and health systems, a consortium of Federally Qualified Health Centers, and two Department of Veterans Affairs hospitals. CAPriCORN builds on the strengths of our institutions to develop a cross-cutting infrastructure for sustainable and patient-centered comparative effectiveness research in Chicago. Unique aspects include collaboration with the University HealthSystem Consortium to aggregate data across sites, a centralized communication center to integrate patient recruitment with the data infrastructure, and a centralized institutional review board to ensure a strong and efficient human subject protection program. With coordination by the Chicago Community Trust and the Illinois Medical District Commission, CAPriCORN will model how healthcare institutions can overcome barriers of data integration, marketplace competition, and care fragmentation to develop, test, and implement strategies to improve care for diverse populations and reduce health disparities.
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Redox-dependent conformational switching of diphenylacetylenes.
Molecules
PUBLISHED: 04-28-2014
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Herein we describe the design and synthesis of a redox-dependent single-molecule switch. Appending a ferrocene unit to a diphenylacetylene scaffold gives a redox-sensitive handle, which undergoes reversible one-electron oxidation, as demonstrated by cyclic voltammetry analysis. (1)H-NMR spectroscopy of the partially oxidized switch and control compounds suggests that oxidation to the ferrocenium cation induces a change in hydrogen bonding interactions that results in a conformational switch.
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Aggregate Features in Multi-Sample Classification Problems.
IEEE J Biomed Health Inform
PUBLISHED: 04-09-2014
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This paper evaluates the classification of multisample problems, such as electromyographic (EMG) data, by making aggregate features available to a per-sample classifier. It is found that the accuracy of this approach is superior to that of traditional methods such as majority-vote for this problem. The classification improvements of this method, in conjunction with a confidence measure expressing the per-sample probability of classification failure (i.e. a hazard function) is described and measured. Results are expected to be of interest in clinical decision support system development.
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Structural reinforcement of microvascular networks using electrostatic layer-by-layer assembly with halloysite nanotubes.
Soft Matter
PUBLISHED: 03-22-2014
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We demonstrate a method for tailoring local mechanical properties near channel surfaces of vascular structural polymers in order to achieve high structural performance in microvascular systems. While synthetic vascularized materials have been created by a variety of manufacturing techniques, unreinforced microchannels act as stress concentrators and lead to the initiation of premature failure. Taking inspiration from biological tissues such as dentin and bone, these mechanical deficiencies can be mitigated by complex hierarchical structural features near to channel surfaces. By employing electrostatic layer-by-layer assembly (ELbL) to deposit films containing halloysite nanotubes onto scaffold surfaces followed by matrix infiltration and scaffold removal, we are able to controllably deposit nanoscale reinforcement onto 200 micron diameter channel surface interiors in microvascular networks. High resolution strain measurements on reinforced networks under load verify that the halloysite reduces strain concentrations and improves mechanical performance.
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Exposure factors for wastewater-irrigated Asian vegetables and a probabilistic rotavirus disease burden model for their consumption.
Risk Anal.
PUBLISHED: 02-27-2014
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Many farmers in water-scarce regions of developing countries use wastewater to irrigate vegetables and other agricultural crops, a practice that may expand with climate change. There are a number of health risks associated with wastewater irrigation for human food crops, particularly with surface irrigation techniques common in the developing world. The World Health Organization (WHO) recommends using quantitative microbial risk assessment (QMRA) to determine if the irrigation scheme meets health standards. However, only a few vegetables have been studied for wastewater risk and little information is known about the disease burden of wastewater-irrigated vegetable consumption in China. To bridge this knowledge gap, an experiment was conducted to determine volume of water left on Asian vegetables and lettuce after irrigation. One hundred samples each of Chinese chard (Brassica rapa var. chinensis), Chinese broccoli (Brassica oleracea var. alboglabra), Chinese flowering cabbage (Brassica rapa var. parachinensis), and lettuce (Lactuca sativa) were harvested after overhead sprinkler irrigation. Chinese broccoli and flowering cabbage were found to capture the most water and lettuce the least. QMRAs were then constructed to estimate rotavirus disease burden from consumption of wastewater-irrigated Asian vegetables in Beijing. Results indicate that estimated risks from these reuse scenarios exceed WHO guideline thresholds for acceptable disease burden for wastewater use, signifying that reduction of pathogen concentration or stricter risk management is necessary for safe reuse. Considering the widespread practice of wastewater irrigation for food production, particularly in developing countries, incorporation of water retention factors in QMRAs can reduce uncertainty regarding health risks for consumers worldwide.
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The old-world Zygonini tr. nov. (Hemiptera, Cercopoidea, Clastopteridae), with new taxa from the related Machaerotinae.
Zootaxa
PUBLISHED: 02-26-2014
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Three new species of old-world Clastopteridae belonging to Machaerotinae are described, two in new monobasic genera: Allox transfigurata (Hindolini) from Borneo and Irridiculum deformatum (Machaerotini) from Sulawesi. One new species Machaeropsis dramatica (Hindolini) is described from Borneo. It is the first male known from the genus and shows that Machaeropsis Melichar is not synonymous with Metaenderleinia Lallemand. Five other new species are described, belonging to a new, related tribe Zygonini. Two of these new species (Ambonga lanceolata and Pseudomachaerota cucullata) belong to formerly monobasic genera from Madagascar incorrectly assigned to Cercopidae and Aphrophoridae respectively. These are related to 3 new genera: (1) from Madagascar, Pseudoclastoptera with new species P. irrubesco and P. invidia; from sub-Saharan Africa, (2) Zygon with 1 new species Z. desegregatum, and (3) Hemizygon, the latter with 2 new combinations from Pseudomachaerota: H. grande (Maa) and H. saturnus (Linnavuori). Zygon is possibly the most basal genus in Clastopteridae, according to its remarkable antennal characters with 5 different types of sensilla that show how basiconic and coeloconic sensilla are homodynamous. Genera related to Zygon are widely divergent from other spittlebugs as measured by mDNA "barcode" data from the COI gene.
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Diphenylacetylene-linked peptide strands induce bidirectional ?-sheet formation.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 02-19-2014
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In the search for synthetic mimics of protein secondary structures relevant to the mediation of protein-protein interactions, we have synthesized a series of tetrasubstituted diphenylacetylenes that display ?-sheet structures in two directions. Extensive X-ray crystallographic and NMR solution phase studies are consistent with these proteomimetics adopting sheet structures, displaying both hydrophobic and hydrophilic amino acid side chains.
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Inhibition of the HIF1?-p300 interaction by quinone- and indandione-mediated ejection of structural Zn(II).
Eur J Med Chem
PUBLISHED: 02-11-2014
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Protein-protein interactions between the hypoxia inducible factor (HIF) and the transcriptional coactivators p300/CBP are potential cancer targets due to their role in the hypoxic response. A natural product based screen led to the identification of indandione and benzoquinone derivatives that reduce the tight interaction between a HIF-1? fragment and the CH1 domain of p300. The indandione derivatives were shown to fragment to give ninhydrin, which was identified as the active species. Both the naphthoquinones and ninhydrin were observed to induce Zn(II) ejection from p300 and the catalytic domain of the histone demethylase KDM4A. Together with previous reports on the effects of related compounds on HIF-1? and other systems, the results suggest that care should be taken in interpreting biological results obtained with highly electrophilic/thiol modifying compounds.
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Effect of preoperative obstructive sleep apnea on the frequency of atrial fibrillation after coronary artery bypass grafting.
Am. J. Cardiol.
PUBLISHED: 01-28-2014
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Patients with obstructive sleep apnea (OSA) have intermittent hypoxia leading to atrial remodeling and this has been associated with the development of atrial fibrillation (AF). Postoperative AF is a common complication of coronary artery bypass grafting (CABG). The aim of this prospective study was to determine whether the presence of OSA predicts the occurrence of post-CABG AF (PCAF). This was a prospective single-center study. Patients undergoing elective CABG were evaluated and categorized as confirmed, high-risk, or low-risk OSA according to a modified Berlin questionnaire. PCAF was evaluated by 24-hour cardiac monitoring strip or 12-lead electrocardiography during the postoperative period, and validated by an electrophysiologist. We included 277 patients. OSA prevalence was 47.7%, with body mass index (31.0 vs 26.9 kg/m(2), p ?0.001), advanced age (63.7 vs 66.4 years, p = 0.031), hypertension (78.0% vs 64.8%, p = 0.015), and diabetes (45.5% vs 28.3%, p = 0.003) more prevalent in the OSA group. PCAF was found to occur in 37.2% of all patients and OSA was found to be a strong predictor of PCAF (45.5% vs 29.7%, p = 0.007). PCAF was also associated with continuous positive airway pressure use (12.6% vs 5.2%, p = 0.027). Increased length of stay was associated with PCAF (6.5 vs 5.3 days, p = 0.006), as was longer time from surgery to occurrence of PCAF (p = 0.001). In conclusion, OSA was found to be a strong predictor of PCAF, which in turn was found to be associated with increased length of stay.
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A probabilistic quantitative microbial risk assessment model of norovirus disease burden from wastewater irrigation of vegetables in Shepparton, Australia.
Water Res.
PUBLISHED: 01-24-2014
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Wastewater can be an important resource for water-scarce regions of the world, but a major barrier to its use is the associated health risk. Quantitative microbial risk assessment (QMRA) is a probabilistic modeling technique used to determine the health risks from wastewater reuse, but only a handful of QMRA studies have examined the norovirus health risks from consumption of vegetables irrigated with human wastewater, even though norovirus is a, if not the most, significant microbial cause of diarrheal disease world-wide. Furthermore, the majority of these studies have focused only on risks from lettuce consumption. To meet the knowledge gap in health risks for other vegetables, a QMRA model was constructed for agricultural wastewater irrigation in the regional city of Shepparton, Australia, using fecal shedding rates to estimate norovirus concentration in raw sewage. Annual norovirus disease burden was estimated for the consumption of lettuce, broccoli, cabbage, Asian vegetables, and cucumber after irrigation with treated wastewater. Results indicate that the waste stabilization pond treatment did not have sufficient virus removal to meet the World Health Organization (WHO) threshold for acceptable level of risk for wastewater reuse, but addition of disinfection treatments provided acceptable results for consumption of cucumber and broccoli. This is the first QMRA study to incorporate virus accumulation from previous wastewater irrigation events.
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Mesenchymal stem cell delivery strategies to promote cardiac regeneration following ischemic injury.
Biomaterials
PUBLISHED: 01-23-2014
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Myocardial infarction (MI) is one of the leading causes of mortality worldwide and is associated with irreversible cardiomyocyte death and pathological remodeling of cardiac tissue. In the past 15 years, several animal models have been developed for pre-clinical testing to assess the potential of stem cells for functional tissue regeneration and the attenuation of left ventricular remodeling. The promising results obtained in terms of improved cardiac function, neo-angiogenesis and reduction in infarct size have motivated the initiation of clinical trials in humans. Despite the potential, the results of these studies have highlighted that the effective delivery and retention of viable cells within the heart remain significant challenges that have limited the therapeutic efficacy of cell-based therapies for treating the ischemic myocardium. In this review, we discuss key elements for designing clinically translatable cell-delivery approaches to promote myocardial regeneration. Key topics addressed include cell selection, with a focus on mesenchymal stem cells derived from the bone marrow (bMSCs) and adipose tissue (ASCs), including a discussion of their potential mechanisms of action. Natural and synthetic biomaterials that have been investigated as injectable cell delivery vehicles for cardiac applications are critically reviewed, including an analysis of the role of the biomaterials themselves in the therapeutic scheme.
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?-Helix mimetics: outwards and upwards.
Bioorg. Med. Chem. Lett.
PUBLISHED: 01-18-2014
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?-Helices are common secondary structural elements forming key parts of the large, generally featureless interfacial regions of many therapeutically-relevant protein-protein interactions (PPIs). The rational design of helix mimetics is an appealing small-molecule strategy for the mediation of aberrant PPIs, however the first generation of scaffolds presented a relatively small number of residues on a single recognition surface. Increasingly, helices involved in PPIs are found to have more complex binding modes, utilizing two or three recognition surfaces, or binding with extended points of contact. To address these unmet needs the design and synthesis of new generations of multi-sided, extended, and supersecondary structures are underway.
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Characterizing EMG data using machine-learning tools.
Comput. Biol. Med.
PUBLISHED: 01-11-2014
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Effective electromyographic (EMG) signal characterization is critical in the diagnosis of neuromuscular disorders. Machine-learning based pattern classification algorithms are commonly used to produce such characterizations. Several classifiers have been investigated to develop accurate and computationally efficient strategies for EMG signal characterization. This paper provides a critical review of some of the classification methodologies used in EMG characterization, and presents the state-of-the-art accomplishments in this field, emphasizing neuromuscular pathology. The techniques studied are grouped by their methodology, and a summary of the salient findings associated with each method is presented.
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Comparison of Human Adipose-Derived Stem Cells Isolated from Subcutaneous, Omental, and Intrathoracic Adipose Tissue Depots for Regenerative Applications.
Stem Cells Transl Med
PUBLISHED: 12-20-2013
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Adipose tissue is an abundant source of multipotent progenitor cells that have shown promise in regenerative medicine. In humans, fat is primarily distributed in the subcutaneous and visceral depots, which have varying biochemical and functional properties. In most studies to date, subcutaneous adipose tissue has been investigated as the adipose-derived stem cell (ASC) source. In this study, we sought to develop a broader understanding of the influence of specific adipose tissue depots on the isolated ASC populations through a systematic comparison of donor-matched abdominal subcutaneous fat and omentum, and donor-matched pericardial adipose tissue and thymic remnant samples. We found depot-dependent and donor-dependent variability in the yield, viability, immunophenotype, clonogenic potential, doubling time, and adipogenic and osteogenic differentiation capacities of the ASC populations. More specifically, ASCs isolated from both intrathoracic depots had a longer average doubling time and a significantly higher proportion of CD34(+) cells at passage 2, as compared with cells isolated from subcutaneous fat or the omentum. Furthermore, ASCs from subcutaneous and pericardial adipose tissue demonstrated enhanced adipogenic differentiation capacity, whereas ASCs isolated from the omentum displayed the highest levels of osteogenic markers in culture. Through cell culture analysis under hypoxic (5% O2) conditions, oxygen tension was shown to be a key mediator of colony-forming unit-fibroblast number and osteogenesis for all depots. Overall, our results suggest that depot selection is an important factor to consider when applying ASCs in tissue-specific cell-based regenerative therapies, and also highlight pericardial adipose tissue as a potential new ASC source.
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Exploring novel strategies for AIDS protozoal pathogens: ?-helix mimetics targeting a key allosteric protein-protein interaction in C. hominis TS-DHFR.
Medchemcomm
PUBLISHED: 12-11-2013
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The bifunctional enzyme thymidylate synthase-dihydrofolate reductase (TS-DHFR) from the protozoal parasite Cryptosporidium hominis is a potential molecular target for the design of antiparasitic therapies for AIDS-related opportunistic infections. The enzyme exists as a homodimer with each monomer containing a unique swap domain known as a "crossover helix" that binds in a cleft on the adjacent DHFR active site. This crossover helix is absent in species containing monofunctional forms of DHFR such as human. An in-depth understanding of protein-protein interactions between the crossover helix and adjacent DHFR active site that might modulate enzyme integrity or function would allow for insights into rational design of species-specific allosteric inhibitors. Mutational analysis coupled with structural studies and biophysical and kinetic characterization of crossover helix mutants identifies this domain as essential for full enzyme stability and catalytic activity, and pinpoints these effects to distinct faces of the crossover helix important in protein-protein interactions. Moreover, targeting this helical protein interaction with ?-helix mimetics of the crossover helix leads to selective inhibition and destabilization of the C. hominis TS-DHFR enzyme, thus validating this region as a new avenue to explore for species-specific inhibitor design.
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Medication safety after implementation of a commercial electronic health record system in five safety-net practices: A mixed methods approach.
J Am Assoc Nurse Pract
PUBLISHED: 11-14-2013
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This study, conducted in five safety-net practices, including two nurse-managed health centers (NMHCs) and three federally qualified health centers (FQHCs), examined the impact of implementing a commercial electronic health records (EHRs) system on medication safety.
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Age-related impairment of endothelial progenitor cell migration correlates with structural alterations of heparan sulfate proteoglycans.
Aging Cell
PUBLISHED: 10-01-2013
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Aging poses one of the largest risk factors for the development of cardiovascular disease. The increased propensity toward vascular pathology with advancing age maybe explained, in part, by a reduction in the ability of circulating endothelial progenitor cells to contribute to vascular repair and regeneration. Although there is evidence to suggest that colony forming unit-Hill cells and circulating angiogenic cells are subject to age-associated changes that impair their function, the impact of aging on human outgrowth endothelial cell (OEC) function has been less studied. We demonstrate that OECs isolated from cord blood or peripheral blood samples from young and old individuals exhibit different characteristics in terms of their migratory capacity. In addition, age-related structural changes were discovered in OEC heparan sulfate (HS), a glycocalyx component that is essential in many signalling pathways. An age-associated decline in the migratory response of OECs toward a gradient of VEGF significantly correlated with a reduction in the relative percentage of the trisulfated disaccharide, 2-O-sulfated-uronic acid, N, 6-O-sulfated-glucosamine (UA[2S]-GlcNS[6S]), within OEC cell surface HS polysaccharide chains. Furthermore, disruption of cell surface HS reduced the migratory response of peripheral blood-derived OECs isolated from young subjects to levels similar to that observed for OECs from older individuals. Together these findings suggest that aging is associated with alterations in the fine structure of HS on the cell surface of OECs. Such changes may modulate the migration, homing, and engraftment capacity of these repair cells, thereby contributing to the progression of endothelial dysfunction and age-related vascular pathologies.
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Fixed sized samples for type-specific surveillance of human papillomavirus in genital warts.
Sex Health
PUBLISHED: 07-16-2013
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Surveillance data suggest that human papillomavirus (HPV) vaccination in Australia is reducing the incidence of genital warts. However, existing surveillance measures do not assess the proportion of the remaining cases of warts that are caused by HPV types other than 6 or 11, against which the vaccine has no demonstrated effectiveness. Using computer simulation rather than sample size formulae, we established that genotyping at least 60 warts can accurately test whether the proportion of warts due to HPV types not targeted by the vaccine has increased (Type I error probability ? 0.05, Type II error probability <0.07). Standard formulae for calculating sample size, in contrast, suggest that a sample size of more than 130 would be required for this task, but using these formulae entails making several strong assumptions. Our methods require fewer assumptions and demonstrate that a smaller sample size than anticipated could be used to address the question of what proportion of post-vaccination cases of warts are due to nonvaccine types. In conjunction with indications of incidence and prevalence provided by existing surveillance measures, this could indicate the number of cases of post-vaccination warts due to nonvaccine types and hence whether type replacement is occurring.
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Pathogen reduction requirements for direct potable reuse in Antarctica: evaluating human health risks in small communities.
Sci. Total Environ.
PUBLISHED: 04-15-2013
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Small, remote communities often have limited access to energy and water. Direct potable reuse of treated wastewater has recently gained attention as a potential solution for water-stressed regions, but requires further evaluation specific to small communities. The required pathogen reduction needed for safe implementation of direct potable reuse of treated sewage is an important consideration but these are typically quantified for larger communities and cities. A quantitative microbial risk assessment (QMRA) was conducted, using norovirus, giardia and Campylobacter as reference pathogens, to determine the level of treatment required to meet the tolerable annual disease burden of 10(-6) DALYs per person per year, using Davis Station in Antarctica as an example of a small remote community. Two scenarios were compared: published municipal sewage pathogen loads and estimated pathogen loads during a gastroenteritis outbreak. For the municipal sewage scenario, estimated required log10 reductions were 6.9, 8.0 and 7.4 for norovirus, giardia and Campylobacter respectively, while for the outbreak scenario the values were 12.1, 10.4 and 12.3 (95th percentiles). Pathogen concentrations are higher under outbreak conditions as a function of the relatively greater degree of contact between community members in a small population, compared with interactions in a large city, resulting in a higher proportion of the population being at risk of infection and illness. While the estimates of outbreak conditions may overestimate sewage concentration to some degree, the results suggest that additional treatment barriers would be required to achieve regulatory compliance for safe drinking water in small communities.
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Late gadolinium enhancement is common in patients with hypertrophic cardiomyopathy and no clinical risk factors for sudden cardiac death: A single centre experience.
Cardiol J
PUBLISHED: 03-03-2013
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Cardiac magnetic resonance (CMR) is used in the diagnosis and risk stratification of hypertrophic cardiomyopathy (HCM) and can detect myocardial replacement fibrosis (an independent predictor of adverse cardiac outcomes) using late gadolinium enhancement. We retrospectively analysed CMR studies carried out over a 2 year period identifying those which were diagnostic of HCM. 117 cases were analysed. Mean age of subjects was 53 years and 78 (67%) were male. Mean ejection fraction was 68.3% with a mean LV mass index of 89.4 g/m². Hypertrophy was predominantly asymmetric in 94 (80%). All subjects received gadolinium and 80 (68%) had evidence of LGE. LV ejection fraction was lower (67 vrs 71% p = 0.015 ) and LV mass index higher (94 vrs 81 g/m2 p = 0.007) in the LGE group. The proportion of patients with at least 1 clinical risk factor for SCD was similar in groups with and without LGE (48% vrs 32% p = 0.160). In this study, a significant proportion (62%) of patients without clinical risk factors for SCD were found to have LGE on CMR. These patients would not currently be considered for therapy with an implantable cardiac defibrillator.
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Breaking it down: the ubiquitin proteasome system in neuronal morphogenesis.
Neural Plast.
PUBLISHED: 02-14-2013
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The ubiquitin-proteasome system (UPS) is most widely known for its role in intracellular protein degradation; however, in the decades since its discovery, ubiquitination has been associated with the regulation of a wide variety of cellular processes. The addition of ubiquitin tags, either as single moieties or as polyubiquitin chains, has been shown not only to mediate degradation by the proteasome and the lysosome, but also to modulate protein function, localization, and endocytosis. The UPS plays a particularly important role in neurons, where local synthesis and degradation work to balance synaptic protein levels at synapses distant from the cell body. In recent years, the UPS has come under increasing scrutiny in neurons, as elements of the UPS have been found to regulate such diverse neuronal functions as synaptic strength, homeostatic plasticity, axon guidance, and neurite outgrowth. Here we focus on recent advances detailing the roles of the UPS in regulating the morphogenesis of axons, dendrites, and dendritic spines, with an emphasis on E3 ubiquitin ligases and their identified regulatory targets.
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Quantifying intrinsic ion-driven conformational changes in diphenylacetylene supramolecular switches with cryogenic ion vibrational spectroscopy.
J Phys Chem A
PUBLISHED: 01-27-2013
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We report how two flexible diphenylacetylene (DPA) derivatives distort to accommodate both cationic and anionic partners in the binary X(±)·DPA series with X = TMA(+) (tetramethylammonium), Na(+), Cl(-), Br(-), and I(-). This is accomplished through theoretical analysis of X(±)·DPA·2D2 vibrational spectra, acquired by predissociation of the weakly bound D2 adducts formed in a 10 K ion trap. DPA binds the weakly coordinating TMA(+) ion with an arrangement similar to that of the neutral compound, whereas the smaller Na(+) ion breaks all intramolecular H-bonds yielding a structure akin to the transition state for interconversion of the two conformations in neutral DPA. Halides coordinate to the urea NH donors in a bidentate H-bonded configuration analogous to the single intramolecular H-bonded motif identified at high chloride concentrations in solution. Three positions of the "switch" are thus identified in the intrinsic ion accommodation profile that differ by the number of intramolecular H-bonds (0, 1, or 2) at play.
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Targeting protein prenylation for cancer therapy.
Nat. Rev. Cancer
PUBLISHED: 10-25-2011
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Protein farnesylation and geranylgeranylation, together referred to as prenylation, are lipid post-translational modifications that are required for the transforming activity of many oncogenic proteins, including some RAS family members. This observation prompted the development of inhibitors of farnesyltransferase (FT) and geranylgeranyl-transferase 1 (GGT1) as potential anticancer drugs. In this Review, we discuss the mechanisms by which FT and GGT1 inhibitors (FTIs and GGTIs, respectively) affect signal transduction pathways, cell cycle progression, proliferation and cell survival. In contrast to their preclinical efficacy, only a small subset of patients responds to FTIs. Identifying tumours that depend on farnesylation for survival remains a challenge, and strategies to overcome this are discussed. One GGTI has recently entered the clinic, and the safety and efficacy of GGTIs await results from clinical trials.
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Neurogenic changes in the upper airway of patients with obstructive sleep apnea.
Am. J. Respir. Crit. Care Med.
PUBLISHED: 10-20-2011
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Controversy persists regarding the presence and importance of hypoglossal nerve dysfunction in obstructive sleep apnea (OSA).
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Differential solute gas response in ionic-liquid-based QCM arrays: elucidating design factors responsible for discriminative explosive gas sensing.
Anal. Chem.
PUBLISHED: 09-26-2011
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An eight-sensor array coupling a chemoselective room-temperature ionic liquid (RTIL) with quartz crystal microbalance (QCM) transduction is presented in this work in order to demonstrate the power of this approach in differentiating closely related analytes in sensory devices. The underlying mechanism behind the specific sensory response was explored by (i) studying mass loading and viscoelasticity effects of the sensing layers, predominantly through variation in damping impedance, the combination of which determines the sensitivity; (ii) creation of a solvation model based on Abrahams solvation descriptors which reveals the fact that polarizability and lipophilicity are the main factors influencing the dissolution of gas analytes into the RTILs; and (iii) determination of enthalpy and entropy values for the studied interactions and comparison via a simulation model, which is also effective for pattern discrimination, in order to establish a foundation for the analytical scientist as well as inspiration for synthetic pathways and innovative research into next-generation sensory approaches. The reported sensors displayed an excellent sensitivity with detection limit of <0.2%, fast response and recovery, and a workable temperature range of 27-55 °C and even higher. Linear discriminant analysis (LDA) showed a discrimination accuracy of 86-92% for nitromethane and 1-ethyl-2-nitrobenzene, 71% for different mixtures of nitromethane, and 100% for these analytes when thermodynamic parameters were used as input data. We envisage applications to detecting other nitroaromatics and security-related gas targets, and high-temperature or real-time situations where manual access is restricted, opening up new horizons in chemical sensing.
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pH-dependent conformational switching in 2,6-benzamidodiphenylacetylenes.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 09-02-2011
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The conformational equilibrium of a pH-dependent switch based on an intramolecularly H-bonded diphenylacetylene can be predictably biased by using electron-donating or -withdrawing groups. Furthermore, protonation of the electron-donating dimethylamino group converts it into an electron-withdrawing dimethylammonium cation with a concomitant switch in conformation.
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A partnership model for implementing electronic health records in resource-limited primary care settings: experiences from two nurse-managed health centers.
J Am Med Inform Assoc
PUBLISHED: 08-09-2011
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To present a partnership-based and community-oriented approach designed to ease provider anxiety and facilitate the implementation of electronic health records (EHR) in resource-limited primary care settings.
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Detection of antibodies against Paracoccidioides brasiliensis melanin in in vitro and in vivo studies during infection.
Clin. Vaccine Immunol.
PUBLISHED: 08-03-2011
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Several cell wall constituents, including melanins or melanin-like compounds, have been implicated in the pathogenesis of a wide variety of microbial diseases caused by diverse species of pathogenic bacteria, fungi, and helminthes. Among these microorganisms, the dimorphic fungal pathogen Paracoccidioides brasiliensis produces melanin in its conidial and yeast forms. In the present study, melanin particles from P. brasiliensis were injected into BALB/c mice in order to produce monoclonal antibodies (MAbs). We identified five immunoglobulin G1 (IgG1) ?-chain and four IgM melanin-binding MAbs. The five IgG1 ?-chain isotypes are the first melanin-binding IgG MAbs ever reported. The nine MAbs labeled P. brasiliensis conidia and yeast cells both in vitro and in pulmonary tissues. The MAbs cross-reacted with melanin-like purified particles from other fungi and also with commercial melanins, such as synthetic and Sepia officinalis melanin. Melanization during paracoccidioidomycosis (PCM) was also further supported by the detection of IgG antibodies reactive to melanin from P. brasiliensis conidia and yeast in sera and bronchoalveolar lavage fluids from P. brasiliensis-infected mice, as well as in sera from human patients with PCM. Serum specimens from patients with other mycoses were also tested for melanin-binding antibodies by enzyme-linked immunosorbent assay, and cross-reactivities were detected for melanin particles from different fungal sources. These results suggest that melanin from P. brasiliensis is an immunologically active fungal structure that activates a strong IgG humoral response in humans and mice.
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Oligophenylenaminones as scaffolds for ?-helix mimicry.
J. Org. Chem.
PUBLISHED: 08-03-2011
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The design and synthesis of small molecule ?-helix mimetics has been a productive field over the past decade. These compounds have performed well in a variety of biological systems as functional disruptors of ?-helix-mediated protein-protein interactions. In our studies we have continued to develop novel, more biologically compatible scaffolds, which are often easier to assemble and capable of mimicking longer and/or more diverse helices. To this end, we have constructed a new series of i, i+4, i+7 ?-helix mimics based on the enaminone scaffold. These molecules represent a step forward in the pursuit of idealized monofacial ?-helix mimetics.
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Optimization of the precordial leads of the 12-lead electrocardiogram may improve detection of ST-segment elevation myocardial infarction.
J Electrocardiol
PUBLISHED: 06-28-2011
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For the assessment of patients with chest pain, the 12-lead electrocardiogram (ECG) is the initial investigation. Major management decisions are based on the ECG findings, both for attempted coronary artery revascularization and risk stratification. The aim of this study was to determine if the current 6 precordial leads (V(1)-V(6)) are optimally located for the detection of ST-segment elevation in ST-segment elevation myocardial infarction (STEMI).
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Hydrogen-bonded synthetic mimics of protein secondary structure as disruptors of protein-protein interactions.
Curr. Top. Microbiol. Immunol.
PUBLISHED: 05-27-2011
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Small molecules which can mimic the key structural facets of protein secondary structure, in particular the ?-helix, ?-strand, and ?-sheet, have been shown to be potent disruptors of protein-protein interactions. Researchers have recently taken the organizational imitation of protein secondary structure to a new level by using intramolecular hydrogen bonds as stabilizing forces in these small molecule mimetics. The inclusion of these interactions invokes a conformational bias of the system, allowing for greater control of the appearance, and thus often function, of these molecules by design.
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Combination of farnesyltransferase and Akt inhibitors is synergistic in breast cancer cells and causes significant breast tumor regression in ErbB2 transgenic mice.
Clin. Cancer Res.
PUBLISHED: 05-04-2011
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The Akt activation inhibitor triciribine and the farnesyltransferase inhibitor tipifarnib have modest to little activity in clinical trials when used as single agents. In this article, preclinical data show that the combination is more effective than single agents both in cultured cells and in vivo. Combination index data analysis shows that this combination is highly synergistic at inhibiting anchorage-dependent growth of breast cancer cells. This synergistic interaction is also observed with structurally unrelated inhibitors of Akt (MK-2206) and farnesyltransferase (FTI-2153). The triciribine/tipifarnib synergistic effects are seen with several cancer cell lines including those from breast, leukemia, multiple myeloma and lung tumors with different genetic alterations such as K-Ras, B-Raf, PI3K (phosphoinositide 3-kinase), p53 and pRb mutations, PTEN, pRB and Ink4a deletions, and ErbB receptor overexpression. Furthermore, the combination is synergistic at inhibiting anchorage-independent growth and at inducing apoptosis in breast cancer cells. The combination is also more effective at inhibiting the Akt/mTOR/S6 kinase pathway. In an ErbB2-driven breast tumor transgenic mouse model, the combination, but not single agent, treatment with triciribine and tipifarnib induces significant breast tumor regression. Our findings warrant further investigation of the combination of farnesyltransferase and Akt inhibitors.
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ProExC triage of atypical glandular cells on liquid-based cervical cytology specimens.
J Low Genit Tract Dis
PUBLISHED: 04-13-2011
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Morphologic distinction between atypical glandular cells not otherwise specified (AGC-NOS) and AGC-favor neoplasia (AGC-FN) can be difficult. Distinction between these entities is important as the American Society for Colposcopy and Cervical Pathology 2006 consensus guidelines state that management of AGC-NOS differs from that of AGC-FN. The objective of this study was to determine the potential role of ProExC immunocytochemical triage of AGC-NOS.
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Decorin GAG synthesis and TGF-? signaling mediate Ox-LDL-induced mineralization of human vascular smooth muscle cells.
Arterioscler. Thromb. Vasc. Biol.
PUBLISHED: 01-04-2011
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Decorin and oxidized low-density lipoprotein (Ox-LDL) independently induce osteogenic differentiation of vascular smooth muscle cells (VSMCs). We aimed to determine whether decorin glycosaminoglycan (GAG) chain synthesis contributes to Ox-LDL-induced differentiation and calcification of human VSMCs in vitro.
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A review of clinical quantitative electromyography.
Crit Rev Biomed Eng
PUBLISHED: 12-24-2010
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Information regarding the morphology of motor unit potentials (MUPs) and motor unit firing patterns can be used to help diagnose, treat, and manage neuromuscular disorders. In a conventional electromyographic (EMG) examination, a clinician manually assesses the characteristics of needle-detected EMG signals across a number of distinct needle positions and forms an overall impression of the condition of the muscle. Such a subjective assessment is highly dependent on the skills and level of experience of the clinician, and is prone to a high error rate and operator bias. Quantitative methods have been developed to characterize MUP waveforms using statistical and probabilistic techniques that allow for greater objectivity and reproducibility in supporting the diagnostic process. In this review, quantitative EMG (QEMG) techniques ranging from simple reporting of numeric MUP values to interpreted muscle characterizations are presented and reviewed in terms of their clinical potential to improve status quo methods. QEMG techniques are also evaluated in terms of their suitability for use in a clinical decision support system based on previously established criteria. Aspects of prototype clinical decision support systems are then presented to illustrate some of the concepts of QEMG-based decision making.
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Intramuscular EMG signal decomposition.
Crit Rev Biomed Eng
PUBLISHED: 12-24-2010
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Information regarding motor unit potentials (MUPs) and motor unit fi ring patterns during muscle contractions is useful for physiological investigation and clinical examinations either for the understanding of motor control or for the diagnosis of neuromuscular disorders. In order to obtain such information, composite electromyographic (EMG) signals are decomposed (i.e., resolved into their constituent motor unit potential trains [MUPTs]). The goals of automatic decomposition techniques are to create a MUPT for each motor unit that contributed significant MUPs to the original composite signal. Diagnosis can then be facilitated by decomposing a needle-detected EMG signal, extracting features of MUPTs, and finally analyzing the extracted features (i.e., quantitative electromyography). Herein, the concepts of EMG signals and EMG signal decomposition techniques are explained. The steps involved with the decomposition of an EMG signal and the methods developed for each step, along with their strengths and limitations, are discussed and compared. Finally, methods developed to evaluate decomposition algorithms and assess the validity of the obtained MUPTs are reviewed and evaluated.
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The BH3 alpha-helical mimic BH3-M6 disrupts Bcl-X(L), Bcl-2, and MCL-1 protein-protein interactions with Bax, Bak, Bad, or Bim and induces apoptosis in a Bax- and Bim-dependent manner.
J. Biol. Chem.
PUBLISHED: 12-09-2010
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A critical hallmark of cancer cell survival is evasion of apoptosis. This is commonly due to overexpression of anti-apoptotic proteins such as Bcl-2, Bcl-X(L), and Mcl-1, which bind to the BH3 ?-helical domain of pro-apoptotic proteins such as Bax, Bak, Bad, and Bim, and inhibit their function. We designed a BH3 ?-helical mimetic BH3-M6 that binds to Bcl-X(L) and Mcl-1 and prevents their binding to fluorescently labeled Bak- or Bim-BH3 peptides in vitro. Using several approaches, we demonstrate that BH3-M6 is a pan-Bcl-2 antagonist that inhibits the binding of Bcl-X(L), Bcl-2, and Mcl-1 to multi-domain Bax or Bak, or BH3-only Bim or Bad in cell-free systems and in intact human cancer cells, freeing up pro-apoptotic proteins to induce apoptosis. BH3-M6 disruption of these protein-protein interactions is associated with cytochrome c release from mitochondria, caspase-3 activation and PARP cleavage. Using caspase inhibitors and Bax and Bak siRNAs, we demonstrate that BH3-M6-induced apoptosis is caspase- and Bax-, but not Bak-dependent. Furthermore, BH3-M6 disrupts Bcl-X(L)/Bim, Bcl-2/Bim, and Mcl-1/Bim protein-protein interactions and frees up Bim to induce apoptosis in human cancer cells that depend for tumor survival on the neutralization of Bim with Bcl-X(L), Bcl-2, or Mcl-1. Finally, BH3-M6 sensitizes cells to apoptosis induced by the proteasome inhibitor CEP-1612.
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Evaluation of motor unit placement algorithms for EMG simulation.
Conf Proc IEEE Eng Med Biol Soc
PUBLISHED: 11-25-2010
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Motor unit layout algorithms have a significant effect on motor unit fibre densities recorded. Motor unit fibre densities are affected by both the method used to place the motor unit territories, and the mechanism by which muscle fibres are assigned to motor units. The first of these should emulate the process by which separate motor neurons create overlapping territories that cover the muscle cross section, while the second should have some relation to the processes involved with axonal arborization and development of the spatial dispersion of the neuro-muscular junctions. The success of an algorithm in creating physiologically realistic motor unit layouts may be evaluated, in part, by examining the distribution of the muscle fibres assigned to the motor units. This paper examines the motor unit fibre densities found in muscles created by two recent algorithms, and explores the degree to which the concepts used by these algorithms may be shared.
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Structure-based design and synthesis of potent, ethylenediamine-based, mammalian farnesyltransferase inhibitors as anticancer agents.
J. Med. Chem.
PUBLISHED: 09-09-2010
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A potent class of anticancer, human farnesyltransferase (hFTase) inhibitors has been identified by "piggy-backing" on potent, antimalarial inhibitors of Plasmodium falciparum farnesyltransferase (PfFTase). On the basis of a 4-fold substituted ethylenediamine scaffold, the inhibitors are structurally simple and readily derivatized, facilitating the extensive structure-activity relationship (SAR) study reported herein. Our most potent inhibitor is compound 1f, which exhibited an in vitro hFTase IC(50) value of 25 nM and a whole cell H-Ras processing IC(50) value of 90 nM. Moreover, it is noteworthy that several of our inhibitors proved highly selective for hFTase (up to 333-fold) over the related prenyltransferase enzyme geranylgeranyltransferase-I (GGTase-I). A crystal structure of inhibitor 1a co-crystallized with farnesyl pyrophosphate (FPP) in the active site of rat FTase illustrates that the para-benzonitrile moiety of 1a is stabilized by a ?-? stacking interaction with the Y361? residue, suggesting a structural explanation for the observed importance of this component of our inhibitors.
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No haploinsufficiency but loss of heterozygosity for EXT in multiple osteochondromas.
Am. J. Pathol.
PUBLISHED: 09-02-2010
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Multiple osteochondromas (MO) is an autosomal dominant disorder caused by germline mutations in EXT1 and/or EXT2. In contrast, solitary osteochondroma (SO) is nonhereditary. Products of the EXT gene are involved in heparan sulfate (HS) biosynthesis. In this study, we investigated whether osteochondromas arise via either loss of heterozygosity (2 hits) or haploinsufficiency. An in vitro three-dimensional chondrogenic pellet model was used to compare heterozygous bone marrow-derived mesenchymal stem cells (MSCs EXT(wt/-)) of MO patients with normal MSCs and the corresponding tumor specimens (presumed EXT(-/-)). We demonstrated a second hit in EXT in five of eight osteochondromas. HS chain length and structure, in vitro chondrogenesis, and EXT expression levels were identical in both EXT(wt/-) and normal MSCs. Immunohistochemistry for HS, HS proteoglycans, and HS-dependent signaling pathways (eg, TGF-?/BMP, Wnt, and PTHLH) also showed no differences. The cartilaginous cap of osteochondroma contained a mixture of HS-positive and HS-negative cells. Because a heterozygous EXT mutation does not affect chondrogenesis, EXT, HS, or downstream signaling pathways in MSCs, our results refute the haploinsufficiency theory. We found a second hit in 63% of analyzed osteochondromas, supporting the hypothesis that osteochondromas arise via loss of heterozygosity. The detection of the second hit may depend on the ratio of HS-positive (normal) versus HS-negative (mutated) cells in the cartilaginous cap of the osteochondroma.
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Assessing motor deficits in compressive neuropathy using quantitative electromyography.
J Neuroeng Rehabil
PUBLISHED: 08-11-2010
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Studying the changes that occur in motor unit potential trains (MUPTs) may provide insight into the extent of motor unit loss and neural re-organization resulting from nerve compression injury. The purpose of this study was to determine the feasibility of using decomposition-based quantitative electromyography (DQEMG) to study the pathophysiological changes associated with compression neuropathy.
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Designed molecular switches: controlling the conformation of benzamido-diphenylacetylenes.
Org. Lett.
PUBLISHED: 07-31-2010
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With the goal of creating a molecular switch, the hydrogen-bonded diphenylacetylene structure has been modified such that an equilibrium now exists between two intramolecular H-bonded states. Through X-ray crystallography and (1)H NMR analysis it is shown that this equilibrium can be biased in a predictable manner by modulating the relative acidity of the amide NHs.
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Combinatorial protein recognition as an alternative approach to antibody-mimetics.
Curr Opin Chem Biol
PUBLISHED: 07-12-2010
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Current approaches to medical diagnostics and drug design are largely based on the ability of monoclonal antibodies or synthetic molecules to bind proteins with high affinity and selectivity. In recent years, however, an alternative approach to protein recognition has emerged, in which proteins are identified using non-specific receptor arrays that are inspired by the olfactory neural system. An ultimate challenge for such systems is realizing a single, high-throughput analytical device that can effectively diagnose a range of medicinally relevant proteins. Such devices might overcome the difficulties associated with designing potent synthetic receptors for proteins and hence, could open up new possibilities in medical diagnostics, pathogen detection, and proteomics. Here we summarize recent developments in this area and also highlight its limitations and the challenges that this exciting interdisciplinary field faces. In particular, the goal of this review is to underscore the basic parameters required for obtaining combinatorial sensors for proteins and more importantly, to elucidate the rational methodologies that can be applied for systematically improving these promising analytical devices.
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Objective cough frequency in Idiopathic Pulmonary Fibrosis.
Cough
PUBLISHED: 06-21-2010
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Cough is a common presenting symptom in patients with Idiopathic Pulmonary Fibrosis (IPF). This study measured cough rates in IPF patients and investigated the association between cough and measures of health related quality of life and subjective cough assessments. In addition, IPF cough rates were related to measures of physiological disease severity and compared to cough rates in health and other respiratory conditions.
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Quantifying uncertainty in estimation of tropical arthropod species richness.
Am. Nat.
PUBLISHED: 05-12-2010
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There is a bewildering range of estimates for the number of arthropods on Earth. Several measures are based on extrapolation from species specialized to tropical rain forest, each using specific assumptions and justifications. These approaches have not provided any sound measure of uncertainty associated with richness estimates. We present two models that account for parameter uncertainty by replacing point estimates with probability distributions. The models predict medians of 3.7 million and 2.5 million tropical arthropod species globally, with 90% confidence intervals of [2.0, 7.4] million and [1.1, 5.4] million, respectively. Estimates of 30 million or greater are predicted to have <0.00001 probability. Sensitivity analyses identified uncertainty in the proportion of canopy arthropod species that are beetles as the most influential parameter, although uncertainties associated with three other parameters were also important. Using the median estimates suggests that in spite of 250 years of taxonomy and around 855,000 species of arthropods already described, approximately 70% await description.
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Altered binding of a multimeric protein by changing the self-assembling properties of its substrate.
J. Am. Chem. Soc.
PUBLISHED: 04-27-2010
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Artificially controlled cell recognition has potentially far-reaching applications in both the understanding and altering of biological function. The event of recognition often involves a multimeric protein binding a cellular membrane. While such an interaction is energetically favorable, it has been surprisingly underexploited in artificial control of recognition. Herein we describe how changing properties of substrate (phosphocholine, PC) self-assembly can affect both binding behavior and substrate affinity to a pentameric recognition protein (C-reactive protein, CRP). PC was modified with a short, self-assembling DNA strand to make the substrate self-assembly sensitive and responsive to ionic environment. A significant shift in CRP binding affinity was observed when substrates were assembled in the presence of Cs(+) rather than K(+). Furthermore, alteration of the linker length tethering PC to DNA showed trends similar to other multivalent systems. In optimizing these linker lengths, positive cooperativity increased and K(d) of the substrate assembly to CRP improved roughly 1000-fold. Such experiments both inform our understanding of biological, multivalent interactions in self-assembling systems and present a potential method to exogenously control events in cell recognition.
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Validating motor unit firing patterns extracted by EMG signal decomposition.
Med Biol Eng Comput
PUBLISHED: 03-03-2010
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Motor unit (MU) firing pattern information can be used clinically or for physiological investigation. It can also be used to enhance and validate electromyographic (EMG) signal decomposition. However, in all instances the validity of the extracted MU firing patterns must first be determined. Two supervised classifiers that can be used to validate extracted MU firing patterns are proposed. The first classifier, the single/merged classifier (SMC), determines whether a motor unit potential train (MUPT) represents the firings of a single MU or the merged activity of more than one MU. The second classifier, the single/contaminated classifier (SCC), determines whether the estimated number of false-classification errors in a MUPT is acceptable or not. Each classifier was trained using simulated data and tested using simulated and real data. The accuracy of the SMC in categorizing a train correctly is 99% and 96% for simulated and real data, respectively. The accuracy of the SCC is 84% and 81% for simulated and real data, respectively. The composition of these classifiers, their objectives, how they were trained, and the evaluation of their performances using both simulated and real data are presented in detail.
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A multicenter randomized controlled trial to assess the feasibility of testing modified ultrafiltration as a blood conservation technology in cardiac surgery.
J. Thorac. Cardiovasc. Surg.
PUBLISHED: 02-24-2010
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Modified ultrafiltration is a technique after cardiopulmonary bypass whereby blood withdrawn from the aortic cannula is passed across a semipermeable membrane to hemoconcentrate. Unblinded trials have suggested that modified ultrafiltration is efficacious for blood conservation. The objective of this trial was to assess the feasibility of a model testing modified ultrafiltration in which all members of the surgical team were blinded to the intervention.
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Bayesian aggregation versus majority vote in the characterization of non-specific arm pain based on quantitative needle electromyography.
J Neuroeng Rehabil
PUBLISHED: 02-15-2010
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Methods for the calculation and application of quantitative electromyographic (EMG) statistics for the characterization of EMG data detected from forearm muscles of individuals with and without pain associated with repetitive strain injury are presented.
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Synthetic mimetics of protein secondary structure domains.
Philos Trans A Math Phys Eng Sci
PUBLISHED: 02-04-2010
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Proteins modulate the majority of all biological functions and are primarily composed of highly organized secondary structural elements such as helices, turns and sheets. Many of these functions are affected by a small number of key protein-protein contacts, often involving one or more of these well-defined structural elements. Given the ubiquitous nature of these protein recognition domains, their mimicry by peptidic and non-peptidic scaffolds has become a major focus of contemporary research. This review examines several key advances in secondary structure mimicry over the past several years, particularly focusing upon scaffolds that show not only promising projection of functional groups, but also a proven effect in biological systems.
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MicroRNA in erythrocytes.
Biochem. Soc. Trans.
PUBLISHED: 01-16-2010
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Mammalian erythrocytes are generally thought to lack RNA and therefore to be unable to translate new proteins in response to internal or external signals. Support for this long-standing view has accumulated from diverse studies, most of which have focused on the total content of RNA or the overall level of translation. However, more recent work on specific types of RNA has shown the presence in human erythrocytes of both Y RNA and microRNA. The latter seem particularly incongruous given that their normal role is to attenuate the translation of mRNA. Y RNA binds the Ro autoantigen which may have a role in cellular RNA quality control. Therefore the presence of both of these non-coding RNAs indicates the possible existence of other cryptic RNAs in erythrocytes. It also suggests either the existence of low levels of translation or new uncharacterized processes involving microRNA in these cells.
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Programing the formation of DNA and PNA quadruplexes by pi-pi-stacking interactions.
Chem. Commun. (Camb.)
PUBLISHED: 01-13-2010
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Guanine (G) rich G(4)T(4)G(4) DNA and homologous PNA strands tend to form antiparallel dimeric quadruplexes. In contrast, the same DNA strands carrying planar aromatic 5-residues preferentially form parallel DNA quadruplex. Conformation and composition of the DNA quadruplexes can be programed by pi-pi-stacking interaction exerted by the 5-residues.
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Disrupting protein-protein interactions with non-peptidic, small molecule alpha-helix mimetics.
Curr Opin Chem Biol
PUBLISHED: 01-12-2010
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Many biological processes are regulated by protein-protein interactions (PPIs) and as such their misregulation can cause a multitude of diseases. Often the interactions between large proteins are mediated by small protein secondary structural domains, which project a minimum number of specifically arranged residues into the complementary surface of an interacting protein. Nature has the advantage of time, and over time has optimized those secondary structures, such as alpha-helices, beta-sheets and beta-strands, found at the interfaces of PPIs. Inspired by Natures extensive optimization, chemists have used these secondary structures as templates in the design of small molecules that may act as structural and functional mimics of large rhenylogically organized protein secondary structures. Herein recent applications of the indane, terphenyl, terphenyl-inspired templates, polycyclic ether and benzodiazepinedione scaffolds, as non-peptidic, small molecule alpha-helix mimetics, to disrupt PPIs are detailed.
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Discovery of a synthetic dual inhibitor of HIV and HCV infection based on a tetrabutoxy-calix[4]arene scaffold.
Bioorg. Med. Chem. Lett.
PUBLISHED: 01-08-2010
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A potential anti-HIV and HCV drug candidate is highly desirable as coinfection has become a worldwide public health challenge. A potent compound based on a tetrabutoxy-calix[4]arene scaffold that possesses dual inhibition for both HIV and HCV is described. Structural activity relationship studies demonstrate the effects of lower-rim alkylation in maintaining cone conformation and upper-rim interacting head groups on the calix[4]arene play key roles for its potent dual antiviral activities.
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Transesophageal echocardiography of a dislodged left atrial appendage thrombus and its subsequent surgical removal during coronary artery bypass graft surgery.
J Am Soc Echocardiogr
PUBLISHED: 01-07-2010
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Left atrial appendage (LAA) thrombus is a common finding in patients with atrial fibrillation and a major source of emboli that cause strokes. The incidental finding of an LAA thrombus during cardiac surgery is an infrequent finding during routine intraoperative echocardiography, and optimal management is not well defined. A case of a large, incidentally discovered LAA thrombus that became mobile on initiation of cardiopulmonary bypass in a patient undergoing coronary artery bypass graft surgery is presented. Intraoperative transesophageal echocardiography diagnosed the thrombus, discovered its dislodgement from the LAA, and very interestingly demonstrated its surgical removal. This case demonstrates the ability of intraoperative transesophageal echocardiography to alter surgical management and provides support for its routine use in cases in which LAA thrombi are likely.
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Validation of motor unit potential trains using motor unit firing pattern information.
Conf Proc IEEE Eng Med Biol Soc
PUBLISHED: 12-08-2009
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A robust and fast method to assess the validity of a motor unit potential train (MUPT) obtained by decomposing a needle-detected EMG signal is proposed. This method determines whether a MUPT represents the firings of a single motor unit (MU) or the merged activity of more than one MU, and if is a single train it identifies whether the estimated levels of missed and false classification errors in the MUPT are acceptable. Two supervised classifiers, the Single/Merged classifier (SMC) and the Error Rate classifier (ERC), and a linear model for estimating the level of missed classification error have been developed for this objective. Experimental results using simulated data show that the accuracy of the SMC and the ERC in correctly categorizing a train is 99% and %84 respectively.
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Ultrafast energy transfer within pyropheophorbide-a tethered to self-assembling DNA quadruplex.
Chem. Commun. (Camb.)
PUBLISHED: 12-07-2009
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A DNA quadruplex system that exhibits ultrafast intramolecular energy transfer is discussed.
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Combined solid/solution phase synthesis of large surface area scaffolds derived from aminomethyl-benzoates.
Tetrahedron Lett.
PUBLISHED: 12-02-2009
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A set of macrocycles was generated by solid phase synthesis of linear trimers of 5-aminoacyl-3-aminomethyl-benzoates followed by resin cleavage and solution phase macrocyclization. These scaffolds can serve as useful building blocks for molecular recognition studies, especially where differentially functionalized molecular platforms spanning large surface areas are required.
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A novel class of meso-tetrakis-porphyrin derivatives exhibits potent activities against hepatitis C virus genotype 1b replicons in vitro.
Antimicrob. Agents Chemother.
PUBLISHED: 11-09-2009
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Recent years have seen the rapid advancement of new therapeutic agents against hepatitis C virus (HCV) in response to the need for treatment that is unmet by interferon (IFN)-based therapies. Most antiviral drugs discovered to date are small molecules that modulate viral enzyme activities. In the search for highly selective protein-binding molecules capable of disrupting the viral life cycle, we have identified a class of anionic tetraphenylporphyrins as potent and specific inhibitors of the HCV replicons. Based on the structure-activity relationship studies reported herein, meso-tetrakis-(3,5-dicarboxy-4,4-biphenyl) porphyrin was found to be the most potent inhibitor of HCV genotype 1b (Con1) replicon systems but was less effective against the genotype 2a (JFH-1) replicon. This compound induced a reduction of viral RNA and protein levels when acting in the low nanomolar range. Moreover, the compound could suppress replicon rebound in drug-treated cells and exhibited additive to synergistic effects when combined with protease inhibitor BILN 2061 or with IFN-alpha-2a. Our results demonstrate the potential use of tetracarboxyphenylporphyrins as potent anti-HCV agents.
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Design and evaluation of nonfluorous CO2-soluble oligomers and polymers.
J Phys Chem B
PUBLISHED: 10-23-2009
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Ab initio molecular modeling is used to design nonfluorous polymers that are potentially soluble in liquid CO2. We have used calculations to design three nonfluorous compounds meant to model the monomeric repeat units of polymers that exhibit multiple favorable binding sites for CO2. These compounds are methoxy isopropyl acetate, 2-methoxy ethoxy-propane, and 2-methoxy methoxy-propane. We have synthesized oligomers or polymers based on these small compounds and have tested their solubility in CO2. All three of these exhibit appreciable solubility in CO2. At 25 degrees C, oligo(3-acetoxy oxetane)6 is 5 wt % soluble at 25 MPa, the random copolymer (vinyl methoxymethyl ether30-co-vinyl acetate9) is 5 wt % soluble at 70 MPa and random copolymer (vinyl 1-methoxyethyl ether30-co-vinyl acetate9) is 3 wt % soluble at 120 MPa. These oligomers and polymers represent new additions to the very short list of nonfluorous CO2-soluble polymers. However, none of these are more soluble than poly(vinyl acetate), which exhibits the highest CO2 solubility of any known polymer containing only the elements C, H, and O.
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Cocoa Pod Borer (Conopomorpha cramerella Snellen) in Papua New Guinea: biosecurity models for New Ireland and the autonomous region of Bougainville.
Risk Anal.
PUBLISHED: 09-17-2009
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Cocoa Pod Borer (Conopomorpha cramerella Snellen) (CPB) is an important pest of cocoa. Following its emergence as a pest in East New Britain, Papua New Guinea, in 2006, it was considered relevant to assess its potential spread to other cocoa growing regions. Its likelihood of introduction to the islands of Bougainville and New Ireland from East New Britain Province, Papua New Guinea, was modeled using Monte Carlo simulation. This dispersal model was based around different scenarios, identifying trends rather than explicitly attempting to encapsulate true values. The model suggested that CPB is far more likely to establish on New Ireland than on Bougainville. More important, incertitude resulting from incomplete knowledge of the amount and frequency of cocoa transported between islands had a significant effect on model outputs. Quarantine and agriculture officials will be able to refine these parameter values, and then use the relevant scenarios from those presented here as a guide to develop quarantine procedures. In addition, a contingency model was employed to estimate the optimal sampling effort to use following an incursion of CPB into Bougainville or New Ireland and the seemingly successful implementation of an initial eradication program. The model suggests that at a 1% infestation level, sampling should continue for 2.5-2.7 years (90% CI) after claiming eradication, and this estimate changed little for higher infestation levels. Through modeling variations in sampling intensity, the model also suggested that determining the full spread of CPB is more important than increased sampling within one region.
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Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats.
Chemistry
PUBLISHED: 09-12-2009
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Isoguanine (2-oxo-6-amino-guanine), a natural but non-standard base, exhibits unique self-association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. The guanine-containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI-MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads.
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Novel 7-(dimethylamino)fluorene-based fluorescent probes and their binding to human serum albumin.
Org. Biomol. Chem.
PUBLISHED: 08-14-2009
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A novel solvatochromic fluorescent molecule, 9,9-dibutyl-7-(dimethylamino)-2-fluorenesulfonate 2 was synthesized from 2-nitrofluorene in moderate yield. The fluorescence spectra of 2 and 7-(dimethylamino)-2-fluorenesulfonate 1 shift to shorter wavelengths as the polarity of the medium decreases. Both 1 and 2 bind to hydrophobic sites of human serum albumin (HSA). The apparent binding constants were determined by fluorescence titration to be 0.37 x 10(6) M(-1) for 1 and 2.2 x 10(6) M(-1) for 2. The energy of the Trp-214 fluorescence of HSA is transferred to the HSA-bound fluorophores with near 100% efficiency. The covalent bonding of acrylodan (AC) to Cys-34 has little effect on the binding affinity of 2 to HSA or fluorescent behavior of HSA-bound 2. Bound 2 also has little effect on the fluorescence of AC, but 2-->AC and Trp-214-->2-->AC resonance energy transfers were observed. Competitive binding between the fluorene compounds and other ligands such as 1-anilino-8-naphthalenesulfonate, aspirin, S-(+)-ibuprofen and phenylbutazone were also studied fluorometrically. The results indicated that the primary binding site of 2 to HSA is site II in domain IIIA, whereas 1 binds to site I in domain IIA, but a different region from the phenylbutazone binding site. Because of its large molar absorptivity, strong fluorescence, sensitivity to its environment, and high binding constant to HSA, 2 can be used successfully in the study of proteins and their binding properties.
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Digital analysis of protein properties by an ensemble of DNA quadruplexes.
J. Am. Chem. Soc.
PUBLISHED: 07-02-2009
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Here we show how different principles developed in the area of molecular logic gates can be applied to diagnostic technologies for proteins. Simultaneous operation of YES NOT and PASS 1 logic gates, produced by a protein sensing ensemble of DNA G-quadruplexes, is used to encode concentration levels of medicinally important proteins. An AND logic gate is another example, where molecular computation can be used to follow the interaction between proteins and metal ions. Combination of molecular Boolean logic with combinatorial sensing is demonstrated as a general strategy to realizing small scale, real time diagnosis of a variety of protein samples.
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Structurally simple inhibitors of lanosterol 14alpha-demethylase are efficacious in a rodent model of acute Chagas disease.
J. Med. Chem.
PUBLISHED: 05-26-2009
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We report structure-activity studies of a large number of dialkyl imidazoles as inhibitors of Trypanosoma cruzi lanosterol-14alpha-demethylase (L14DM). The compounds have a simple structure compared to posaconazole, another L14DM inhibitor that is an anti-Chagas drug candidate. Several compounds display potency for killing T. cruzi amastigotes in vitro with values of EC(50) in the 0.4-10 nM range. Two compounds were selected for efficacy studies in a mouse model of acute Chagas disease. At oral doses of 20-50 mg/kg given after establishment of parasite infection, the compounds reduced parasitemia in the blood to undetectable levels, and analysis of remaining parasites by PCR revealed a lack of parasites in the majority of animals. These dialkyl imidazoles are substantially less expensive to produce than posaconazole and are appropriate for further development toward an anti-Chagas disease clinical candidate.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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