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Find video protocols related to scientific articles indexed in Pubmed.
Indirect genetic effects from competition in the clonal herb Sedum album (Crassulaceae).
PLoS ONE
PUBLISHED: 08-29-2014
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Recent years have seen increasing interest in indirect genetic effects, i.e. influences on the phenotype that depend on the genotype of other conspecific individuals; however, the empirical evidence for such effects is still limited, especially in wild plant species. The present study of the clonal herb Sedum album assessed direct and indirect genetic effects on performance-related traits in a 4-year experiment with clonally replicated genotypes, grown in pairs and differing in anthocyanin pigmentation to allow separation of individuals during data collection. In agreement with the existence of indirect genetic effects, the experimentally-paired plants not only expressed their own genotype but were also affected by the genotype of their pair mate. The effect of neighbour genotype explained up to one-fourth of the variation in performance and most likely resulted from competition, imposed by the close physical contact between paired individuals and the limiting conditions used in the garden environment. Indirect genetic effects from competition have the potential to enhance the efficacy of group-level selection relative to individual selection, given the nutrient-poor and spatially-confined substrate available to plants of S. album in the natural habitat.
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Potential of multi-photon upconversion emissions for fluorescence diffuse optical imaging.
Opt Express
PUBLISHED: 08-05-2014
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The spatial resolution of fluorescence molecular imaging is a critical issue for the success of the technique in biomedical applications. One important method for increasing the imaging resolution is to utilize multi-photon emissions. In this study, we thoroughly investigate the potential of the multi-photon upconversion emissions from rare-earth-doped upconverting nanoparticles for the improvement in spatial resolution of diffuse optical imaging. It is found that the imaging resolution is increased by a factor of 1.45 through employing two-photon upconversion emission compared with using the linear emission, and can be further elevated by a factor of 1.23 by using three-photon upconversion emission. In addition, we demonstrate that the pulsed excitation approach holds the promise of overcoming the low quantum yield associated with the high-order upconversion emissions.
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Design and validation of a fiber optic point probe instrument for therapy guidance and monitoring.
J Biomed Opt
PUBLISHED: 02-11-2014
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Optical techniques for tissue diagnostics currently are experiencing tremendous growth in biomedical applications, mainly due to their noninvasive, inexpensive, and real-time functionality. Here, we demonstrate a hand-held fiber optic probe instrument based on fluorescence/reflectance spectroscopy for precise tumor delineation. It is mainly aimed for brain tumor resection guidance with clinical adaptation to minimize the disruption of the standard surgical workflow and is meant as a complement to the state-of-the-art fluorescence surgical microscopy technique. Multiple light sources with fast pulse modulation and detection enable precise quantification of protoporphyrin IX (PpIX), tissue optical properties, and ambient light suppression. Laboratory measurements show the system is insensitive to strong ambient light. Validation measurements of tissue phantoms using nonlinear least squares support vector machines (LS-SVM) regression analysis demonstrate an error of <5% for PpIX concentration ranging from 400 to 1000 nM, even in the presence of large variations in phantom optical properties. The mean error is 3% for reduced scattering coefficient and 5% for blood concentration. Diagnostic precision of 100% was obtained by LS-SVM classification for in vivo skin tumors with topically applied 5-aminolevulinic acid during photodynamic therapy. The probe could easily be generalized to other tissue types and fluorophores for therapy guidance and monitoring.
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Broadband photon time-of-flight spectroscopy of pharmaceuticals and highly scattering plastics in the VIS and close NIR spectral ranges.
Opt Express
PUBLISHED: 10-10-2013
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We present extended spectroscopic analysis of pharmaceutical tablets in the close near infrared spectral range performed using broadband photon time-of-flight (PTOF) absorption and scattering spectra measurements. We show that the absorption spectra can be used to perform evaluation of the chemical composition of pharmaceutical tablets without need for chemo-metric calibration. The spectroscopic analysis was performed using an advanced PTOF spectrometer operating in the 650 to 1400 nm spectral range. By employing temporal stabilization of the system we achieve the high precision of 0.5% required to evaluate the concentration of tablet ingredients. In order to further illustrate the performance of the system, we present the first ever reported broadband evaluation of absorption and scattering spectra from pure and doped Spectralon®.
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Noninvasive monitoring of gas in the lungs and intestines of newborn infants using diode lasers: feasibility study.
J Biomed Opt
PUBLISHED: 09-23-2013
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ABSTRACT. Preterm newborn infants have a high morbidity rate. The most frequently affected organs where free gas is involved are the lungs and intestines. In respiratory distress syndrome, both hyperexpanded and atelectatic (collapsed) areas occur, and in necrotizing enterocolitis, intramural gas may appear in the intestine. Today, these conditions are diagnosed with x-ray radiography. A bed-side, rapid, nonintrusive, and gas-specific technique for in vivo gas sensing would improve diagnosis. We report the use of noninvasive laser spectroscopy, for the first time, to assess gas content in the lungs and intestines of three full-term infants. Water vapor and oxygen were studied with two low-power diode lasers, illuminating the skin and detecting light a few centimeters away. Water vapor was easily detected in the intestines and was also observed in the lungs. The relatively thick chest walls of the infants prevented detection of the weaker oxygen signal in this study. However, results from a previous phantom study, together with scaling of the results presented here to the typical chest-wall thickness of preterm infants, suggest that oxygen also should be detectable in their lungs.
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Deep tissue optical imaging of upconverting nanoparticles enabled by exploiting higher intrinsic quantum yield through use of millisecond single pulse excitation with high peak power.
Nanoscale
PUBLISHED: 08-22-2013
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We have accomplished deep tissue optical imaging of upconverting nanoparticles at 800 nm, using millisecond single pulse excitation with high peak power. This is achieved by carefully choosing the pulse parameters, derived from time-resolved rate-equation analysis, which result in higher intrinsic quantum yield that is utilized by upconverting nanoparticles for generating this near infrared upconversion emission. The pulsed excitation approach thus promises previously unreachable imaging depths and shorter data acquisition times compared with continuous wave excitation, while simultaneously keeping the possible thermal side-effects of the excitation light moderate. These key results facilitate means to break through the general shallow depth limit of upconverting-nanoparticle-based fluorescence techniques, necessary for a range of biomedical applications, including diffuse optical imaging, photodynamic therapy and remote activation of biomolecules in deep tissues.
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Pharmacokinetic and biodistribution study following systemic administration of Fospeg® - a Pegylated liposomal mTHPC formulation in a murine model.
J Biophotonics
PUBLISHED: 08-19-2013
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Fospeg® is a newly developed photosensitizer formulation based on meso-tetra(hydroxyphenyl)chlorin (mTHPC), with hydrophilic liposomes to carry the hydrophobic photosensitizer to the target tissue. In this study the pharmacokinetics and biodistribution of Fospeg® were investigated by high performance liquid chromatography at various times (0.5-18 hours) following systemic i.v. administration. As a model an experimental HT29 colon tumor in NMRI nu/nu mice was employed. Our study indicates a higher plasma peak concentration, a longer circulation time and a better tumor-to-skin ratio than those of Foslip®, another liposomal mTHPC formulation. Data from ex vivo tissue fluorescence and reflectance imaging exhibit good correlation with chemical extraction. Our results have shown that optical imaging provides the potential for fluorophore quantification in biological tissues. (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim).
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Effects of mating system on adaptive potential for leaf morphology in Crepis tectorum (Asteraceae).
Ann. Bot.
PUBLISHED: 08-01-2013
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A shift from outcrossing to selfing is thought to reduce the long-term survival of populations by decreasing the genetic variation necessary for adaptation to novel ecological conditions. However, theory also predicts an increase in adaptive potential as more of the existing variation becomes expressed as homozygous genotypes. So far, relatively few studies have examined how a transition to selfing simultaneously affects means, variances and covariances for characters that might be under stabilizing selection for a spatially varying optimum, e.g. characters describing leaf morphology.
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Balancing power density based quantum yield characterization of upconverting nanoparticles for arbitrary excitation intensities.
Nanoscale
PUBLISHED: 04-22-2013
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Upconverting nanoparticles (UCNPs) have recently shown great potential as contrast agents in biological applications. In developing different UCNPs, the characterization of their quantum yield (QY) is a crucial issue, as the typically drastic decrease in QY for low excitation power densities can either impose a severe limitation or provide an opportunity in many applications. The power density dependence of the QY is governed by the competition between the energy transfer upconversion (ETU) rate and the linear decay rate in the depopulation of the intermediate state of the involved activator in the upconversion process. Here we show that the QYs of Yb(3+) sensitized two-photon upconversion emissions can be well characterized by the balancing power density, at which the ETU rate and the linear decay rate have equal contributions, and its corresponding QY. The results in this paper provide a method to fully describe the QY of upconverting nanoparticles for arbitrary excitation power densities, and is a fast and simple approach for assessing the applicability of UCNPs from the perspective of energy conversion.
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Estrogen receptor ? and 17?-hydroxysteroid dehydrogenase type 6, a growth regulatory pathway that is lost in prostate cancer.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 11-23-2011
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Estrogen receptor ? (ER?) is activated in the prostate by 5?-androstane-3?,17?-diol (3?-Adiol) where it exerts antiproliferative activity. The proliferative action of the androgen receptor is activated by 5?-dihydrotestosterone (DHT). Thus, prostate growth is governed by the balance between androgen receptor and ER? activation. 3?-Adiol is a high-affinity ligand and agonist of ER? and is derived from DHT by 3-keto reductase/3?-hydroxysteroid dehydrogenase enzymes. Here, we demonstrate that, when it is expressed in living cells containing an estrogen response element-luciferase reporter, 17?-hydroxysteroid dehydrogenase type 6 (17?HSD6) converts the androgen DHT to the estrogen 3?-Adiol, and this leads to activation of the ER? reporter. This conversion of DHT occurs at concentrations that are in the physiological range of this hormone in the prostate. Immunohistochemical analysis revealed that 17?HSD6 is expressed in ER?-positive epithelial cells of the human prostate and that, in prostate cancers of Gleason grade higher than 3, both ER? and 17?HSD6 are undetectable. Both proteins were present in benign prostatic hyperplasia samples. These observations reveal that formation of 3?-Adiol via 17?HSD6 from DHT is an important growth regulatory pathway that is lost in prostate cancer.
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Physiological influence of basic perturbations assessed by non-invasive optical techniques in humans.
Appl Physiol Nutr Metab
PUBLISHED: 11-23-2011
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New non-invasive techniques enabling frequent or continuous assessments of various pathophysiological conditions might be used to improve in-hospital outcome by enabling earlier and more reliable bedside detection of medical deterioration. In this preclinical study, three modern non-invasive optical techniques, laser Doppler imaging (LDI), near-infrared spectroscopy (NIRS), and tissue viability imaging (TVI), were all evaluated with respect to the influence of basic physiological perturbations (including local changes in arm positioning, skin temperature, and regional blood flow conditions) on quasi simultaneously obtained values of skin perfusion, muscle tissue oxygenation (StO?), and skin blood volume, recorded in eighteen healthy volunteers. Skin perfusion measured by LDI responded prominently to changes in positioning of the arm, whereas muscle StO? measured by NIRS did not change significantly. Total haemoglobin count (HbT) measured by NIRS and blood volume estimated by TVI both increased significantly on lowering of the limb. On local cooling, the perfusion and blood volume were both found to increase considerably, while StO? and HbT did not change. Local heating induced a more than 10-fold increase in skin perfusion and a small increase in blood volume. On progressive venoarterial occlusion, the perfusion, StO?, HbT, and blood volume values decreased, after transient increases in HbT and blood volume before full arterial occlusion occurred, and all values approached the baseline level on release of the occlusion with a slight overshoot of the StO?. The results obtained have potential bearing on future utilization of these non-invasive techniques in the management of severely injured and (or) critically ill patients.
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An overview on preclinical and clinical experiences with photodynamic therapy for bladder cancer.
Can J Urol
PUBLISHED: 08-23-2011
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Photodynamic therapy (PDT) is one of the most interesting methods of photo treatment. In general, PDT is a modality for the treatment of non-muscle invasive tumors. PDT is very well suited in managing bladder cancer, as the bladder is accessible by endoscopy and the tumors are most often limited to the mucosa or sub-mucosa. PDT is likely more useful for patients with recurrent tumors after conventional therapies, as well as for patients with diffuse non-muscle invasive bladder carcinomas that are refractory to standard treatments before the commitment to radical extirpative surgery, particularly in patients at surgical high risk. The treatment of tumors with PDT includes three major parameters: presence of oxygen in tumor tissue, administration of a photosensitizer, and subsequent exposure to light. The PDT mechanism relies on the in situ generation of cytotoxic agents by the activation of a light-sensitive drug, resulting in cell death. In this review, we present past and current advances in the use of PDT with urinary bladder cancer and discuss the future roles for this type of therapy in the treatment of bladder cancer.
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A theoretical and experimental study on translational and internal energies of H2O and OH from the 157 nm irradiation of amorphous solid water at 90 K.
Phys Chem Chem Phys
PUBLISHED: 08-09-2011
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The photodesorption of H(2)O in its vibrational ground state, and of OH radicals in their ground and first excited vibrational states, following 157 nm photoexcitation of amorphous solid water has been studied using molecular dynamics simulations and detected experimentally by resonance-enhanced multiphoton ionization techniques. There is good agreement between the simulated and measured energy distributions. In addition, signals of H(+) and OH(+) were detected in the experiments. These are inferred to originate from vibrationally excited H(2)O molecules that are ejected from the surface by two distinct mechanisms: a direct desorption mechanism and desorption induced by secondary recombination of photoproducts at the ice surface. This is the first reported experimental evidence of photodesorption of vibrationally excited H(2)O molecules from water ice.
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Effects of probe geometry on transscleral diffuse optical spectroscopy.
Biomed Opt Express
PUBLISHED: 07-18-2011
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The purpose of this study was to investigate how the geometry of a fiber optic probe affects the transmission and reflection of light through the scleral eye wall. Two geometrical parameters of the fiber probe were investigated: the source-detector distance and the fiber protrusion, i.e. the length of the fiber extending from the flat surface of the fiber probe. For optimization of the fiber optic probe geometry, fluorescence stained choroidal tumor phantoms in ex vivo porcine eyes were measured with both diffuse reflectance- and laser-induced fluorescence spectroscopy. The strength of the fluorescence signal compared to the excitation signal was used as a measure for optimization. Intraocular pressure (IOP) and temperature were monitored to assess the impact of the probe on the eye. For visualizing any possible damage caused by the probe, the scleral surface was imaged with scanning electron microscopy after completion of the spectroscopic measurements. A source-detector distance of 5 mm with zero fiber protrusion was considered optimal in terms of spectroscopic contrast, however, a slight fiber protrusion of 0.5 mm is argued to be advantageous for clinical measurements. The study further indicates that transscleral spectroscopy can be safely performed in human eyes under in vivo conditions, without leading to an unacceptable IOP elevation, a significant rise in tissue temperature, or any visible damage to the scleral surface.
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Drug quantification in turbid media by fluorescence imaging combined with light-absorption correction using white Monte Carlo simulations.
J Biomed Opt
PUBLISHED: 07-05-2011
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Accurate quantification of photosensitizers is in many cases a critical issue in photodynamic therapy. As a noninvasive and sensitive tool, fluorescence imaging has attracted particular interest for quantification in pre-clinical research. However, due to the absorption of excitation and emission light by turbid media, such as biological tissue, the detected fluorescence signal does not have a simple and unique dependence on the fluorophore concentration for different tissues, but depends in a complex way on other parameters as well. For this reason, little has been done on drug quantification in vivo by the fluorescence imaging technique. In this paper we present a novel approach to compensate for the light absorption in homogeneous turbid media both for the excitation and emission light, utilizing time-resolved fluorescence white Monte Carlo simulations combined with the Beer-Lambert law. This method shows that the corrected fluorescence intensity is almost proportional to the absolute fluorophore concentration. The results on controllable tissue phantoms and murine tissues are presented and show good correlations between the evaluated fluorescence intensities after the light-absorption correction and absolute fluorophore concentrations. These results suggest that the technique potentially provides the means to quantify the fluorophore concentration from fluorescence images.
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Using 915 nm laser excited Tm³+/Er³+/Ho³+- doped NaYbF4 upconversion nanoparticles for in vitro and deeper in vivo bioimaging without overheating irradiation.
ACS Nano
PUBLISHED: 05-02-2011
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Successful further development of superhigh-constrast upconversion (UC) bioimaging requires addressing the existing paradox: 980 nm laser light is used to excite upconversion nanoparticles (UCNPs), while 980 nm light has strong optical absorption of water and biological specimens. The overheating caused by 980 nm excitation laser light in UC bioimaging is computationally and experimentally investigated for the first time. A new promising excitation approach for better near-infrared to near-infrared (NIR-to-NIR) UC photoluminescence in vitro or in vivo imaging is proposed employing a cost-effective 915 nm laser. This novel laser excitation method provides drastically less heating of the biological specimen and larger imaging depth in the animals or tissues due to quite low water absorption. Experimentally obtained thermal-graphic maps of the mouse in response to the laser heating are investigated to demonstrate the less heating advantage of the 915 nm laser. Our tissue phantom experiments and simulations verified that the 915 nm laser is superior to the 980 nm laser for deep tissue imaging. A novel and facile strategy for surface functionalization is utilized to render UCNPs hydrophilic, stable, and cell targeting. These as-prepared UCNPs were characterized by TEM, emission spectroscopy, XRD, FTIR, and zeta potential. Specifically targeting UCNPs excited with a 915 nm laser have shown very high contrast UC bioimaging. Highly stable DSPE-mPEG-5000-encapsulated UCNPs were injected into mice to perform in vivo imaging. Imaging and spectroscopy analysis of UC photoluminescence demonstrated that a 915 nm laser can serve as a new promising excitation light for UC animal imaging.
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Interstitial laser thermotherapy of a rat liver tumour: effect of hepatic inflow occlusion.
Lasers Surg Med
PUBLISHED: 01-22-2011
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Interstitial laser thermotherapy was used to treat rat liver tumours. The aim was to investigate the influence of temperature and temporary hepatic inflow occlusion on tumour growth and blood perfusion.
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Fluorescence spectroscopy measurements in ultrasonic navigated resection of malignant brain tumors.
Lasers Surg Med
PUBLISHED: 01-22-2011
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Glioblastoma multiforme is a highly malignant primary brain tumor. It has no border but at best a marginal zone, however, invisible to the surgeon. An optical touch pointer (OTP) enabling differentiation of healthy and tumor tissue by means of fiber-optic fluorescence spectroscopy has been developed. In combination with an ultrasonic navigation system, the OTP may be used for demarcation of resectable tumor tissue. The aim of the study was to evaluate the clinical performance of OTP during surgery of malignant brain tumors.
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Transscleral visible/near-infrared spectroscopy for quantitative assessment of haemoglobin in experimental choroidal tumours.
Acta Ophthalmol
PUBLISHED: 12-14-2010
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To study the feasibility of using transscleral visible/near-infrared spectroscopy (Vis/NIRS) to estimate the content of haemoglobin in choroidal tumour phantoms of ex vivo porcine eyes.
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System for interstitial photodynamic therapy with online dosimetry: first clinical experiences of prostate cancer.
J Biomed Opt
PUBLISHED: 11-09-2010
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The first results from a clinical study for Temoporfin-mediated photodynamic therapy (PDT) of low-grade (T1c) primary prostate cancer using online dosimetry are presented. Dosimetric feedback in real time was applied, for the first time to our knowledge, in interstitial photodynamic therapy. The dosimetry software IDOSE provided dose plans, including optical fiber positions and light doses based on 3-D tissue models generated from ultrasound images. Tissue optical property measurements were obtained using the same fibers used for light delivery. Measurements were taken before, during, and after the treatment session. On the basis of these real-time measured optical properties, the light-dose plan was recalculated. The aim of the treatment was to ablate the entire prostate while minimizing exposure to surrounding organs. The results indicate that online dosimetry based on real-time tissue optical property measurements enabled the light dose to be adapted and optimized. However, histopathological analysis of tissue biopsies taken six months post-PDT treatment showed there were still residual viable cancer cells present in the prostate tissue sections. The authors propose that the incomplete treatment of the prostate tissue could be due to a too low light threshold dose, which was set to 5 J?cm2.
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Photodynamic therapy: superficial and interstitial illumination.
J Biomed Opt
PUBLISHED: 08-31-2010
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Photodynamic therapy (PDT) is reviewed using the treatment of skin tumors as an example of superficial lesions and prostate cancer as an example of deep-lying lesions requiring interstitial intervention. These two applications are among the most commonly studied in oncological PDT, and illustrate well the different challenges facing the two modalities of PDT-superficial and interstitial. They thus serve as good examples to illustrate the entire field of PDT in oncology. PDT is discussed based on the Lund University groups over 20 yr of experience in the field. In particular, the interplay between optical diagnostics and dosimetry and the delivery of the therapeutic light dose are highlighted. An interactive multiple-fiber interstitial procedure to deliver the required therapeutic dose based on the assessment of light fluence rate and sensitizer concentration and oxygen level throughout the tumor is presented.
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Use of nonlinear upconverting nanoparticles provides increased spatial resolution in fluorescence diffuse imaging.
Opt Lett
PUBLISHED: 08-19-2010
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Fluorescence diffuse imaging (FDI) suffers from limited spatial resolution. In this Letter, we report a scanning imaging approach to increase the resolution of FDI using nonlinear fluorophores. The resolution of a linear fluorophore was compared with nonlinear upconverting nanoparticles (NaYF(4):Yb(3+)/Tm(3+)) in a tissue phantom. A resolution improvement of a factor of 1.3 was found experimentally. Simulations suggested a maximum resolution improvement of a factor of 1.45. Usage of nonlinear fluorophores is a promising method for increasing the spatial resolution in FDI.
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Next-generation acceleration and code optimization for light transport in turbid media using GPUs.
Biomed Opt Express
PUBLISHED: 07-09-2010
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A highly optimized Monte Carlo (MC) code package for simulating light transport is developed on the latest graphics processing unit (GPU) built for general-purpose computing from NVIDIA - the Fermi GPU. In biomedical optics, the MC method is the gold standard approach for simulating light transport in biological tissue, both due to its accuracy and its flexibility in modelling realistic, heterogeneous tissue geometry in 3-D. However, the widespread use of MC simulations in inverse problems, such as treatment planning for PDT, is limited by their long computation time. Despite its parallel nature, optimizing MC code on the GPU has been shown to be a challenge, particularly when the sharing of simulation result matrices among many parallel threads demands the frequent use of atomic instructions to access the slow GPU global memory. This paper proposes an optimization scheme that utilizes the fast shared memory to resolve the performance bottleneck caused by atomic access, and discusses numerous other optimization techniques needed to harness the full potential of the GPU. Using these techniques, a widely accepted MC code package in biophotonics, called MCML, was successfully accelerated on a Fermi GPU by approximately 600x compared to a state-of-the-art Intel Core i7 CPU. A skin model consisting of 7 layers was used as the standard simulation geometry. To demonstrate the possibility of GPU cluster computing, the same GPU code was executed on four GPUs, showing a linear improvement in performance with an increasing number of GPUs. The GPU-based MCML code package, named GPU-MCML, is compatible with a wide range of graphics cards and is released as an open-source software in two versions: an optimized version tuned for high performance and a simplified version for beginners (http://code.google.com/p/gpumcml).
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Optical porosimetry and investigations of the porosity experienced by light interacting with porous media.
Opt Lett
PUBLISHED: 06-03-2010
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We investigate how light samples disordered porous materials such as ceramics and pharmaceutical materials. By combining photon time-of-flight spectroscopy and sensitive laser-based gas sensing, we obtain information on the extent to which light interacts with solid and pore volumes, respectively. Comparison with mercury intrusion porosimetry shows that light predominantly interacts with the solid. Analysis based on a two-state model does not fully explain observations, revealing a need for refined modeling. Nonetheless, excellent correlation between actual porosity and the porosity experienced by photons demonstrates the potential of nondestructive optical porosimetry based on gas absorption.
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A desorption mechanism of water following vacuum-ultraviolet irradiation on amorphous solid water at 90 K.
J Chem Phys
PUBLISHED: 05-06-2010
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Following 157 nm photoexcitation of amorphous solid water and polycrystalline water ice, photodesorbed water molecules (H(2)O and D(2)O), in the ground vibrational state, have been observed using resonance-enhanced multiphoton ionization detection methods. Time-of-flight and rotationally resolved spectra of the photodesorbed water molecules were measured, and the kinetic and internal energy distributions were obtained. The measured energy distributions are in good accord with those predicted by classical molecular dynamics calculations for the kick-out mechanism of a water molecule from the ice surface by a hot hydrogen (deuterium) atom formed by photodissociation of a neighboring water molecule. Desorption of D(2)O following 193 nm photoirradiation of a D(2)O/H(2)S mixed ice was also investigated to provide further direct evidence for the operation of a kick-out mechanism.
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Multibeam fluorescence diffuse optical tomography using upconverting nanoparticles.
Opt Lett
PUBLISHED: 03-03-2010
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Fluorescence diffuse optical tomography (FDOT) is a biomedical imaging modality that can be used for localization and quantification of fluorescent molecules inside turbid media. In this ill-posed problem, the reconstruction quality is directly determined by the amount and quality of the information obtained from the boundary measurements. Regularly, more information can be obtained by increasing the number of excitation positions in an FDOT system. However, the maximum number of excitation positions is limited by the finite size of the excitation beam. In the present work, we demonstrate a method in FDOT to exploit the unique nonlinear power dependence of upconverting nanoparticles to further increase the amount of information in a raster-scanning setup by including excitation with two beams simultaneously. We show that the additional information can be used to obtain more accurate reconstructions.
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Optical touch pointer for fluorescence guided glioblastoma resection using 5-aminolevulinic acid.
Lasers Surg Med
PUBLISHED: 01-16-2010
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Total tumor resection in patients with glioblastoma multiforme (GBM) is difficult to achieve due to the tumors infiltrative way of growing and morphological similarity to the surrounding functioning brain tissue. The diagnosis is usually subjectively performed using a surgical microscope. The objective of this study was to develop and evaluate a hand-held optical touch pointer using a fluorescence spectroscopy system to quantitatively distinguish healthy from malignant brain tissue intraoperatively.
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Quantitative genetic effects of bottlenecks: experimental evidence from a wild plant species, Nigella degenii.
J. Hered.
PUBLISHED: 11-27-2009
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Understanding the genetic consequences of changes in population size is fundamental in a variety of contexts, such as adaptation and conservation biology. In the study presented here, we have performed a replicated experiment with the plant Nigella degenii to explore the quantitative genetic effects of a single-founder bottleneck. In agreement with additive theory, the bottleneck reduced the mean (co)variance within lines and caused stochastic, line-specific changes in the genetic (co)variance structure. However, a significant portion of the (co)variance structure was conserved, and 2 characters-leaf and flower (sepal) size-turned out to be positively correlated in all data sets, indicating a potential for correlated evolution in these characters, even after a severe bottleneck. The hierarchical partitioning of genetic variance for flower size was in good agreement with predictions from additive theory, whereas the remaining characters showed an excess of within-line variance and a deficiency of among-line variance. The latter discrepancies were most likely a result of selection, given the small proportion of lines (23%) that remained viable until the end of the experiment. Our results suggest that bottlenecked populations of N. degenii generally have a lower adaptive potential than the ancestral population but also highlight the idiosyncratic nature of bottleneck effects.
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Desorption of hydroxyl radicals in the vacuum ultraviolet photolysis of amorphous solid water at 90 K.
J Chem Phys
PUBLISHED: 08-14-2009
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We have studied the desorption dynamics of OH radicals from the 157 nm photodissociation of amorphous solid water (ASW) as well as H(2)O(2) deposited on an ASW surface at 90 K. The translational and internal energy distributions of OH were measured using resonance-enhanced multiphoton ionization methods. These distributions are compared to reported molecular dynamics calculations for the condensed phase photodissociation of water ice and also reported results for the gas phase photodissociation of H(2)O at 157 nm. We have confirmed that OH radicals are produced from two different mechanisms: one from primary photolysis of surface H(2)O of ASW, and the other being secondary photolysis of H(2)O(2) photoproducts on the ASW surface after prolonged irradiation at 157 nm.
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Transscleral visible/near-infrared spectroscopy for quantitative assessment of melanin in a uveal melanoma phantom of ex vivo porcine eyes.
Exp. Eye Res.
PUBLISHED: 08-10-2009
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Optical spectroscopy has been used as a supplement to conventional techniques for analyzing and diagnosing cancer in many human organs. Because ocular tumors may be characterized by their different melanin content, we investigated the feasibility of using transscleral visible/near-infrared spectroscopy (Vis/NIRS) to estimate the quantity of melanin in a novel uveal melanoma phantom of ex vivo porcine eyes. The phantoms were made by injecting a freshly prepared suspension of 15% (wt/vol) gelatin, 10 mg/ml titanium dioxide (TiO(2)), and natural melanin, isolated from the ink sac of cuttlefish (Sepia officinalis), into the suprachoroidal space of 30 enucleated porcine eyes. The melanin concentrations used were 1 mg/ml, 2 mg/ml, and 3 mg/ml, with 10 eyes in each group. After gelation, the size and location of the phantoms were documented by B-scan ultrasonography and transillumination. Vis/NIRS recordings, covering the wavelength region from 550 to 1000 nm, were performed with two optical fibers separated by 6 mm to deliver and collect the light through the sclera. During all measurements, the exact pressure exerted by the fiber probe on the scleral surface was monitored by placing the eye on an electronic scale. Transscleral Vis/NIRS was performed across the phantom inclusion, as well as on the opposite (normal) side of each eye. A total of three consecutive measurements were carried out alternately on each side of the globe. The spectral data were analyzed using partial least squares regression. In the melanin concentration groups of 1 mg/ml (n = 10), 2 mg/ml (n = 10), and 3 mg/ml (n = 10), the largest basal phantom diameters (mean +/- SD) were 14.9 +/- 1.6 mm, 14.6 +/- 1.5 mm, and 14.3 +/- 1.0 mm, respectively (p > 0.05). The largest phantom thicknesses (mean +/- SD) were 4.0 +/- 0.5 mm, 4.4 +/- 0.7 mm, and 4.5 +/- 0.5 mm, respectively (p > 0.05). Statistical regression modeling of the Vis/NIRS data revealed that it was possible to correctly classify the phantoms according to their melanin concentrations in 84.4% of cases. The correct classification rate for phantoms with the lowest (1 mg/ml) and highest (3 mg/ml) melanin concentrations was 99.2%. The study demonstrates that transscleral Vis/NIRS is a feasible and accurate method for predicting the content of melanin in choroidal lesions.
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Near-infrared photon time-of-flight spectroscopy of turbid materials up to 1400 nm.
Rev Sci Instrum
PUBLISHED: 07-02-2009
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Photon time-of-flight spectroscopy (PTOFS) is a powerful tool for analysis of turbid materials. We have constructed a time-of-flight spectrometer based on a supercontinuum fiber laser, acousto-optical tunable filtering, and an InP/InGaAsP microchannel plate photomultiplier tube. The system is capable of performing PTOFS up to 1400 nm, and thus covers an important region for vibrational spectroscopy of solid samples. The development significantly increases the applicability of PTOFS for analysis of chemical content and physical properties of turbid media. The great value of the proposed approach is illustrated by revealing the distinct absorption features of turbid epoxy resin. Promising future applications of the approach are discussed, including quantitative assessment of pharmaceuticals, powder analysis, and calibration-free near-infrared spectroscopy.
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The dynamics of the H2 + CO+ reaction on an interpolated potential energy surface.
J Chem Phys
PUBLISHED: 07-02-2009
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A potential energy surface that describes the title reaction has been constructed by interpolation of ab initio data. Classical trajectory studies on this surface show that the total reaction rate is close to that predicted by a Langevin model, although the mechanism is more complicated than simple ion-molecule capture. Only the HCO(+) + H product is observed classically. An estimate of the magnitude of rotational inelastic scattering is also reported.
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Comparison of quantum dynamics and quantum transition state theory estimates of the H + CH4 reaction rate.
J Phys Chem A
PUBLISHED: 03-12-2009
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Thermal rate constants are calculated for the H + CH(4) --> CH(3) + H(2) reaction employing the potential energy surface of Espinosa-Garcia (Espinosa-Garcia, J. J. Chem. Phys. 2002, 116, 10664). Two theoretical approaches are used. First, we employ the multiconfigurational time-dependent Hartree method combined with flux correlation functions. In this way rate constants in the range 225-400 K are obtained and compared with previous results using the same theoretical method but the potential energy surface of Wu et al. (Wu, T.; Werner, H.-J.; Manthe, U. Science 2004, 306, 2227). It is found that the Espinosa-Garcia surface results in larger rate constants. Second, a harmonic quantum transition state theory (HQTST) implementation of instanton theory is used to obtain rate constants in a temperature interval from 20 K up to the crossover temperature at 296 K. The HQTST estimates are larger than MCTDH ones by a factor of about three in the common temperature range. Comparison is also made with various tunneling corrections to transition state theory and quantum instanton theory.
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A matrix-free algorithm for multiple wavelength fluorescence tomography.
Opt Express
PUBLISHED: 03-05-2009
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In the recent years, there has been an increase in applications of non-contact diffusion optical tomography. Especially when the objective is the recovery of fluorescence targets. The non-contact acquisition systems with the use of a CCD-camera produce much denser sampled boundary data sets than fibre-based systems. When model-based reconstruction methods are used, that rely on the inversion of a derivative operator, the large number of measurements poses a challenge since the explicit formulation and storage of the Jacobian matrix could be in general not feasible. This problem is aggravated further in applications, where measurements at multiple wavelengths are used. We present a matrix-free model-based reconstruction method, that addresses the problems of large data sets and reduces the computational cost and memory requirements for the reconstruction. The idea behind the matrix-free method is that information about the Jacobian matrix could be available through matrix times vector products so that the creation and storage of big matrices can be avoided. We tested the method for multiple wavelength fluorescence tomography with simulated and experimental data from phantom experiments, and we found substantial benefits in computational times and memory requirements.
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In vivo photosensitizer tomography inside the human prostate.
Opt Lett
PUBLISHED: 02-03-2009
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Interstitial photodynamic therapy (IPDT) provides a promising means to treat large cancerous tumors and solid organs inside the human body. The treatment outcome is dependent on the distributions of light, photosensitizer, and tissue oxygenation. We present a scheme for reconstructing the spatial distribution of a fluorescent photosensitizer. The reconstruction is based on measurements performed in the human prostate, acquired during an ongoing IPDT clinical trial, as well as in optical phantoms. We show that in an experimental setup we can quantitatively reconstruct a fluorescent inclusion in a fluorescent background. We also show reconstructions from a patient showing a heterogeneous distribution of the photosensitizer mTHPC in the human prostate.
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Evaluation of a radiative transfer equation and diffusion approximation hybrid forward solver for fluorescence molecular imaging.
J Biomed Opt
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The solution of the forward problem in fluorescence molecular imaging strongly influences the successful convergence of the fluorophore reconstruction. The most common approach to meeting this problem has been to apply the diffusion approximation. However, this model is a first-order angular approximation of the radiative transfer equation, and thus is subject to some well-known limitations. This manuscript proposes a methodology that confronts these limitations by applying the radiative transfer equation in spatial regions in which the diffusion approximation gives decreased accuracy. The explicit integro differential equations that formulate this model were solved by applying the Galerkin finite element approximation. The required spatial discretization of the investigated domain was implemented through the Delaunay triangulation, while the azimuthal discretization scheme was used for the angular space. This model has been evaluated on two simulation geometries and the results were compared with results from an independent Monte Carlo method and the radiative transfer equation by calculating the absolute values of the relative errors between these models. The results show that the proposed forward solver can approximate the radiative transfer equation and the Monte Carlo method with better than 95% accuracy, while the accuracy of the diffusion approximation is approximately 10% lower.
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Quantitative integral cross sections for the H + CO2 ? OH + CO reaction from a density functional theory-based potential energy surface.
Phys Chem Chem Phys
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The OH + CO ? H + CO(2) reaction is important in combustion, atmospheric, and interstellar chemistry. Whereas the direct reaction has been extensively studied both experimentally and theoretically, the reverse reaction has received relatively less attention. Here we carry out a quasiclassical trajectory study of the hyperthermal H + CO(2)? OH + CO reaction on a new interpolated potential energy surface based on the M06-2X density functional. The results reveal for the first time quantitative agreement with experiment for the reaction cross sections in the range of relative translational energies 1.2-2.5 eV. We attribute this excellent agreement to both the quality of the M06-2X energies, which closely reproduce CCSD(T) energies, and to the potential surface construction strategy that emphasizes both the direct and reverse reactions.
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Does inbreeding promote evolutionary reduction of flower size? Experimental evidence from Crepis tectorum (Asteraceae).
Am. J. Bot.
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Small, autogamous flowers have evolved repeatedly in the plant kingdom. While much attention has focused on the mechanisms that promote the shift to autogamy, there is still a paucity of information on the factors that underlie the reduction of flower size so prevalent in selfing lineages. In this study of Crepis tectorum, I examine the role of inbreeding, acting alone or together with selection, in promoting evolutionary reduction of flower size.
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Single-fiber diffuse optical time-of-flight spectroscopy.
Opt Lett
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We demonstrate interstitial diffuse optical time-of-fight spectroscopy based on a single fiber for both light delivery and detection. Detector saturation due to the massive short-time reflection is avoided by ultrafast gating of a single photon avalanche diode. We show that the effects of scattering and absorption are separable and that absorption can be assessed independently of scattering. Measurements on calibrated liquid phantoms and subsequent Monte Carlo-based evaluation illustrate that absorption coefficients can be accurately assessed over a wide range of medically relevant optical properties. Our findings pave the way to simplified and less invasive interstitial in vivo spectroscopy.
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Transscleral optical spectroscopy of uveal melanoma in enucleated human eyes.
Invest. Ophthalmol. Vis. Sci.
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The aims of this study were to use transscleral optical spectroscopy to analyze normal and tumor-infiltrated areas of enucleated human eyes, and to characterize the spectral properties of uveal melanomas in relation to various morphological features.
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Estimation of heritability, evolvability and genetic correlations of two pollen and pistil traits involved in a sexual conflict over timing of stigma receptivity in Collinsia heterophylla (Plantaginaceae).
Ann. Bot.
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Heritable genetic variation is crucial for selection to operate, yet there is a paucity of studies quantifying such variation in interactive male/female sexual traits, especially those of plants. Previous work on the annual plant Collinsia heterophylla, a mixed-mating species, suggests that delayed stigma receptivity is involved in a sexual conflict: pollen from certain donors fertilize ovules earlier than others at the expense of reduced maternal seed set and lower levels of pollen competition.
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High-resolution fluorescence diffuse optical tomography developed with nonlinear upconverting nanoparticles.
ACS Nano
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Fluorescence diffuse optical tomography (FDOT) is an emerging biomedical imaging technique that can be used to localize and quantify deeply situated fluorescent molecules within tissues. However, the potential of this technique is currently limited by its poor spatial resolution. In this work, we demonstrate that the current resolution limit of FDOT can be breached by exploiting the nonlinear power-dependent optical emission property of upconverting nanoparticles doped with rare-earth elements. The rare-earth-doped core-shell nanoparticles, NaYF(4):Yb(3+)/Tm(3+)@NaYF(4) of hexagonal phase, are synthesized through a stoichiometric method, and optical characterization shows that the upconverting emission of the nanoparticles in tissues depends quadratically on the power of excitation. In addition, quantum-yield measurements of the emission from the synthesized nanoparticles are performed over a large range of excitation intensities, for both core and core-shell particles. The measurements show that the quantum yield of the 800 nm emission band of core-shell upconverting nanoparticles is 3.5% under an excitation intensity of 78 W/cm(2). The FDOT reconstruction experiments are carried out in a controlled environment using liquid tissue phantoms. The experiments show that the spatial resolution of the FDOT reconstruction images can be significantly improved by the use of the synthesized upconverting nanoparticles and break the current spatial resolution limits of FDOT images obtained from using conventional linear fluorophores as contrast agents.
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An adiabatic capture theory and quasiclassical trajectory study of C + NO and O + CN on the 2A, 2A", and 4A" potential energy surfaces.
J Phys Chem A
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The adiabatic capture centrifugal sudden approximation (ACCSA) has been applied to the C + NO and O + CN reactions, along with quasiclassical trajectory simulations. Existing global analytic fits to the potential energy surfaces of the CNO system in the (2)A, (2)A", and (4)A" electronic states have been used. Thermal rate constants for reaction in each of the electronic states have been calculated. In all cases a strong temperature dependence is evident in the calculated rate constants. The agreement between the calculated adiabatic capture and quasiclassical trajectory rate constants is excellent in some cases, but these rate constants differ considerably in other cases. This behavior is analyzed in terms of the anisotropy of the potential energy surfaces. On the basis of this analysis, we propose a new diagnostic for the reliability of ACCSA capture calculations.
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In vivo measurements of diffuse reflectance and time-resolved autofluorescence emission spectra of basal cell carcinomas.
J Biophotonics
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We present a clinical investigation of diffuse reflectance and time-resolved autofluorescence spectra of skin cancer with an emphasis on basal cell carcinoma. A total of 25 patients were measured using a compact steady-state diffuse reflectance/fluorescence spectrometer and a fibre-optic-coupled multispectral time-resolved spectrofluorometer. Measurements were performed in vivo prior to surgical excision of the investigated region. Singular value decomposition was used to reduce the dimensionality of steady state diffuse reflectance and fluorescence spectra. Linear discriminant analysis was then applied to the measurements of basal cell carcinomas (BCCs) and used to predict the tissue disease state with a leave-one-out methodology. This approach was able to correctly diagnose 87% of the BCCs. With 445 nm excitation a decrease in the spectrally averaged fluorescence lifetime was observed between normal tissue and BCC lesions with a mean value of 886 ps. Furthermore, the fluorescence lifetime for BCCs was lower than that of the surrounding healthy tissue in all cases and statistical analysis of the data revealed that this decrease was significant (p = 0.002).
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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

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