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Find video protocols related to scientific articles indexed in Pubmed.
Spatial variability and temporal trends in water-use efficiency of European forests.
Glob Chang Biol
PUBLISHED: 09-22-2014
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The increasing carbon dioxide (CO2 ) concentration in the atmosphere in combination with climatic changes throughout the last century are likely to have had a profound effect on the physiology of trees: altering the carbon and water fluxes passing through the stomatal pores. However, the magnitude and spatial patterns of such changes in natural forests remain highly uncertain. Here, stable carbon isotope ratios from a network of 35 tree-ring sites located across Europe are investigated to determine the intrinsic water-use efficiency (iWUE), the ratio of photosynthesis to stomatal conductance from 1901 to 2000. The results were compared with simulations of a dynamic vegetation model (LPX-Bern 1.0) that integrates numerous ecosystem and land-atmosphere exchange processes in a theoretical framework. The spatial pattern of tree-ring derived iWUE of the investigated coniferous and deciduous species and the model results agreed significantly with a clear south-to-north gradient, as well as a general increase in iWUE over the 20th century. The magnitude of the iWUE increase was not spatially uniform, with the strongest increase observed and modelled for temperate forests in Central Europe, a region where summer soil-water availability decreased over the last century. We were able to demonstrate that the combined effects of increasing CO2 and climate change leading to soil drying have resulted in an accelerated increase in iWUE. These findings will help to reduce uncertainties in the land surface schemes of global climate models, where vegetation-climate feedbacks are currently still poorly constrained by observational data.
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Climate change. Six centuries of variability and extremes in a coupled marine-terrestrial ecosystem.
Science
PUBLISHED: 09-20-2014
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Reported trends in the mean and variability of coastal upwelling in eastern boundary currents have raised concerns about the future of these highly productive and biodiverse marine ecosystems. However, the instrumental records on which these estimates are based are insufficiently long to determine whether such trends exceed preindustrial limits. In the California Current, a 576-year reconstruction of climate variables associated with winter upwelling indicates that variability increased over the latter 20th century to levels equaled only twice during the past 600 years. This modern trend in variance may be unique, because it appears to be driven by an unprecedented succession of extreme, downwelling-favorable, winter climate conditions that profoundly reduce productivity for marine predators of commercial and conservation interest.
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Toward high-performance digital logic technology with carbon nanotubes.
ACS Nano
PUBLISHED: 09-05-2014
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The slow-down in traditional silicon complementary metal-oxide-semiconductor (CMOS) scaling (Moore's law) has created an opportunity for a disruptive innovation to bring the semiconductor industry into a postsilicon era. Due to their ultrathin body and ballistic transport, carbon nanotubes (CNTs) have the intrinsic transport and scaling properties to usher in this new era. The remaining challenges are largely materials-related and include obtaining purity levels suitable for logic technology, placement of CNTs at very tight (?5 nm) pitch to allow for density scaling and source/drain contact scaling. This review examines the potential performance advantages of a CNT-based computing technology, outlines the remaining challenges, and describes the recent progress on these fronts. Although overcoming these issues will be challenging and will require a large, sustained effort from both industry and academia, the recent progress in the field is a cause for optimism that these materials can have an impact on future technologies.
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Human thalamic and amygdala modulation in emotional scene perception.
Brain Res.
PUBLISHED: 08-27-2014
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Emotional scene perception is associated with enhanced activity in ventral occipitotemporal cortex and amygdala. While a growing body of research supports the perspective that emotional perception is organized via amygdala feedback to rostral ventral visual cortex, the contributions of high-order thalamic structures strongly associated with visual attention, specifically the mediodorsal nucleus and pulvinar, have not been well investigated. Here we sample the activity of amygdala, MDN, pulvinar, and extrastriate ventral visual regions with fMRI as a group of participants view a mixed series of pleasant, neutral, and unpleasant natural scenes, balanced for basic perceptual characteristics. The results demonstrate that all regions showed enhanced activity during emotionally arousing relative to neutral scene perception. Consistent with recent research, the latency of emotional discrimination across subcortical and visual cortical regions suggests a role for the amygdala in the early evaluation of scene emotion. These data support the perspective that higher order visual thalamic structures are sensitive to the emotional value of complex scene stimuli, and may serve in concert with amygdala and fusiform gyrus to modulate visual attention toward motivationally relevant cues.
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Interstellar dust. Evidence for interstellar origin of seven dust particles collected by the Stardust spacecraft.
Science
PUBLISHED: 08-16-2014
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Seven particles captured by the Stardust Interstellar Dust Collector and returned to Earth for laboratory analysis have features consistent with an origin in the contemporary interstellar dust stream. More than 50 spacecraft debris particles were also identified. The interstellar dust candidates are readily distinguished from debris impacts on the basis of elemental composition and/or impact trajectory. The seven candidate interstellar particles are diverse in elemental composition, crystal structure, and size. The presence of crystalline grains and multiple iron-bearing phases, including sulfide, in some particles indicates that individual interstellar particles diverge from any one representative model of interstellar dust inferred from astronomical observations and theory.
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A tree-ring perspective on the terrestrial carbon cycle.
Oecologia
PUBLISHED: 08-14-2014
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Tree-ring records can provide valuable information to advance our understanding of contemporary terrestrial carbon cycling and to reconstruct key metrics in the decades preceding monitoring data. The growing use of tree rings in carbon-cycle research is being facilitated by increasing recognition of reciprocal benefits among research communities. Yet, basic questions persist regarding what tree rings represent at the ecosystem level, how to optimally integrate them with other data streams, and what related challenges need to be overcome. It is also apparent that considerable unexplored potential exists for tree rings to refine assessments of terrestrial carbon cycling across a range of temporal and spatial domains. Here, we summarize recent advances and highlight promising paths of investigation with respect to (1) growth phenology, (2) forest productivity trends and variability, (3) CO2 fertilization and water-use efficiency, (4) forest disturbances, and (5) comparisons between observational and computational forest productivity estimates. We encourage the integration of tree-ring data: with eddy-covariance measurements to investigate carbon allocation patterns and water-use efficiency; with remotely sensed observations to distinguish the timing of cambial growth and leaf phenology; and with forest inventories to develop continuous, annually-resolved and long-term carbon budgets. In addition, we note the potential of tree-ring records and derivatives thereof to help evaluate the performance of earth system models regarding the simulated magnitude and dynamics of forest carbon uptake, and inform these models about growth responses to (non-)climatic drivers. Such efforts are expected to improve our understanding of forest carbon cycling and place current developments into a long-term perspective.
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High risk and little knowledge: Overdose experiences and knowledge among young adult nonmedical prescription opioid users.
Int. J. Drug Policy
PUBLISHED: 07-31-2014
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Opioid-involved overdoses in the United States have dramatically increased in the last 15 years, largely due to a rise in prescription opioid (PO) use. Yet few studies have examined the overdose knowledge and experience of nonmedical PO users.
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Coupling gas chromatography and electronic nose detection for detailed cigarette smoke aroma characterization.
J Chromatogr A
PUBLISHED: 07-07-2014
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Aroma characterization of whole cigarette smoke samples using sensory panels or electronic nose (E-nose) devices is difficult due to the masking effect of major constituents and solvent used for the extraction step. On the other hand, GC in combination with olfactometry detection does not allow to study the delicate balance and synergetic effect of aroma solutes. To overcome these limitations a new instrumental set-up consisting of heart-cutting gas chromatography using a capillary flow technology based Deans switch and low thermal mass GC in combination with an electronic nose device is presented as an alternative to GC-olfactometry. This new hyphenated GC-E-nose configuration is used for the characterization of cigarette smoke aroma. The system allows the transfer, combination or omission of selected GC fractions before injection in the E-nose. Principal component analysis (PCA) and discriminant factor analysis (DFA) allowed clear visualizing of the differences among cigarette brands and classifying them independently of their nicotine content. Omission and perceptual interaction tests could also be carried out using this configuration. The results are promising and suggest that the GC-E-nose hyphenation is a good approach to measure the contribution level of individual compounds to the whole cigarette smoke.
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Contribution of semi-arid ecosystems to interannual variability of the global carbon cycle.
Nature
PUBLISHED: 04-10-2014
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The land and ocean act as a sink for fossil-fuel emissions, thereby slowing the rise of atmospheric carbon dioxide concentrations. Although the uptake of carbon by oceanic and terrestrial processes has kept pace with accelerating carbon dioxide emissions until now, atmospheric carbon dioxide concentrations exhibit a large variability on interannual timescales, considered to be driven primarily by terrestrial ecosystem processes dominated by tropical rainforests. We use a terrestrial biogeochemical model, atmospheric carbon dioxide inversion and global carbon budget accounting methods to investigate the evolution of the terrestrial carbon sink over the past 30 years, with a focus on the underlying mechanisms responsible for the exceptionally large land carbon sink reported in 2011 (ref. 2). Here we show that our three terrestrial carbon sink estimates are in good agreement and support the finding of a 2011 record land carbon sink. Surprisingly, we find that the global carbon sink anomaly was driven by growth of semi-arid vegetation in the Southern Hemisphere, with almost 60 per cent of carbon uptake attributed to Australian ecosystems, where prevalent La Niña conditions caused up to six consecutive seasons of increased precipitation. In addition, since 1981, a six per cent expansion of vegetation cover over Australia was associated with a fourfold increase in the sensitivity of continental net carbon uptake to precipitation. Our findings suggest that the higher turnover rates of carbon pools in semi-arid biomes are an increasingly important driver of global carbon cycle inter-annual variability and that tropical rainforests may become less relevant drivers in the future. More research is needed to identify to what extent the carbon stocks accumulated during wet years are vulnerable to rapid decomposition or loss through fire in subsequent years.
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Kinetics of tracheid development explain conifer tree-ring structure.
New Phytol.
PUBLISHED: 03-31-2014
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Conifer tree rings are generally composed of large, thin-walled cells of light earlywood followed by narrow, thick-walled cells of dense latewood. Yet, how wood formation processes and the associated kinetics create this typical pattern remains poorly understood. We monitored tree-ring formation weekly over 3 yr in 45 trees of three conifer species in France. Data were used to model cell development kinetics, and to attribute the relative importance of the duration and rate of cell enlargement and cell wall deposition on tree-ring structure. Cell enlargement duration contributed to 75% of changes in cell diameter along the tree rings. Remarkably, the amount of wall material per cell was quite constant along the rings. Consequently, and in contrast with widespread belief, changes in cell wall thickness were not principally attributed to the duration and rate of wall deposition (33%), but rather to the changes in cell size (67%). Cell enlargement duration, as the main driver of cell size and wall thickness, contributed to 56% of wood density variation along the rings. This mechanistic framework now forms the basis for unraveling how environmental stresses trigger deviations (e.g. false rings) from the normal tree-ring structure.
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Multidimensional gas chromatography in combination with accurate mass, tandem mass spectrometry, and element-specific detection for identification of sulfur compounds in tobacco smoke.
J Chromatogr A
PUBLISHED: 03-18-2014
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A method is developed for identification of sulfur compounds in tobacco smoke extract. The method is based on large volume injection (LVI) of 10?L of tobacco smoke extract followed by selectable one-dimensional ((1)D) or two-dimensional ((2)D) gas chromatography (GC) coupled to a hybrid quadrupole time-of-flight mass spectrometer (Q-TOF-MS) using electron ionization (EI) and positive chemical ionization (PCI), with parallel sulfur chemiluminescence detection (SCD). In order to identify each individual sulfur compound, sequential heart-cuts of 28 sulfur fractions from (1)D GC to (2)D GC were performed with the three MS detection modes (SCD/EI-TOF-MS, SCD/PCI-TOF-MS, and SCD/PCI-Q-TOF-MS). Thirty sulfur compounds were positively identified by MS library search, linear retention indices (LRI), molecular mass determination using PCI accurate mass spectra, formula calculation using EI and PCI accurate mass spectra, and structure elucidation using collision activated dissociation (CAD) of the protonated molecule. Additionally, 11 molecular formulas were obtained for unknown sulfur compounds. The determined values of the identified and unknown sulfur compounds were in the range of 10-740ngmg total particulate matter (TPM) (RSD: 1.2-12%, n=3).
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The influence of sampling design on tree-ring-based quantification of forest growth.
Glob Chang Biol
PUBLISHED: 03-05-2014
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Tree-rings offer one of the few possibilities to empirically quantify and reconstruct forest growth dynamics over years to millennia. Contemporaneously with the growing scientific community employing tree-ring parameters, recent research has suggested that commonly applied sampling designs (i.e. how and which trees are selected for dendrochronological sampling) may introduce considerable biases in quantifications of forest responses to environmental change. To date, a systematic assessment of the consequences of sampling design on dendroecological and-climatological conclusions has not yet been performed. Here, we investigate potential biases by sampling a large population of trees and replicating diverse sampling designs. This is achieved by retroactively subsetting the population and specifically testing for biases emerging for climate reconstruction, growth response to climate variability, long-term growth trends, and quantification of forest productivity. We find that commonly applied sampling designs can impart systematic biases of varying magnitude to any type of tree-ring-based investigations, independent of the total number of samples considered. Quantifications of forest growth and productivity are particularly susceptible to biases, whereas growth responses to short-term climate variability are less affected by the choice of sampling design. The world's most frequently applied sampling design, focusing on dominant trees only, can bias absolute growth rates by up to 459% and trends in excess of 200%. Our findings challenge paradigms, where a subset of samples is typically considered to be representative for the entire population. The only two sampling strategies meeting the requirements for all types of investigations are the (i) sampling of all individuals within a fixed area; and (ii) fully randomized selection of trees. This result advertises the consistent implementation of a widely applicable sampling design to simultaneously reduce uncertainties in tree-ring-based quantifications of forest growth and increase the comparability of datasets beyond individual studies, investigators, laboratories, and geographical boundaries.
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Reduced Medial Prefrontal-Subcortical Connectivity in Dysphoria: Granger Causality Analyses of Rapid Functional Magnetic Resonance Imaging.
Brain Connect
PUBLISHED: 03-01-2014
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Abstract A cortico-limbic network consisting of the amygdala, medial prefrontal cortex (mPFC), and ventral striatum (vSTR) has been associated with altered function in emotional disorders. Here we used rapidly sampled functional magnetic resonance imaging and Granger causality analyses to assess the directional connectivity between these brain structures in a sample of healthy and age-matched participants endorsing moderate to severe depressive symptomatology as they viewed a series of natural scene stimuli varying systematically in pleasantness and arousal. Specifically during pleasant scene perception, dysphoric participants showed reduced activity in mPFC and vSTR, relative to healthy participants. In contrast, amygdala activity was enhanced to pleasant as well as unpleasant arousing scenes in both participant groups. Granger causality estimates of influence between mPFC and vSTR were significantly reduced in dysphoric relative to control participants during all picture contents. These findings provide direct evidence that during visual perception of evocative emotional stimuli, reduced reward-related activity in dysphoria is associated with dysfunctional causal connectivity between mPFC, amygdala, and vSTR.
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Utility of electrocardiogram in the assessment and monitoring of pulmonary hypertension (idiopathic or secondary to pulmonary developmental abnormalities) in patients?18 years of age.
Am. J. Cardiol.
PUBLISHED: 02-27-2014
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Electrocardiograms have utility in disease stratification and monitoring in adult pulmonary arterial hypertension (PAH). We examined the electrocardiographic findings that are common in pediatric PAH and assessed for correlation with disease severity and progression. We retrospectively identified patients aged?18 years followed at a single institution from January 2001 to June 2012 with catheterization-confirmed diagnosis of idiopathic PAH and PAH secondary to pulmonary developmental abnormalities. Patients with an electrocardiography performed within 60 days of catheterization were included. Primary and secondary outcomes are the prevalence of abnormal electrocardiographic findings at the time of catheterization and the association between electrocardiographic and hemodynamic findings and electrocardiographic changes with disease progression on follow-up catheterization, respectively. Of the 100 electrocardiography-catheterization pairs derived from the 46 patients identified, 93% had an electrocardiographic abnormality: 78% had right ventricular hypertrophy (RVH) and 52% had right axis deviation (RAD) for age. In patients with idiopathic PAH, the presence of RVH and RAD correlated with pulmonary vascular resistance and transpulmonary gradient. RAD and RVH on baseline electrocardiogram was associated with an increased risk of disease progression on subsequent catheterization (odds ratio 11.0, 95% confidence interval 1.3 to 96.2, p=0.03) after adjusting for PAH subgroup. The sensitivity, specificity, and positive and negative predictive values of RAD and RVH on baseline electrocardiogram for disease progression were 92%, 48%, 33%, and 95%, respectively. In conclusion, electrocardiographic abnormalities are common in pediatric PAH. RAD and RVH on electrocardiogram were associated with worse hemodynamics, whereas their absence is suggestive of a lack of disease progression.
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STAT3 induction of miR-146b forms a feedback loop to inhibit the NF-?B to IL-6 signaling axis and STAT3-driven cancer phenotypes.
Sci Signal
PUBLISHED: 01-30-2014
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Interleukin-6 (IL-6)-mediated activation of signal transducer and activator of transcription 3 (STAT3) is a mechanism by which chronic inflammation can contribute to cancer and is a common oncogenic event. We discovered a pathway, the loss of which is associated with persistent STAT3 activation in human cancer. We found that the gene encoding the tumor suppressor microRNA miR-146b is a direct STAT3 target gene, and its expression was increased in normal breast epithelial cells but decreased in tumor cells. Methylation of the miR-146b promoter, which inhibited STAT3-mediated induction of expression, was increased in primary breast cancers. Moreover, we found that miR-146b inhibited nuclear factor ?B (NF-?B)-dependent production of IL-6, subsequent STAT3 activation, and IL-6/STAT3-driven migration and invasion in breast cancer cells, thereby establishing a negative feedback loop. In addition, higher expression of miR-146b was positively correlated with patient survival in breast cancer subtypes with increased IL6 expression and STAT3 phosphorylation. Our results identify an epigenetic mechanism of crosstalk between STAT3 and NF-?B relevant to constitutive STAT3 activation in malignancy and the role of inflammation in oncogenesis.
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STAT3 Activity and Function in Cancer: Modulation by STAT5 and miR-146b.
Cancers (Basel)
PUBLISHED: 01-24-2014
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The transcription factor STAT3 regulates genes that control critical cellular processes such as proliferation, survival, pluripotency, and motility. Thus, under physiological conditions, the transcriptional function of STAT3 is tightly regulated as one part of a complex signaling matrix. When these processes are subverted through mutation or epigenetic events, STAT3 becomes highly active and drives elevated expression of genes underlying these phenotypes, leading to malignant cellular behavior. However, even in the presence of activated STAT3, other cellular modulators can have a major impact on the biological properties of a cancer cell, which is reflected in the clinical behavior of a tumor. Recent evidence has suggested that two such key modulators are the activation status of other STAT family members, particularly STAT5, and the expression of STAT3-regulated genes that are part of negative feedback circuits, including microRNAs such as miR-146b. With attention to these newly emerging areas, we will gain greater insight into the consequence of STAT3 activation in the biology of human cancers. In addition, understanding these subtleties of STAT3 signaling in cancer pathogenesis will allow the development of more rational molecular approaches to cancer therapy.
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Fold change of nuclear NF-?B determines TNF-induced transcription in single cells.
Mol. Cell
PUBLISHED: 01-24-2014
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In response to tumor necrosis factor (TNF), NF-?B enters the nucleus and promotes inflammatory and stress-responsive gene transcription. Because NF-?B deregulation is associated with disease, one might expect strict control of NF-?B localization. However, nuclear NF-?B levels exhibit considerable cell-to-cell variability, even in unstimulated cells. To resolve this paradox and determine how transcription-inducing signals are encoded, we quantified single-cell NF-?B translocation dynamics and transcription in the same cells. We show that TNF-induced transcription correlates best with fold change in nuclear NF-?B, not absolute nuclear NF-?B abundance. Using computational modeling, we find that an incoherent feedforward loop, from competition for binding to ?B motifs, could provide memory of the preligand state necessary for fold-change detection. Experimentally, we observed three gene-specific transcriptional patterns that our model recapitulates by modulating competition strength alone. Fold-change detection buffers against stochastic variation in signaling molecules and explains how cells tolerate variability in NF-?B abundance and localization.
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Targeting STAT5 in hematologic malignancies through inhibition of the bromodomain and extra-terminal (BET) bromodomain protein BRD2.
Mol. Cancer Ther.
PUBLISHED: 01-16-2014
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The transcription factor signal STAT5 is constitutively activated in a wide range of leukemias and lymphomas, and drives the expression of genes necessary for proliferation, survival, and self-renewal. Thus, targeting STAT5 is an appealing therapeutic strategy for hematologic malignancies. Given the importance of bromodomain-containing proteins in transcriptional regulation, we considered the hypothesis that a pharmacologic bromodomain inhibitor could inhibit STAT5-dependent gene expression. We found that the small-molecule bromodomain and extra-terminal (BET) bromodomain inhibitor JQ1 decreases STAT5-dependent (but not STAT3-dependent) transcription of both heterologous reporter genes and endogenous STAT5 target genes. JQ1 reduces STAT5 function in leukemia and lymphoma cells with constitutive STAT5 activation, or inducibly activated by cytokine stimulation. Among the BET bromodomain subfamily of proteins, it seems that BRD2 is the critical mediator for STAT5 activity. In experimental models of acute T-cell lymphoblastic leukemias, where activated STAT5 contributes to leukemia cell survival, Brd2 knockdown or JQ1 treatment shows strong synergy with tyrosine kinase inhibitors (TKI) in inducing apoptosis in leukemia cells. In contrast, mononuclear cells isolated form umbilical cord blood, which is enriched in normal hematopoietic precursor cells, were unaffected by these combinations. These findings indicate a unique functional association between BRD2 and STAT5, and suggest that combinations of JQ1 and TKIs may be an important rational strategy for treating leukemias and lymphomas driven by constitutive STAT5 activation.
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Seasonal transfer of oxygen isotopes from precipitation and soil to the tree ring: source water versus needle water enrichment.
New Phytol.
PUBLISHED: 01-08-2014
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For accurate interpretation of oxygen isotopes in tree rings (?(18) O), it is necessary to disentangle the mechanisms underlying the variations in the tree's internal water cycle and to understand the transfer of source versus leaf water ?(18) O to phloem sugars and stem wood. We studied the seasonal transfer of oxygen isotopes from precipitation and soil water through the xylem, needles and phloem to the tree rings of Larix decidua at two alpine sites in the Lötschental (Switzerland). Weekly resolved ?(18) O records of precipitation, soil water, xylem and needle water, phloem organic matter and tree rings were developed. Week-to-week variations in needle-water (18) O enrichment were strongly controlled by weather conditions during the growing season. These short-term variations were, however, not significantly fingerprinted in tree-ring ?(18) O. Instead, seasonal trends in tree-ring ?(18) O predominantly mirrored trends in the source water, including recent precipitation and soil water pools. Modelling results support these findings: seasonal tree-ring ?(18) O variations are captured best when the week-to-week variations of the leaf water signal are suppressed. Our results suggest that climate signals in tree-ring ?(18) O variations should be strongest at temperate sites with humid conditions and precipitation maxima during the growing season.
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A meta-analysis of cambium phenology and growth: linear and non-linear patterns in conifers of the northern hemisphere.
Ann. Bot.
PUBLISHED: 11-07-2013
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Background and Aims Ongoing global warming has been implicated in shifting phenological patterns such as the timing and duration of the growing season across a wide variety of ecosystems. Linear models are routinely used to extrapolate these observed shifts in phenology into the future and to estimate changes in associated ecosystem properties such as net primary productivity. Yet, in nature, linear relationships may be special cases. Biological processes frequently follow more complex, non-linear patterns according to limiting factors that generate shifts and discontinuities, or contain thresholds beyond which responses change abruptly. This study investigates to what extent cambium phenology is associated with xylem growth and differentiation across conifer species of the northern hemisphere. Methods Xylem cell production is compared with the periods of cambial activity and cell differentiation assessed on a weekly time scale on histological sections of cambium and wood tissue collected from the stems of nine species in Canada and Europe over 1-9 years per site from 1998 to 2011. Key Results The dynamics of xylogenesis were surprisingly homogeneous among conifer species, although dispersions from the average were obviously observed. Within the range analysed, the relationships between the phenological timings were linear, with several slopes showing values close to or not statistically different from 1. The relationships between the phenological timings and cell production were distinctly non-linear, and involved an exponential pattern Conclusions The trees adjust their phenological timings according to linear patterns. Thus, shifts of one phenological phase are associated with synchronous and comparable shifts of the successive phases. However, small increases in the duration of xylogenesis could correspond to a substantial increase in cell production. The findings suggest that the length of the growing season and the resulting amount of growth could respond differently to changes in environmental conditions.
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A bioinformatics approach identifies signal transducer and activator of transcription-3 and checkpoint kinase 1 as upstream regulators of kidney injury molecule-1 after kidney injury.
J. Am. Soc. Nephrol.
PUBLISHED: 10-24-2013
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Kidney injury molecule-1 (KIM-1)/T cell Ig and mucin domain-containing protein-1 (TIM-1) is upregulated more than other proteins after AKI, and it is highly expressed in renal damage of various etiologies. In this capacity, KIM-1/TIM-1 acts as a phosphatidylserine receptor on the surface of injured proximal tubular epithelial cells, mediating phagocytosis of apoptotic cells, and it may also act as a costimulatory molecule for immune cells. Despite recognition of KIM-1 as an important therapeutic target for kidney disease, the regulators of KIM-1 transcription in the kidney remain unknown. Using a bioinformatics approach, we identified upstream regulators of KIM-1 after AKI. In response to tubular injury in rat and human kidneys or oxidant stress in human proximal tubular epithelial cells (HPTECs), KIM-1 expression increased significantly in a manner that corresponded temporally and regionally with increased phosphorylation of checkpoint kinase 1 (Chk1) and STAT3. Both ischemic and oxidant stress resulted in a dramatic increase in reactive oxygen species that phosphorylated and activated Chk1, which subsequently bound to STAT3, phosphorylating it at S727. Furthermore, STAT3 bound to the KIM-1 promoter after ischemic and oxidant stress, and pharmacological or genetic induction of STAT3 in HPTECs increased KIM-1 mRNA and protein levels. Conversely, inhibition of STAT3 using siRNAs or dominant negative mutants reduced KIM-1 expression in a kidney cancer cell line (769-P) that expresses high basal levels of KIM-1. These observations highlight Chk1 and STAT3 as critical upstream regulators of KIM-1 expression after AKI and may suggest novel approaches for therapeutic intervention.
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Intra-annual dynamics of non-structural carbohydrates in the cambium of mature conifer trees reflects radial growth demands.
Tree Physiol.
PUBLISHED: 10-17-2013
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The presence of soluble carbohydrates in the cambial zone, either from sugars recently produced during photosynthesis or from starch remobilized from storage organs, is necessary for radial tree growth. However, considerable uncertainties on carbohydrate dynamics and the consequences on tree productivity exist. This study aims to better understand the variation in different carbon pools at intra-annual resolution by quantifying how cambial zone sugar and starch concentrations fluctuate over the season and in relation to cambial phenology. A comparison between two physiologically different species growing at the same site, i.e., the evergreen Picea abies Karst. and the deciduous Larix decidua Mill., and between L. decidua from two contrasting elevations, is presented to identify mechanisms of growth limitation. Results indicate that the annual cycle of sugar concentration within the cambial zone is coupled to the process of wood formation. The highest sugar concentration is observed when the number of cells in secondary wall formation and lignification stages is at a maximum, subsequent to most radial growth. Starch disappears in winter, while other freeze-resistant non-structural carbohydrates (NSCs) increase. Slight differences in NSC concentration between species are consistent with the differing climate sensitivity of the evergreen and deciduous species investigated. The general absence of differences between elevations suggests that the cambial activity of trees growing at the treeline was not limited by the availability of carbohydrates at the cambial zone but instead by environmental controls on the growing season duration.
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Biodiversity, conservation biology, and rational choice.
Stud Hist Philos Biol Biomed Sci
PUBLISHED: 10-13-2013
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This paper critically discusses two areas of Sahotra Sarkars recent work in environmental philosophy: biodiversity and conservation biology and roles for decision theory in incorporating values explicitly in the environmental policy process. I argue that Sarkars emphasis on the practices of conservation biologists, and especially the role of social and cultural values in the choice of biodiversity constituents, restricts his conception of biodiversity to particular practical conservation contexts. I argue that life scientists have many reasons to measure many types of diversity, and that biodiversity metrics could be value-free. I argue that Sarkars emphasis on the limitations of normative decision theory is in tension with his statement that decision theory can "put science and ethics together." I also challenge his claim that multi-criteria decision tools lacking axiomatic foundations in preference and utility theory are "without a rational basis," by presenting a case of a simple "outranking" multi-criteria decision rule that can violate a basic normative requirement of preferences (transitivity) and ask whether there may nevertheless be contexts in which such a procedure might assist decision makers.
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Targeting transcription factors: promising new strategies for cancer therapy.
Curr Opin Oncol
PUBLISHED: 09-20-2013
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A lack of effective treatments for advanced cancer remains a major challenge in oncology. Because cancer is a disease associated with aberrant gene expression patterns, transcription factors, which serve as the convergence points of oncogenic signaling and are functionally altered in many cancers, hold great therapeutic promise.
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Switching of ferroelectric polarization in epitaxial BaTiO? films on silicon without a conducting bottom electrode.
Nat Nanotechnol
PUBLISHED: 08-27-2013
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Epitaxial growth of SrTiO? on silicon by molecular beam epitaxy has opened up the route to the integration of functional complex oxides on a silicon platform. Chief among them is ferroelectric functionality using perovskite oxides such as BaTiO?. However, it has remained a challenge to achieve ferroelectricity in epitaxial BaTiO? films with a polarization pointing perpendicular to the silicon substrate without a conducting bottom electrode. Here, we demonstrate ferroelectricity in such stacks. Synchrotron X-ray diffraction and high-resolution scanning transmission electron microscopy reveal the presence of crystalline domains with the long axis of the tetragonal structure oriented perpendicular to the substrate. Using piezoforce microscopy, polar domains can be written and read and are reversibly switched with a phase change of 180°. Open, saturated hysteresis loops are recorded. Thus, ferroelectric switching of 8- to 40-nm-thick BaTiO? films in metal-ferroelectric-semiconductor structures is realized, and field-effect devices using this epitaxial oxide stack can be envisaged.
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Above-ground woody carbon sequestration measured from tree rings is coherent with net ecosystem productivity at five eddy-covariance sites.
New Phytol.
PUBLISHED: 08-11-2013
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Attempts to combine biometric and eddy-covariance (EC) quantifications of carbon allocation to different storage pools in forests have been inconsistent and variably successful in the past. We assessed above-ground biomass changes at five long-term EC forest stations based on tree-ring width and wood density measurements, together with multiple allometric models. Measurements were validated with site-specific biomass estimates and compared with the sum of monthly CO2 fluxes between 1997 and 2009. Biometric measurements and seasonal net ecosystem productivity (NEP) proved largely compatible and suggested that carbon sequestered between January and July is mainly used for volume increase, whereas that taken up between August and September supports a combination of cell wall thickening and storage. The inter-annual variability in above-ground woody carbon uptake was significantly linked with wood production at the sites, ranging between 110 and 370 g C m(-2)  yr(-1) , thereby accounting for 10-25% of gross primary productivity (GPP), 15-32% of terrestrial ecosystem respiration (TER) and 25-80% of NEP. The observed seasonal partitioning of carbon used to support different wood formation processes refines our knowledge on the dynamics and magnitude of carbon allocation in forests across the major European climatic zones. It may thus contribute, for example, to improved vegetation model parameterization and provides an enhanced framework to link tree-ring parameters with EC measurements.
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Multi-stir bar sorptive extraction for analysis of odor compounds in aqueous samples.
J Chromatogr A
PUBLISHED: 07-24-2013
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As reproducible coating of stir bars with more polar phases was found to be very difficult, a supporting grid was used in the development of an ethyleneglycol-modified Silicone (EG Silicone) coated stir bar. This new polar coating showed good performance for the extraction of polar solutes, but long term use also showed degradation of the coating due to friction while stirring. In order to address the lower robustness of the EG Silicone stir bar which has a much softer coating compared to a conventional polydimethylsiloxane (PDMS) stir bar, a novel SBSE procedure termed multi-SBSE ((m)SBSE) was developed. (m)SBSE consists of the robust PDMS stir bar stirring at the bottom of the vial and the EG Silicone stir bar attached on the inner side wall of the vial (a magnetic clip is used for the set-up). After extraction, the two stir bars are placed in a single glass desorption liner and are simultaneously thermally desorbed. The desorbed compounds were analyzed by thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS). Compared to conventional SBSE, (m)SBSE provides more uniform enrichment of a wide range of odor compounds in aqueous sample since both stir bars can complement each other, while eliminating the damage of the EG Silicone phase during the extraction. The robustness of the EG Silicone stir bar was dramatically increased and more than 30 extraction and desorption cycles were possible without loss in performance. The recoveries for polar solutes such as 2-acetyl pyrrole (logKow: 0.55), benzyl alcohol (logKow: 1.08), guaiacol (logKow: 1.34), and indole (logKow: 2.05) were increased by a factor of about 2-7. The (m)SBSE-TD-GC-MS method showed good linearity (r(2)>0.9913) and high sensitivity (limit of detection: 0.011-0.071 ng mL(-1)) for the test compounds spiked in water. The feasibility and benefit of the method was demonstrated with analysis of odor compounds in roasted green tea. The normalized areas obtained from (m)SBSE showed the best enrichment for most of the selected compounds compared to conventional SBSE using the PDMS stir bar or the EG Silicone stir bar. Fifteen compounds were determined in the range of 0.15-210 ng mL(-1) (RSD<14%, n=6).
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Climate extremes and the carbon cycle.
Nature
PUBLISHED: 05-29-2013
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The terrestrial biosphere is a key component of the global carbon cycle and its carbon balance is strongly influenced by climate. Continuing environmental changes are thought to increase global terrestrial carbon uptake. But evidence is mounting that climate extremes such as droughts or storms can lead to a decrease in regional ecosystem carbon stocks and therefore have the potential to negate an expected increase in terrestrial carbon uptake. Here we explore the mechanisms and impacts of climate extremes on the terrestrial carbon cycle, and propose a pathway to improve our understanding of present and future impacts of climate extremes on the terrestrial carbon budget.
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STAT5 outcompetes STAT3 to regulate the expression of the oncogenic transcriptional modulator BCL6.
Mol. Cell. Biol.
PUBLISHED: 05-28-2013
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Inappropriate activation of the transcription factors STAT3 and STAT5 has been shown to drive cancer pathogenesis through dysregulation of genes involved in cell survival, growth, and differentiation. Although STAT3 and STAT5 are structurally related, they can have opposite effects on key genes, including BCL6. BCL6, a transcriptional repressor, has been shown to be oncogenic in diffuse large B cell lymphoma. BCL6 also plays an important role in breast cancer pathogenesis, a disease in which STAT3 and STAT5 can be activated individually or concomitantly. To determine the mechanism by which these oncogenic transcription factors regulate BCL6 transcription, we analyzed their effects at the levels of chromatin and gene expression. We found that STAT3 increases expression of BCL6 and enhances recruitment of RNA polymerase II phosphorylated at a site associated with transcriptional initiation. STAT5, in contrast, represses BCL6 expression below basal levels and decreases the association of RNA polymerase II at the gene. Furthermore, the repression mediated by STAT5 is dominant over STAT3-mediated induction. STAT5 exerts this effect by displacing STAT3 from one of the two regulatory regions to which it binds. These findings may underlie the divergent biology of breast cancers containing activated STAT3 alone or in conjunction with activated STAT5.
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Tree growth response along an elevational gradient: climate or genetics?
Oecologia
PUBLISHED: 05-27-2013
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Environment and genetics combine to influence tree growth and should therefore be jointly considered when evaluating forest responses in a warming climate. Here, we combine dendroclimatology and population genetic approaches with the aim of attributing climatic influences on growth of European larch (Larix decidua) and Norway spruce (Picea abies). Increment cores and genomic DNA samples were collected from populations along a ~900-m elevational transect where the air temperature gradient encompasses a ~4 °C temperature difference. We found that low genetic differentiation among populations indicates gene flow is high, suggesting that migration rate is high enough to counteract the selective pressures of local environmental variation. We observed lower growth rates towards higher elevations and a transition from negative to positive correlations with growing season temperature upward along the elevational transect. With increasing elevation there was also a clear increase in the explained variance of growth due to summer temperatures. Comparisons between climate sensitivity patterns observed along this elevational transect with those from Larix and Picea sites distributed across the Alps reveal good agreement, and suggest that tree-ring width (TRW) variations are more climate-driven than genetics-driven at regional and larger scales. We conclude that elevational transects are an extremely valuable platform for understanding climatic-driven changes over time and can be especially powerful when working within an assessed genetic framework.
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Increasing productivity for the analysis of trace contaminants in food by gas chromatography-mass spectrometry using automated liner exchange, backflushing and heart-cutting.
J Chromatogr A
PUBLISHED: 05-03-2013
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Laboratories focusing on residue analysis in food are continuously seeking to increase sample throughput by minimizing sample preparation. Generic sample extraction methods such as QuEChERS lack selectivity and consequently extracts are not free from non-volatile material that contaminates the analytical system. Co-extracted matrix constituents interfere with target analytes, even if highly sensitive and selective GC-MS/MS is used. A number of GC approaches are described that can be used to increase laboratory productivity. These techniques include automated inlet liner exchange and column backflushing for preservation of the performance of the analytical system and heart-cutting two-dimensional GC for increasing sensitivity and selectivity. The application of these tools is illustrated by the analysis of pesticides in vegetables and fruits, PCBs in milk powder and coplanar PCBs in fish. It is demonstrated that considerable increase in productivity can be achieved by decreasing instrument down-time, while analytical performance is equal or better compared to conventional trace contaminant analysis.
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Combination of two anti-CD5 monoclonal antibodies synergistically induces complement-dependent cytotoxicity of chronic lymphocytic leukaemia cells.
Br. J. Haematol.
PUBLISHED: 04-05-2013
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The treatment of chronic lymphocytic leukaemia (CLL) has been improved by introduction of monoclonal antibodies (mAbs) that exert their effect through secondary effector mechanisms. CLL cells are characterized by expression of CD5 and CD23 along with CD19 and CD20, hence anti-CD5 Abs that engage secondary effector functions represent an attractive opportunity for CLL treatment. Here, a repertoire of mAbs against human CD5 was generated and tested for ability to induce complement-dependent cytotoxicity (CDC) and antibody-dependent cell-mediated cytotoxicity (ADCC) both as single mAbs and combinations of two mAbs against non-overlapping epitopes on human CD5. The results demonstrated that combinations of two mAbs significantly increased the level of CDC compared to the single mAbs, while no enhancement of ADCC was seen with anti-CD5 mAb combinations. High levels of CDC and ADCC correlated with low levels of Ab-induced CD5 internalization and degradation. Importantly, an anti-CD5 mAb combination enhanced CDC of CLL cells when combined with the anti-CD20 mAbs rituximab and ofatumumab as well as with the anti-CD52 mAb alemtuzumab. These results suggest that an anti-CD5 mAb combination inducing CDC and ADCC may be effective alone, in combination with mAbs against other targets or combined with chemotherapy for CLL and other CD5-expressing haematological or lymphoid malignancies.
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Early phrenic motor neuron loss and transient respiratory abnormalities after unilateral cervical spinal cord contusion.
J. Neurotrauma
PUBLISHED: 03-29-2013
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Contusion-type cervical spinal cord injury (SCI) is one of the most common forms of SCI observed in patients. In particular, injuries targeting the C3-C5 region affect the pool of phrenic motor neurons (PhMNs) that innervates the diaphragm, resulting in significant and often chronic respiratory dysfunction. Using a previously described rat model of unilateral midcervical C4 contusion with the Infinite Horizon Impactor, we have characterized the early time course of PhMN degeneration and consequent respiratory deficits following injury, as this knowledge is important for designing relevant treatment strategies targeting protection and plasticity of PhMN circuitry. PhMN loss (48% of the ipsilateral pool) occurred almost entirely during the first 24?h post-injury, resulting in persistent phrenic nerve axonal degeneration and denervation at the diaphragm neuromuscular junction (NMJ). Reduced diaphragm compound muscle action potential amplitudes following phrenic nerve stimulation were observed as early as the first day post-injury (30% of pre-injury maximum amplitude), with slow functional improvement over time that was associated with partial reinnervation at the diaphragm NMJ. Consistent with ipsilateral diaphragmatic compromise, the injury resulted in rapid, yet only transient, changes in overall ventilatory parameters measured via whole-body plethysmography, including increased respiratory rate, decreased tidal volume, and decreased peak inspiratory flow. Despite significant ipsilateral PhMN loss, the respiratory system has the capacity to quickly compensate for partially impaired hemidiaphragm function, suggesting that C4 hemicontusion in rats is a model of SCI that manifests subacute respiratory abnormalities. Collectively, these findings demonstrate significant and persistent diaphragm compromise in a clinically relevant model of midcervical contusion SCI; however, the therapeutic window for PhMN protection is restricted to early time points post-injury. On the contrary, preventing loss of innervation by PhMNs and/or inducing plasticity in spared PhMN axons at the diaphragm NMJ are relevant long-term targets.
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Distinct roles of STAT3 and STAT5 in the pathogenesis and targeted therapy of breast cancer.
Mol. Cell. Endocrinol.
PUBLISHED: 01-21-2013
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The transcription factors STAT3 and STAT5 play important roles in the regulation of mammary gland function during pregnancy, lactation, and involution. Given that STAT3 and STAT5 regulate genes involved in proliferation and survival, it is not surprising that inappropriate activation of STAT3 and STAT5 occurs commonly in breast cancer. Although these proteins are structurally similar, they have divergent and opposing effects on gene expression and cellular phenotype. Notably, when STAT5 and STAT3 are activated simultaneously, STAT5 has a dominant effect, and leads to decreased proliferation and increased sensitivity to cell death. Similarly, in breast cancer, activation of both STAT5 and STAT3 is associated with longer patient survival than activation of STAT3 alone. Pharmacological inhibitors of STAT3 and STAT5 are being developed for cancer therapy, though understanding the activation state and functional interaction of STAT3 and STAT5 in a patients tumor may be critical for the optimal use of this strategy.
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Biomarkers of human exposure to personal care products: results from the Flemish Environment and Health Study (FLEHS 2007-2011).
Sci. Total Environ.
PUBLISHED: 01-18-2013
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Personal care products (PCPs), such as soaps, perfumes, cosmetics, lotions, etc., contain a variety of chemicals that have been described as potentially hormone disrupting chemicals. Therefore, it is important to assess the internal exposure of these chemicals in humans. Within the 2nd Flemish Environment and Health Study (FLEHS II, 2007-2011), the human exposure to three classes of pollutants that are present in a wide variety of PCPs--i.e. polycyclic musks (galaxolide, HHCB and tonalide, AHTN in blood), parabens (urinary para-hydroxybenzoic acid, HBA) and triclosan (urinary TCS)--was assessed in 210 Flemish adolescents (14-15 years) and in 204 adults (20-40 years) randomly selected from the general population according to a stratified two stage clustered study design. The aim of this study was to define average levels of exposure in the general Flemish population and to identify determinants of exposure. Average levels (GM (95% CI)) in the Flemish adolescents were 0.717 (0.682-0.753) ?g/L for blood HHCB; 0.118 (0.108-0.128) ?g/L for blood AHTN; 1022 (723-1436) ?g/L for urinary HBA and 2.19 (1.64-2.92) ?g/L for urinary TCS. In the adults, levels of HBA were on average 634 (471-970) ?g/L. Inter-individual variability was small for HHCB and AHTN, intermediate for HBA, and large for TCS. All biomarkers were positively associated with the use of PCPs. Additionally, levels of HHCB and AHTN increased with higher educational level of the adolescents. Both in adults and adolescents, urinary HBA levels were negatively correlated with BMI. We define here Flemish exposure values for biomarkers of PCPs, which can serve as baseline exposure levels to identify exposure trends in future biomonitoring campaigns.
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Whole-exome sequencing identifies a recurrent NAB2-STAT6 fusion in solitary fibrous tumors.
Nat. Genet.
PUBLISHED: 01-13-2013
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Solitary fibrous tumors (SFTs) are rare mesenchymal tumors. Here, we describe the identification of a NAB2-STAT6 fusion from whole-exome sequencing of 17 SFTs. Analysis in 53 tumors confirmed the presence of 7 variants of this fusion transcript in 29 tumors (55%), representing a lower bound for fusion frequency at this locus and suggesting that the NAB2-STAT6 fusion is a distinct molecular feature of SFTs.
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Heart-cutting two-dimensional gas chromatography in combination with isotope ratio mass spectrometry for the characterization of the wax fraction in plant material.
J Chromatogr A
PUBLISHED: 01-03-2013
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Gas chromatography coupled to isotope ratio mass spectrometry after on-line combustion (GC-C-IRMS) and high temperature conversion (GC-HTC-IRMS) is used for compound specific isotope ratio determination. This determination can only be performed successfully if the target solutes are fully resolved from other compounds. A new instrumental set-up consisting of heart-cutting two-dimensional GC based on capillary flow technology and a low thermal mass GC oven in combination with an isotope ratio mass spectrometer is presented. Capillary flow technology was also used in all column and interface connections for robust and leak-free operation. The new configuration was applied to the characterization of wax compounds in tobacco leaf and corresponding smoke samples. It is demonstrated that high accuracy is obtained, both in the determination of ?(13)C and ?(2)H values, allowing the study of biosynthesis and delivery mechanisms of naturally occurring compounds in tobacco.
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Profiling and characterizing skin ceramides using reversed-phase liquid chromatography-quadrupole time-of-flight mass spectrometry.
Anal. Chem.
PUBLISHED: 12-07-2011
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An LC-MS based method for the profiling and characterization of ceramide species in the upper layer of human skin is described. Ceramide samples, collected by tape stripping of human skin, were analyzed by reversed-phase liquid chromatography coupled to high-resolution quadrupole time-of-flight mass spectrometry operated in both positive and negative electrospray ionization mode. All known classes of ceramides could be measured in a repeatable manner. Furthermore, the data set showed several undiscovered ceramides, including a class with four hydroxyl functionalities in its sphingoid base. High-resolution MS/MS fragmentation spectra revealed that each identified ceramide species is composed of several skeletal isomers due to variation in carbon length of the respective sphingoid bases and fatty acyl building blocks. The resulting variety in skeletal isomers has not been previously demonstrated. It is estimated that over 1000 unique ceramide structures could be elucidated in human stratum corneum. Ceramide species with an even and odd number of carbon atoms in both chains were detected in all ceramide classes. Acid hydrolysis of the ceramides, followed by LC-MS analysis of the end-products, confirmed the observed distribution of both sphingoid bases and fatty acyl groups in skin ceramides. The study resulted in an accurate mass retention time library for targeted profiling of skin ceramides. It is furthermore demonstrated that targeted data processing results in an improved repeatability versus untargeted data processing (72.92% versus 62.12% of species display an RSD < 15%).
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The trouble with morality: the effects of 12-step discourse on addicts decision-making.
J Psychoactive Drugs
PUBLISHED: 11-25-2011
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Since its development in the 1960s, researchers have extensively scrutinized methadone maintenance treatment (MMT) as a medical response to heroin addiction. Studies consistently find that MMT is more successful than other treatment models in the reduction of opiate/opioid misuse, the transmission of diseases like HIV/AIDS and hepatitis C, and criminal arrest and conviction rates. Nonetheless, a significant portion of active and former heroin addicts view MMT negatively and-perhaps as a result-MMT is vastly underused. This study examines the effects of 12-Step discourses on the opinions and treatment decisions of active heroin addicts, addicts in MMT, and addicts in 12-Step treatment programs. The study finds the abstinence/morality based discourse of drug addiction and treatment is pervasive among addicts and their non-drug using relations and peers alike; moreover, addicts have internalized this narrative, oftentimes despite their own knowledge of MMTs success and positive personal experiences. The findings suggest that the dominance of abstinence/morality narratives contributes to MMTs poor reputation among, and low use rate by current and former heroin addicts and that the power of the dominant discourse is such that it produces a desire to buy into its values and tenets even when it is against the individuals interests to do so.
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STAT3 Inhibition by Microtubule-Targeted Drugs: Dual Molecular Effects of Chemotherapeutic Agents.
Mol Cell Pharmacol
PUBLISHED: 09-28-2011
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To improve the effectiveness of anti-cancer therapies, it is necessary to identify molecular targets that are essential to a tumor cell but dispensable in a normal cell. Increasing evidence indicates that the transcription factor STAT3, which regulates the expression of genes controlling proliferation, survival, and self-renewal, constitutes such a target. Recently it has been found that STAT3 can associate with the cytoskeleton. Since many of the tumors in which STAT3 is activated, such as breast cancer and ovarian cancer, are responsive to drugs that target microtubules, we examined the effect of these compounds on STAT3. We found that microtubule stabilizers, such as paclitaxel, or microtubule inhibitors, such as vinorelbine, decrease the activating tyrosine phosphorylation of STAT3 in tumor cells and inhibit the expression of STAT3 target genes. Paclitaxel decreases the association between STAT3 and microtubules, and appears to decrease STAT3 phosphorylation through induction of a negative feedback regulator. The cytotoxic activity of paclitaxel in breast cancer cell lines correlates with its ability to decrease STAT3 phosphorylation. However, consistent with the necessity for expression of a negative regulator, treatment of resistant MDA-MB-231 cells with the DNA demethylating agent 5-azacytidine restores the ability of paclitaxel to block STAT3-dependent gene expression. Finally, the combination of paclitaxel and agents that directly target STAT3 has beneficial effects in killing STAT3-dependent cell lines. Thus, microtubule-targeted agents may exert some of their effects by inhibiting STAT3, and understanding this interaction may be important for optimizing rational targeted cancer therapies.
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Reversible resistance induced by FLT3 inhibition: a novel resistance mechanism in mutant FLT3-expressing cells.
PLoS ONE
PUBLISHED: 08-10-2011
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Clinical responses achieved with FLT3 kinase inhibitors in acute myeloid leukemia (AML) are typically transient and partial. Thus, there is a need for identification of molecular mechanisms of clinical resistance to these drugs. In response, we characterized MOLM13 AML cell lines made resistant to two structurally-independent FLT3 inhibitors.
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Pyrimethamine inhibits adult polycystic kidney disease by modulating STAT signaling pathways.
Hum. Mol. Genet.
PUBLISHED: 08-05-2011
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Autosomal dominant polycystic kidney disease (ADPKD) is a commonly inherited disorder mostly caused by mutations in PKD1, encoding polycystin-1 (PC1). The disease is characterized by development and growth of epithelium-lined cyst in both kidneys, often leading to renal failure. There is no specific treatment for this disease. Here, we report a sustained activation of the transcription factor signal transducer and activator of transcription 3 (STAT3) in ischemic injured and uninjured Pkd1 knockout polycystic kidneys and in human ADPKD kidneys. Through a chemical library screen, we identified the anti-parasitic compound pyrimethamine as an inhibitor of STAT3 function. Treatment with pyrimethamine decreases cell proliferation in human ADPKD cells and blocks renal cyst formation in an adult and a neonatal PKD mouse model. Moreover, we demonstrated that a specific STAT3 inhibitor, S3I-201, reduces cyst formation and growth in a neonatal PKD mouse model. Our results suggest that PC1 acts as a negative regulator of STAT3 and that blocking STAT3 signaling with pyrimethamine or similar drugs may be an attractive therapy for human ADPKD.
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In-vial pyrolysis (PyroVial) with pre- and post-sample treatment combined with different chromatographic techniques.
J Chromatogr A
PUBLISHED: 07-20-2011
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A new generic pyrolysis unit (PyroVial) is presented. Pyrolysis is carried out in a 2 mL autosampler vial placed in a XYZ robot for automated pyrolysis as well as for pre- and post-pyrolysis treatment of the sample. Analysis of the volatiles is performed by headspace analysis while the semi- and non-volatiles are extracted from the pyrolysate with an organic solvent. The features of the PyroVial are such that all chromatographic techniques can be applied. The pyrolysis unit is discussed in terms of its technical features and its performance is illustrated with applications including conventional pyrolysis, in situ and post-pyrolysis derivatization, reaction pyrolysis and catalytic cracking.
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RON (MST1R) is a novel prognostic marker and therapeutic target for gastroesophageal adenocarcinoma.
Cancer Biol. Ther.
PUBLISHED: 07-01-2011
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RON (MST1R) is one of two members of the MET receptor tyrosine kinase family, along with parent receptor MET. RON has a putative role in several cancers, but its expression and function is poorly characterized in gastroesophageal adenocarcinoma. A recognized functional role of MET tyrosine kinase in gastroesophageal cancer has led to early phase clinical trials using MET inhibitors, with unimpressive results. Therefore, the role of RON in gastroesophageal cancer, as well as its role in cooperative signaling with MET and as a mechanism of resistance to MET inhibition, was studied in gastroesophageal tissues and cell lines. By IHC, RON was highly over-expressed in 74% of gastroesophageal samples (n=94), and over-expression was prognostic of poor survival (p=0.008); RON and MET co-expression occurred in 43% of samples and was prognostic of worst survival (p=0.03). High MST1R gene copy number by quantitative polymerase chain reaction, and confirmed by fluorescence in situ hybridization and/or array comparative genomic hybridization, was seen in 35.5% (16/45) of cases. High MST1R gene copy number correlated with poor survival (p=0.01), and was associated with high MET and ERBB2 gene copy number. A novel somatic MST1R juxtamembrane mutation R1018G was found in 11% of samples. RON signaling was functional in cell lines, activating downstream effector STAT3, and resulted in increased viability over controls. RON and MET co-stimulation assays led to enhanced malignant phenotypes over stimulation of either receptor alone. Growth inhibition as evidenced by viability and apoptosis assays was optimal using novel blocking monoclonal antibodies to both RON and MET, versus either alone. SU11274, a classic MET small molecule tyrosine kinase inhibitor, blocked signaling of both receptors, and proved synergistic when combined with STAT3 inhibition (combination index < 1). These preclinical studies define RON as an important novel prognostic marker and therapeutic target for gastroesophageal cancer warranting further investigation.
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A chemical biology approach to developing STAT inhibitors: molecular strategies for accelerating clinical translation.
Oncotarget
PUBLISHED: 06-18-2011
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STAT transcription factors transduce signals from the cell surface to the nucleus, where they regulate the expression of genes that control proliferation, survival, self-renewal, and other critical cellular functions. Under normal physiological conditions, the activation of STATs is tightly regulated. In cancer, by contrast, STAT proteins, particularly STAT3 and STAT5, become activated constitutively, thereby driving the malignant phenotype of cancer cells. Since these proteins are largely dispensable in the function of normal adult cells, STATs represent a potentially important target for cancer therapy. Although transcription factors have traditionally been viewed as suboptimal targets for pharmacological inhibition, chemical biology approaches have been particularly fruitful in identifying compounds that can modulate this pathway through a variety of mechanisms. STAT inhibitors have notable anti-cancer effects in many tumor systems, show synergy with other therapeutic modalities, and have the potential to eradicate tumor stem cells. Furthermore, STAT inhibitors identified through the screening of chemical libraries can then be employed in large scale analyses such as gene expression profiling, RNA interference screens, or large-scale tumor cell line profiling. Data derived from these studies can then provide key insights into mechanisms of STAT signal transduction, as well as inform the rational design of targeted therapeutic strategies for cancer patients.
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Causes and consequences of past and projected Scandinavian summer temperatures, 500-2100 AD.
PLoS ONE
PUBLISHED: 05-26-2011
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Tree rings dominate millennium-long temperature reconstructions and many records originate from Scandinavia, an area for which the relative roles of external forcing and internal variation on climatic changes are, however, not yet fully understood. Here we compile 1,179 series of maximum latewood density measurements from 25 conifer sites in northern Scandinavia, establish a suite of 36 subset chronologies, and analyse their climate signal. A new reconstruction for the 1483-2006 period correlates at 0.80 with June-August temperatures back to 1860. Summer cooling during the early 17th century and peak warming in the 1930s translate into a decadal amplitude of 2.9°C, which agrees with existing Scandinavian tree-ring proxies. Climate model simulations reveal similar amounts of mid to low frequency variability, suggesting that internal ocean-atmosphere feedbacks likely influenced Scandinavian temperatures more than external forcing. Projected 21st century warming under the SRES A2 scenario would, however, exceed the reconstructed temperature envelope of the past 1,500 years.
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The JAK2/STAT3 signaling pathway is required for growth of CD44?CD24? stem cell-like breast cancer cells in human tumors.
J. Clin. Invest.
PUBLISHED: 04-13-2011
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Intratumor heterogeneity is a major clinical problem because tumor cell subtypes display variable sensitivity to therapeutics and may play different roles in progression. We previously characterized 2 cell populations in human breast tumors with distinct properties: CD44+CD24- cells that have stem cell-like characteristics, and CD44-CD24+ cells that resemble more differentiated breast cancer cells. Here we identified 15 genes required for cell growth or proliferation in CD44+CD24- human breast cancer cells in a large-scale loss-of-function screen and found that inhibition of several of these (IL6, PTGIS, HAS1, CXCL3, and PFKFB3) reduced Stat3 activation. We found that the IL-6/JAK2/Stat3 pathway was preferentially active in CD44+CD24- breast cancer cells compared with other tumor cell types, and inhibition of JAK2 decreased their number and blocked growth of xenografts. Our results highlight the differences between distinct breast cancer cell types and identify targets such as JAK2 and Stat3 that may lead to more specific and effective breast cancer therapies.
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STAT3 expression, molecular features, inflammation patterns, and prognosis in a database of 724 colorectal cancers.
Clin. Cancer Res.
PUBLISHED: 02-10-2011
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STAT3 is a transcription factor that is constitutively activated in some cancers. It seems to play crucial roles in cell proliferation and survival, angiogenesis, tumor-promoting inflammation, and suppression of antitumor host immune response in the tumor microenvironment. Although the STAT3 signaling pathway is a potential drug target, clinical, pathologic, molecular, or prognostic features of STAT3-activated colorectal cancer remain uncertain.
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Junctional tachycardia in a child with Lyme carditis.
Pediatr Cardiol
PUBLISHED: 02-06-2011
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A 3-year-old girl presented with fatigue, fever, and rash. Tachycardia was noted and an ECG showed junctional tachycardia. Lyme titers were positive and the arrhythmia resolved with intravenous ceftriaxone.
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An autonomous BMP2 regulatory element in mesenchymal cells.
J. Cell. Biochem.
PUBLISHED: 01-27-2011
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BMP2 is a morphogen that controls mesenchymal cell differentiation and behavior. For example, BMP2 concentration controls the differentiation of mesenchymal precursors into myocytes, adipocytes, chondrocytes, and osteoblasts. Sequences within the 3untranslated region (UTR) of the Bmp2 mRNA mediate a post-transcriptional block of protein synthesis. Interaction of cell and developmental stage-specific trans-regulatory factors with the 3UTR is a nimble and versatile mechanism for modulating this potent morphogen in different cell types. We show here, that an ultra-conserved sequence in the 3UTR functions independently of promoter, coding region, and 3UTR context in primary and immortalized tissue culture cells and in transgenic mice. Our findings indicate that the ultra-conserved sequence is an autonomously functioning post-transcriptional element that may be used to modulate the level of BMP2 and other proteins while retaining tissue specific regulatory elements.
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Evaluation of ionic liquid stationary phases for one dimensional gas chromatography-mass spectrometry and comprehensive two dimensional gas chromatographic analyses of fatty acids in marine biota.
J Chromatogr A
PUBLISHED: 01-25-2011
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Ionic liquid stationary phases were tested for one dimensional gas chromatography-mass spectrometry (GC-MS) and comprehensive two dimensional gas chromatography (GC×GC) of fatty acid methyl esters from algae. In comparison with polyethylene glycol and cyanopropyl substituted polar stationary phases, ionic liquid stationary phases SLB-IL 82 and SLB-IL 100 showed comparable resolution, but lower column bleeding with MS detection, resulting in better sensitivity. The selectivity and polarity of the ionic liquid phases are similar to a highly polar biscyanopropyl-silicone phase (e.g. HP-88). In GC×GC, using an apolar polydimethyl siloxane×polar ionic liquid column combination, an excellent group-type separation of fatty acids with different carbon numbers and number of unsaturations was obtained, providing information that is complementary to GC-MS identification.
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2500 years of European climate variability and human susceptibility.
Science
PUBLISHED: 01-13-2011
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Climate variations influenced the agricultural productivity, health risk, and conflict level of preindustrial societies. Discrimination between environmental and anthropogenic impacts on past civilizations, however, remains difficult because of the paucity of high-resolution paleoclimatic evidence. We present tree ring-based reconstructions of central European summer precipitation and temperature variability over the past 2500 years. Recent warming is unprecedented, but modern hydroclimatic variations may have at times been exceeded in magnitude and duration. Wet and warm summers occurred during periods of Roman and medieval prosperity. Increased climate variability from ~250 to 600 C.E. coincided with the demise of the western Roman Empire and the turmoil of the Migration Period. Such historical data may provide a basis for counteracting the recent political and fiscal reluctance to mitigate projected climate change.
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The STAT5 inhibitor pimozide decreases survival of chronic myelogenous leukemia cells resistant to kinase inhibitors.
Blood
PUBLISHED: 01-13-2011
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The transcription factor STAT5 is an essential mediator of the pathogenesis of chronic myelogenous leukemia (CML). In CML, the BCR/ABL fusion kinase causes the constitutive activation of STAT5, thereby driving the expression of genes promoting survival. BCR/ABL kinase inhibitors have become the mainstay of therapy for CML, although CML cells can develop resistance through mutations in BCR/ABL. To overcome this problem, we used a cell-based screen to identify drugs that inhibit STAT-dependent gene expression. Using this approach, we identified the psychotropic drug pimozide as a STAT5 inhibitor. Pimozide decreases STAT5 tyrosine phosphorylation, although it does not inhibit BCR/ABL or other tyrosine kinases. Furthermore, pimozide decreases the expression of STAT5 target genes and induces cell cycle arrest and apoptosis in CML cell lines. Pimozide also selectively inhibits colony formation of CD34(+) bone marrow cells from CML patients. Importantly, pimozide induces similar effects in the presence of the T315I BCR/ABL mutation that renders the kinase resistant to presently available inhibitors. Simultaneously inhibiting STAT5 with pimozide and the kinase inhibitors imatinib or nilotinib shows enhanced effects in inhibiting STAT5 phosphorylation and in inducing apoptosis. Thus, targeting STAT5 may be an effective strategy for the treatment of CML and other myeloproliferative diseases.
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History matters: ecometrics and integrative climate change biology.
Proc. Biol. Sci.
PUBLISHED: 01-12-2011
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Climate change research is increasingly focusing on the dynamics among species, ecosystems and climates. Better data about the historical behaviours of these dynamics are urgently needed. Such data are already available from ecology, archaeology, palaeontology and geology, but their integration into climate change research is hampered by differences in their temporal and geographical scales. One productive way to unite data across scales is the study of functional morphological traits, which can form a common denominator for studying interactions between species and climate across taxa, across ecosystems, across space and through time-an approach we call ecometrics. The sampling methods that have become established in palaeontology to standardize over different scales can be synthesized with tools from community ecology and climate change biology to improve our understanding of the dynamics among species, ecosystems, climates and earth systems over time. Developing these approaches into an integrative climate change biology will help enrich our understanding of the changes our modern world is undergoing.
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Evaluation of automated sample preparation, retention time locked gas chromatography-mass spectrometry and data analysis methods for the metabolomic study of Arabidopsis species.
J Chromatogr A
PUBLISHED: 01-07-2011
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In this paper, automated sample preparation, retention time locked gas chromatography-mass spectrometry (GC-MS) and data analysis methods for the metabolomics study were evaluated. A miniaturized and automated derivatisation method using sequential oximation and silylation was applied to a polar extract of 4 types (2 types×2 ages) of Arabidopsis thaliana, a popular model organism often used in plant sciences and genetics. Automation of the derivatisation process offers excellent repeatability, and the time between sample preparation and analysis was short and constant, reducing artifact formation. Retention time locked (RTL) gas chromatography-mass spectrometry was used, resulting in reproducible retention times and GC-MS profiles. Two approaches were used for data analysis. XCMS followed by principal component analysis (approach 1) and AMDIS deconvolution combined with a commercially available program (Mass Profiler Professional) followed by principal component analysis (approach 2) were compared. Several features that were up- or down-regulated in the different types were detected.
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Ecometrics: the traits that bind the past and present together.
Integr Zool
PUBLISHED: 12-17-2010
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We outline here an approach for understanding the biology of climate change, one that integrates data at multiple spatial and temporal scales. Taxon-free trait analysis, or "ecometrics," is based on the idea that the distribution in a community of ecomorphological traits such as tooth structure, limb proportions, body mass, leaf shape, incubation temperature, claw shape, any aspect of anatomy or physiology can be measured across some subset of the organisms in a community. Regardless of temporal or spatial scale, traits are the means by which organisms interact with their environment, biotic and abiotic. Ecometrics measures these interactions by focusing on traits which are easily measurable, whose structure is closely related to their function, and whose function interacts directly with local environment. Ecometric trait distributions are thus a comparatively universal metric for exploring systems dynamics at all scales. The main challenge now is to move beyond investigating how future climate change will affect the distribution of organisms and how it will impact ecosystem services and to shift the perspective to ask how biotic systems interact with changing climate in general, and how climate change affects the interactions within and between the components of the whole biotic-physical system. We believe that it is possible to provide believable, quantitative answers to these questions. Because of this we have initiated an IUBS program iCCB (integrative Climate Change Biology).
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Climatic warming disrupts recurrent Alpine insect outbreaks.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 11-08-2010
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Climate change has been identified as a causal factor for diverse ecological changes worldwide. Warming trends over the last couple of decades have coincided with the collapse of long-term population cycles in a broad range of taxa, although causal mechanisms are not well-understood. Larch budmoth (LBM) population dynamics across the European Alps, a classic example of regular outbreaks, inexplicably changed sometime during the 1980s after 1,200 y of nearly uninterrupted periodic outbreak cycles. Herein, analysis of perhaps the most extensive spatiotemporal dataset of population dynamics and reconstructed Alpine-wide LBM defoliation records reveals elevational shifts in LBM outbreak epicenters that coincide with temperature fluctuations over two centuries. A population model supports the hypothesis that temperature-mediated shifting of the optimal elevation for LBM population growth is the mechanism for elevational epicenter changes. Increases in the optimal elevation for population growth over the warming period of the last century to near the distributional limit of host larch likely dampened population cycles, thereby causing the collapse of a millennium-long outbreak cycle. The threshold-like change in LBM outbreak pattern highlights how interacting species with differential response rates to climate change can result in dramatic ecological changes.
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Eye movements and strategy shift in skill acquisition: adult age differences.
J Gerontol B Psychol Sci Soc Sci
PUBLISHED: 11-03-2010
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The current article explores age differences in skill acquisition. We validated strategy self-reports, evaluated whether eye movements may be automatic as well as information seeking, and considered the contribution of eye movements to age differences in overall performance.
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Microtubule-targeted chemotherapeutic agents inhibit signal transducer and activator of transcription 3 (STAT3) signaling.
Mol. Pharmacol.
PUBLISHED: 08-06-2010
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The transcription factor signal transducer and activator of transcription 3 (STAT3) is inappropriately activated in the majority of breast tumors, especially in aggressive and invasive ones. In addition to driving the expression of genes promoting malignancy, STAT3 associates with tubulin and can promote cell migration. Because microtubule-targeted drugs are among the most active agents used in the treatment of breast cancer, we examined whether microtubule-based chemotherapy modulates STAT3 activity. When treated with paclitaxel or vinorelbine, breast cancer cells with constitutive activation of STAT3 display a loss of STAT3 phosphorylation, and paclitaxel disrupts the interaction of STAT3 with tubulin. Paclitaxel also inhibits cytokine-induced STAT3 activation. This effect is specific for microtubule-targeted agents, because other chemotherapeutic drugs, such as doxorubicin, have no effect on STAT3. The loss of STAT3 tyrosine phosphorylation is also reflected in an inhibition of expression of STAT3 target genes. This effect is not restricted to breast cancer, because similar effects are also seen in ovarian cancer and prostate cancer cells. Thus, in addition to their role in disrupting microtubule function, microtubule-targeted agents also suppress STAT3 signaling. This may be an important component of their activity, raising the possibility that microtubule targeted therapy may be particularly effective in tumors characterized by STAT3 activation.
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Authors Submission Toolkit: a practical guide to getting your research published.
Curr Med Res Opin
PUBLISHED: 06-24-2010
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Biomedical journals and the pharmaceutical industry share the goals of enhancing transparency and expanding access to peer-reviewed research; both industries have recently instituted new policies and guidelines to effect this change. However, while increasing transparency may elevate standards and bring benefits to readers, it will drive a significant increase in manuscript volume, posing challenges to both the journals and industry sponsors. As a result, there is a need to: (1) increase efficiency in the submission process to accommodate the rising manuscript volume and reduce the resource demands on journals, peer reviewers, and authors; and (2) identify suitable venues to publish this research. These shared goals can only be accomplished through close collaboration among stakeholders in the process.In an effort to foster mutual collaboration, members of the pharmaceutical industry and the International Society for Medical Publication Professionals founded a unique collaborative venture in 2008 - the Medical Publishing Insights and Practices initiative (MPIP). At an MPIP roundtable meeting in September 2009,journal editors, publishers and industry representatives identified and prioritized opportunities to streamline the submission process and requirements, and to support prompt publication and dissemination of clinical trial results in the face of increasing manuscript volume. Journal and sponsor participants agreed that more author education on manuscript preparation and submission was needed to increase efficiency and enhance quality and transparency in the publication of industry-sponsored research. They suggested an authorsguide to help bridge the gap between author practices and editor expectations.To address this unmet educational need, MPIP supported development of an Authors Submission Toolkit to compile best practices in the preparation and submission of manuscripts describing sponsored research.The Toolkit represents a unique collaboration between the pharmaceutical industry and biomedical journals,and reflects both groups perspectives on how authors can help raise standards and increase efficiency in publishing industry-sponsored studies. The information provided in the toolkit can be useful to help authors navigate the manuscript
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Analysis of bacterial fatty acids by flow modulated comprehensive two-dimensional gas chromatography with parallel flame ionization detector/mass spectrometry.
J Chromatogr A
PUBLISHED: 06-10-2010
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Comprehensive two-dimensional gas chromatography (GCxGC) offers an interesting tool for profiling bacterial fatty acids. Flow modulated GCxGC using a commercially available system was evaluated, different parameters such as column flows and modulation time were optimized. The method was tested on bacterial fatty acid methyl esters (BAMEs) from Stenotrophomonas maltophilia LMG 958T by using parallel flame ionization detector (FID)/mass spectrometry (MS). The results are compared to data obtained using a thermal modulated GCxGC system. The data show that flow modulated GCxGC-FID/MS method can be applied in a routine environment and offers interesting perspectives for chemotaxonomy of bacteria.
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Chagas disease risk in Texas.
PLoS Negl Trop Dis
PUBLISHED: 04-05-2010
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Chagas disease, caused by Trypanosoma cruzi, remains a serious public health concern in many areas of Latin America, including México. It is also endemic in Texas with an autochthonous canine cycle, abundant vectors (Triatoma species) in many counties, and established domestic and peridomestic cycles which make competent reservoirs available throughout the state. Yet, Chagas disease is not reportable in Texas, blood donor screening is not mandatory, and the serological profiles of human and canine populations remain unknown. The purpose of this analysis was to provide a formal risk assessment, including risk maps, which recommends the removal of these lacunae.
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Time-dependent effects of dim light at night on re-entrainment and masking of hamster activity rhythms.
J. Biol. Rhythms
PUBLISHED: 03-30-2010
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Bright light has been established as the most ubiquitous environmental cue that entrains circadian timing systems under natural conditions. Light equivalent in intensity to moonlight (<1 lux), however, also strongly modulates circadian function in a number of entrainment paradigms. For example, compared to completely dark nights, dim nighttime illumination accelerated re-entrainment of hamster activity rhythms to 4-hour phase advances and delays of an otherwise standard laboratory photocycle. The purpose of this study was to determine if a sensitive period existed in the night during which dim illumination had a robust influence on speed of re-entrainment. Male Siberian hamsters were either exposed to dim light throughout the night, for half of the night, or not at all. Compared to dark nights, dim illumination throughout the entire night decreased by 29% the time for the midpoint of the active phase to re-entrain to a 4-hour phase advance and by 26% for a 4-hour delay. Acceleration of advances and delays were also achieved with 5 hours of dim light per night, but effects depended on whether dim light was present in the first half, second half, or first and last quarters of the night. Both during phase shifting and steady-state entrainment, partially lit nights also produced strong positive and negative masking effects, as well as entrainment aftereffects in constant darkness. Thus, even in the presence of a strong zeitgeber, light that might be encountered under a natural nighttime sky potently modulates the circadian timing system of hamsters.
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Regulation of kidney development by Shp2: an unbiased stereological analysis.
Anat Rec (Hoboken)
PUBLISHED: 03-15-2010
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Genes that regulate renal branching morphogenesis are likely to indirectly regulate nephron endowment, but few have been validated to do so in vivo. PTPN11, which encodes the nonreceptor protein tyrosine phosphatase Shp2, acts downstream of receptor tyrosine kinases to modulate the Ras-MAPK pathway and has been implicated in branching morphogenesis in vitro and in invertebrates, and is therefore a candidate in vivo regulator of nephron number. In this work, heterozygous null mutant Shp2(+/-) mice at postnatal days 30-35 were compared with their wild-type (WT) littermates using unbiased stereology to determine if, indeed, the former had decreased nephron number due to their 50% decrease in gene/protein dosage. Although there was a trend toward decreases in total glomerular (nephron) number and kidney volume in Shp2(+/-) mice compared with WT, neither difference was statistically significant (11310 vs. 12198 glomeruli, P = 0.22; 62.8 mm(3) vs. 66.0 mm(3) renal volume; P = 0.40). We conclude that loss of 50% gene/protein dosage of PTPN11/Shp2 is insufficient to affect glomerular (and thereby nephron) number in mouse kidneys in vivo.
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RIP-CHIP in drug development.
Methods Mol. Biol.
PUBLISHED: 03-11-2010
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Microarrays are extensively used to evaluate the effects of compounds on gene expression in the cells. Most of the studies so far have analyzed the transcriptome of the cell. The basic assumption of this approach is that the changes in gene expression occur at the level of transcription of a gene. However, changes often occur at the posttranscriptional level and are not reflected in the analysis of whole transcriptome. We have pioneered the development of "ribonomic profiling" as a high-throughput method to study posttranscriptional regulation of gene expression in the cell. This method is also often referred to as RIP-CHIP. In this chapter, we describe how to use the RIP-CHIP technology to assess the posttranscriptional changes occurring in the cell in response to treatment with a drug.
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Determination of alternate splicing events using the Affymetrix Exon 1.0 ST arrays.
Methods Mol. Biol.
PUBLISHED: 03-11-2010
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Alternative splicing plays an important role in regulation of normal cellular function. Alternative splicing of pre-mRNA leads to the diversity of downstream protein products in the cell. The Affymetrix Exon arrays allow for a high throughput evaluation of the differences in spliced mRNA expressed in a biological system. In this study, we describe a method using this technology to study the generation of alternative mRNA transcripts in breast cancer cells that differ in the levels of a particular integrin, alpha3beta1.
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Chorioamnionitis stimulates angiogenesis in saccular stage fetal lungs via CC chemokines.
Am. J. Physiol. Lung Cell Mol. Physiol.
PUBLISHED: 02-19-2010
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The fetal lung vasculature forms in tandem with developing airways. Whereas saccular airway morphogenesis is arrested in bronchopulmonary dysplasia (BPD), the potential vascular phenotype in BPD at this stage of development is less well-understood. As inflammation increases the risk of BPD and induces arrest of saccular airway morphogenesis, we tested the effects of Escherichia coli LPS on fetal mouse lung vascular development. Injecting LPS into the amniotic fluid of Tie2-lacZ endothelial reporter mice at embryonic day 15 stimulated angiogenesis in the saccular stage fetal lung mesenchyme. LPS also increased the number of endothelial cells in saccular stage fetal mouse lung explants. Inflammation appeared to directly promote vascular development, as LPS stimulated pulmonary microvascular endothelial cell angiogenesis, cell migration, and proliferation in vitro. Whereas LPS did not increase expression of VEGF, angiopoietin-1 (Ang-1), Tie2, fetal liver kinase-1 (Flk-1), fms-like tyrosine kinase-1 (Flt-1), PDGFA, PDGFB, heparin-binding EGF-like growth factor (HB-EGF), or connective tissue growth factor (CTGF), LPS did stimulate the production of the angiogenic CC chemokines macrophage inflammatory protein-1? (MIP-1?) and monocyte chemoattractant protein-1 (MCP-1). Both MIP-1? and MCP-1 increased angiogenesis in fetal mouse lung explants. In addition, inhibitory antibodies against MIP-1? and MCP-1 blocked the effects of LPS on fetal lung vascular development, suggesting these chemokines are downstream mediators of LPS-induced angiogenesis. We speculate that an inflammation-mediated surge in angiogenesis could lead to formation of aberrant alveolar capillaries in the lungs of patients developing BPD.
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Comprehensive blood plasma lipidomics by liquid chromatography/quadrupole time-of-flight mass spectrometry.
J Chromatogr A
PUBLISHED: 02-08-2010
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A lipidomics strategy, combining high resolution reversed-phase liquid chromatography (RPLC) with high resolution quadrupole time-of-flight mass spectrometry (QqTOF), is described. The method has carefully been assessed in both a qualitative and a quantitative fashion utilizing human blood plasma. The inherent low technical variability associated with the lipidomics method allows to measure 65% of the features with an intensity RSD value below 10%. Blood plasma lipid spike-in experiments demonstrate that relative concentration differences smaller than 25% can readily be revealed by means of a t-test. Utilizing an advanced identification strategy, it is shown that the detected features mainly originate from (lyso-)phospholipids, sphingolipids, mono-, di- and triacylglycerols and cholesterol esters. The high resolution offered by the up-front RPLC step further allows to discriminate various isomeric species associated with the different lipid classes. The added value of utilizing a Jetstream electrospray ionization (ESI) source over a regular ESI source in lipidomics is for the first time demonstrated. In addition, the application of ultra high performance LC (UHPLC) up to 1200bar to extend the peak capacity or increase productivity is discussed.
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The utility of sulfonate salts in drug development.
J Pharm Sci
PUBLISHED: 01-30-2010
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The issue of controlling genotoxic impurities in novel active pharmaceutical ingredients (APIs) is a significant challenge. Much of the current regulatory concern, has been focused on the formation and control of genotoxic sulfonate esters. This is linked with the withdrawal of Viracept (Nefinavir mesilate) from European markets in mid-2007, over concerns about elevated levels of ethyl methanesulfonate (EMS). This issue has resulted in calls from European regulators to assess risk mitigation strategies for all marketed products employing a sulfonic acid counter-ion to ensure that the sulfonate esters that could be potentially formed are controlled to threshold of toxicological concern (TTC)-based limits. This has even led to calls to avoid sulfonic acids as salt counter-ions. However, sulfonic acid salts possess a range of properties that are useful to both synthetic and formulation chemists. Whilst sulfonate salts are not a universal panacea to some of the problems of salt formation they do offer significant advantages as alternatives to other salt forming moieties under certain circumstances. This review thus sets out to define some of the advantages provided through utilization of sulfonic acids, explaining the importance of their retention as part of a thorough salt selection process.
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What is Visualize?

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

How does it work?

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

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

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