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1.
Nanoscale ; 15(41): 16601-16611, 2023 Oct 26.
Article in English | MEDLINE | ID: mdl-37812063

ABSTRACT

The photoluminescence (PL) of lanthanide-doped nanocrystals can be quenched by energy transfer to vibrations of molecules located within a few nanometers from the dopants. Such short-range electronic-to-vibrational energy transfer (EVET) is often undesired as it reduces the photoluminescence efficiency. On the other hand, EVET may be exploited to extract information about molecular vibrations in the local environment of the nanocrystals. Here, we investigate the influence of solvent and gas environments on the PL properties of NaYF4:Er3+,Yb3+ upconversion nanocrystals. We relate changes in the PL spectrum and excited-state lifetimes in different solvents and their deuterated analogues to quenching of specific lanthanide levels by EVET to molecular vibrations. Similar but weaker changes are induced when we expose a film of nanocrystals to a gas environment with different amounts of H2O or D2O vapor. Quenching of green- and red-emitting levels of Er3+ can be explained in terms of EVET-mediated quenching that involves molecular vibrations with energies resonant with the gap between the energy levels of the lanthanide. Quenching of the near-infrared-emitting level is more complex and may involve EVET to combination-vibrations or defect-mediated quenching. EVET-mediated quenching holds promise as a mechanism to probe the local chemical environment-both for nanocrystals dispersed in a liquid and for nanocrystals exposed to gaseous molecules that adsorb onto the nanocrystal surface.

2.
J Phys Chem Lett ; 13(42): 9950-9956, 2022 Oct 27.
Article in English | MEDLINE | ID: mdl-36260410

ABSTRACT

Impurity doping of low-dimensional semiconductors is an interesting route towards achieving control over carrier dynamics and energetics, e.g., to improve hot carrier extraction, or to obtain strongly Stokes shifted luminescence. Such studies remain, however, underexplored for the emerging family of III-V colloidal quantum dots (QDs). Here, we show through a detailed global analysis of multiresonant pump-probe spectroscopy that electron cooling in copper-doped InP quantum dot (QDs) proceeds on subpicosecond time scales. Conversely, hole localization on Cu dopants is remarkably slow (1.8 ps), yet still leads to very efficient subgap emission. Due to this slow hole localization, common Auger assisted pathways in electron cooling cannot be blocked by Cu doping III-V systems, in contrast with the case of II-VI QDs. Finally, we argue that the structural relaxation around the Cu dopants, estimated to impart a reorganization energy of 220 meV, most likely proceeds simultaneously with the localization itself leading to efficient luminescence.

3.
ACS Nanosci Au ; 2(2): 111-118, 2022 Apr 20.
Article in English | MEDLINE | ID: mdl-35481224

ABSTRACT

Many phosphor materials rely on energy transfer (ET) between optically active dopant ions. Typically, a donor species absorbs light of one color and transfers the energy to an acceptor species that emits light of a different color. For many applications, it is beneficial, or even crucial, that the phosphor is of nanocrystalline nature. Much unlike the widely recognized finite-size effects on the optical properties of quantum dots, the behavior of optically active ions is generally assumed to be independent of the size or shape of the optically inactive host material. Here, we demonstrate that ET between optically active dopants is also impacted by finite-size effects: Donor ions close to the surface of a nanocrystal (NC) are likely to have fewer acceptors in proximity compared to donors in a bulk-like coordination. As such, the rate and efficiency of ET in nanocrystalline phosphors are low in comparison to that of their bulk counterparts. Surprisingly, these undesired finite-size effects should be considered already for NCs with diameters as large as 12 nm. If we suppress radiative decay of the donor by embedding the NCs in media with low refractive indices, we can compensate for finite-size effects on the ET rate. Experimentally, we demonstrate these finite-size effects and how to compensate for them in YPO4 NCs co-doped with Tb3+ and Yb3+.

4.
Nano Lett ; 21(1): 658-665, 2021 Jan 13.
Article in English | MEDLINE | ID: mdl-33395305

ABSTRACT

The luminescence of CuInS2 quantum dots (QDs) is slower and spectrally broader than that of many other types of QDs. The origin of this anomalous behavior is still under debate. Single-QD experiments could help settle this debate, but studies by different groups have yielded conflicting results. Here, we study the photophysics of single core-only CuInS2 and core/shell CuInS2/CdS QDs. Both types of single QDs exhibit broad PL spectra with fluctuating peak position and single-exponential photoluminescence decay with a slow but fluctuating lifetime. Spectral diffusion of CuInS2-based QDs is qualitatively and quantitatively different from CdSe-based QDs. The differences reflect the dipole moment of the CuInS2 excited state and hole localization on a preferred site in the QD. Our results unravel the highly dynamic photophysics of CuInS2 QDs and highlight the power of the analysis of single-QD property fluctuations.

5.
J Phys Chem C Nanomater Interfaces ; 124(14): 8047-8054, 2020 Apr 09.
Article in English | MEDLINE | ID: mdl-32421082

ABSTRACT

Metal-halide perovskite nanocrystals show promise as the future active material in photovoltaics, lighting, and other optoelectronic applications. The appeal of these materials is largely due to the robustness of the optoelectronic properties to structural defects. The photoluminescence quantum yield (PLQY) of most types of perovskite nanocrystals is nevertheless below unity, evidencing the existence of nonradiative charge-carrier decay channels. In this work, we experimentally elucidate the nonradiative pathways in CsPbBr3 nanoplatelets, before and after chemical treatment with PbBr2 that improves the PLQY. A combination of picosecond streak camera and nanosecond time-correlated single-photon counting measurements is used to probe the excited-state dynamics over 6 orders of magnitude in time. We find that up to 40% of the nanoplatelets from a synthesis batch are entirely nonfluorescent and cannot be turned fluorescent through chemical treatment. The other nanoplatelets show fluorescence, but charge-carrier trapping leads to losses that are prevented by chemical treatment. Interestingly, even without chemical treatment, some losses due to trapping are mitigated because trapped carriers spontaneously detrap on nanosecond-to-microsecond timescales. Our analysis shows that multiple nonradiative pathways are active in perovskite nanoplatelets, which are affected differently by chemical treatment with PbBr2. More generally, our work highlights that in-depth studies using a combination of techniques are necessary to understand nonradiative pathways in fluorescent nanocrystals. Such understanding is essential to optimize synthesis and treatment procedures.

6.
Am J Disaster Med ; 14(1): 9-15, 2019.
Article in English | MEDLINE | ID: mdl-31441024

ABSTRACT

OBJECTIVE: Improve documentation during a mass casualty incident (MCI). DESIGN: This is a retrospective chart review. SETTING: This chart review was done in the Major Incident Hospital (MIH). The MIH is a highly prepared back-up hospital in the center of the Netherland that can be deployed in case of a major incident. PATIENTS, PARTICIPANTS: Until recently, the MIH used an extensive paper medical record: the hospital in special circumstances medical record (HSCMR). A concise primary survey form was developed and attached to the HSCMR, forming the pilot disaster medical record (pDMR). In this retrospective chart review, primary survey data documented in the HSCMR (during a MCI) were compared to the pDMR (during a drill exercise). Three triage categories were used: T1, immediate; T2, urgent; and T3, delayed. MAIN OUTCOME: The MIH hypothesized that a dedicated, concise, and practical primary survey form could improve quantitative patient documentation during an MCI. Significant differences were tested with the chi square and Fisher exact test (p < 0.05). RESULTS: The pDMR was used significantly more often 61 percent vs 89 percent (p = 0.001), especially in T1 and T2 patients. Quantitative documentation in the pDMR improved significantly on airway, breathing, breathing frequency, saturation, circulation, heart rate, blood pressure, Glasgow Coma Score, exposure, and medication given but not in cervical spine and temperature. CONCLUSION: Significantly more primary survey forms were used and more data were documented using the pDMR, especially in the most critical patients. An MCI medical record should be simple and concise and should not deviate from daily routine.


Subject(s)
Disaster Planning , Mass Casualty Incidents , Medical Records/standards , Triage/methods , Humans , Retrospective Studies
7.
J Phys Chem C Nanomater Interfaces ; 123(14): 8892-8901, 2019 Apr 11.
Article in English | MEDLINE | ID: mdl-31001369

ABSTRACT

On-surface synthesis has emerged in the last decade as a method to create graphene nanoribbons (GNRs) with atomic precision. The underlying premise of this bottom-up strategy is that precursor molecules undergo a well-defined sequence of inter- and intramolecular reactions, leading to the formation of a single product. As such, the structure of the GNR is encoded in the precursors. However, recent examples have shown that not only the molecule, but also the coinage metal surface on which the reaction takes place, plays a decisive role in dictating the nanoribbon structure. In this work, we use scanning probe microscopy and X-ray photoelectron spectroscopy to investigate the behavior of 10,10'-dichloro-9,9'-bianthryl (DCBA) on Ag(111). Our study shows that Ag(111) can induce the formation of both seven-atom wide armchair GNRs (7-acGNRs) and 3,1-chiral GNRs (3,1-cGNRs), demonstrating that a single molecule on a single surface can react to different nanoribbon products. We additionally show that coadsorbed dibromoperylene can promote surface-assisted dehydrogenative coupling in DCBA, leading to the exclusive formation of 3,1-cGNRs.

8.
J Phys Chem Lett ; 10(7): 1600-1616, 2019 Apr 04.
Article in English | MEDLINE | ID: mdl-30883139

ABSTRACT

Colloidal nanocrystals of ternary I-III-VI2 semiconductors are emerging as promising alternatives to Cd- and Pb-chalcogenide nanocrystals because of their inherently lower toxicity, while still offering widely tunable photoluminescence. These properties make them promising materials for a variety of applications. However, the realization of their full potential has been hindered by both their underdeveloped synthesis and the poor understanding of their optoelectronic properties, whose origins are still under intense debate. In this Perspective, we provide novel insights on the latter aspect by critically discussing the accumulated body of knowledge on I-III-VI2 nanocrystals. From our analysis, we conclude that the luminescence in these nanomaterials most likely originates from the radiative recombination of a delocalized conduction band electron with a hole localized at the group-I cation, which results in broad bandwidths, large Stokes shifts, and long exciton lifetimes. Finally, we highlight the remaining open questions and propose experiments to address them.

9.
ACS Nano ; 12(7): 7048-7056, 2018 Jul 24.
Article in English | MEDLINE | ID: mdl-29939719

ABSTRACT

With the advent of atomically precise synthesis and consequent precise tailoring of their electronic properties, graphene nanoribbons (GNRs) have emerged as promising building blocks for nanoelectronics. Before being applied as such, it is imperative that their charge transport properties are investigated. Recently, formation of a molecular junction through the controlled attachment of nanoribbons to the probe of a scanning tunneling microscope (STM) and subsequent lifting allowed for the first conductance measurements. Drawbacks are the perturbation of the intrinsic electronic properties through interaction with the metal surface, as well as the risk of current-induced defect formation which largely restricts the measurements to low bias voltages. Here, we show that resonant transport-essential for device applications-can be measured by lifting electronically decoupled GNRs from an ultrathin layer of NaCl. By varying the applied voltage and tip-sample distance, we can probe resonant transport through frontier orbitals and its dependence on junction length. This technique is used for two distinct types of GNRs: the 7 atom wide armchair GNR and the 3,1-chiral GNR. The features in the conductance maps can be understood and modeled in terms of the intrinsic electronic properties of the ribbons as well as capacitive coupling to tip and substrate. We demonstrate that we can simultaneously measure the current decay with increasing junction length and bias voltage by using a double modulation spectroscopy technique. The strategy described in this work is widely applicable and will lead to a better understanding of electronic transport through molecular junctions in general.

10.
Biomed Opt Express ; 8(7): 3292-3316, 2017 Jul 01.
Article in English | MEDLINE | ID: mdl-28717568

ABSTRACT

We developed a fully automated system using a convolutional neural network (CNN) for total retina segmentation in optical coherence tomography (OCT) that is robust to the presence of severe retinal pathology. A generalized U-net network architecture was introduced to include the large context needed to account for large retinal changes. The proposed algorithm outperformed qualitative and quantitatively two available algorithms. The algorithm accurately estimated macular thickness with an error of 14.0 ± 22.1 µm, substantially lower than the error obtained using the other algorithms (42.9 ± 116.0 µm and 27.1 ± 69.3 µm, respectively). These results highlighted the proposed algorithm's capability of modeling the wide variability in retinal appearance and obtained a robust and reliable retina segmentation even in severe pathological cases.

11.
Invest Ophthalmol Vis Sci ; 58(4): 2318-2328, 2017 04 01.
Article in English | MEDLINE | ID: mdl-28437528

ABSTRACT

Purpose: To evaluate a machine learning algorithm that automatically grades age-related macular degeneration (AMD) severity stages from optical coherence tomography (OCT) scans. Methods: A total of 3265 OCT scans from 1016 patients with either no signs of AMD or with signs of early, intermediate, or advanced AMD were randomly selected from a large European multicenter database. A machine learning system was developed to automatically grade unseen OCT scans into different AMD severity stages without requiring retinal layer segmentation. The ability of the system to identify high-risk AMD stages and to assign the correct severity stage was determined by using receiver operator characteristic (ROC) analysis and Cohen's κ statistics (κ), respectively. The results were compared to those of two human observers. Reproducibility was assessed in an independent, publicly available data set of 384 OCT scans. Results: The system achieved an area under the ROC curve of 0.980 with a sensitivity of 98.2% at a specificity of 91.2%. This compares favorably with the performance of human observers who achieved sensitivities of 97.0% and 99.4% at specificities of 89.7% and 87.2%, respectively. A good level of agreement with the reference was obtained (κ = 0.713) and was in concordance with the human observers (κ = 0.775 and κ = 0.755, respectively). Conclusions: A machine learning system capable of automatically grading OCT scans into AMD severity stages was developed and showed similar performance as human observers. The proposed automatic system allows for a quick and reliable grading of large quantities of OCT scans, which could increase the efficiency of large-scale AMD studies and pave the way for AMD screening using OCT.


Subject(s)
Macula Lutea/pathology , Macular Degeneration/diagnosis , Tomography, Optical Coherence/methods , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , ROC Curve , Reproducibility of Results , Severity of Illness Index
12.
PLoS One ; 11(11): e0167336, 2016.
Article in English | MEDLINE | ID: mdl-27898729

ABSTRACT

Glycosaminoglycans (GAGs) are linear negatively charged polysaccharides and important components of extracellular matrices and cell surface glycan layers such as the endothelial glycocalyx. The GAG family includes sulfated heparin, heparan sulfate (HS), dermatan sulfate (DS), chondroitin sulfate (CS), keratan sulfate, and non-sulfated hyaluronan. Because relative expression of GAGs is dependent on cell-type and niche, isolating GAGs from cell cultures and tissues may provide insight into cell- and tissue-specific GAG structure and functions. In our objective to obtain structural information about the GAGs expressed on a specialized mouse glomerular endothelial cell culture (mGEnC-1) we adapted a recently published GAG isolation protocol, based on cell lysis, proteinase K and DNase I digestion. Analysis of the GAGs contributing to the mGEnC-1 glycocalyx indicated a large HS and a minor CS content on barium acetate gel. However, isolated GAGs appeared resistant to enzymatic digestion by heparinases. We found that these GAG extracts were heavily contaminated with RNA, which co-migrated with HS in barium acetate gel electrophoresis and interfered with 1,9-dimethylmethylene blue (DMMB) assays, resulting in an overestimation of GAG yields. We hypothesized that RNA may be contaminating GAG extracts from other cell cultures and possibly tissue, and therefore investigated potential RNA contaminations in GAG extracts from two additional cell lines, human umbilical vein endothelial cells and retinal pigmental epithelial cells, and mouse kidney, liver, spleen and heart tissue. GAG extracts from all examined cell lines and tissues contained varying amounts of contaminating RNA, which interfered with GAG quantification using DMMB assays and characterization of GAGs by barium acetate gel electrophoresis. We therefore recommend routinely evaluating the RNA content of GAG extracts and propose a robust protocol for GAG isolation that includes an RNA digestion step.


Subject(s)
Glycosaminoglycans/chemistry , Kidney/metabolism , Liver/metabolism , RNA/isolation & purification , Spleen/metabolism , Alginates/chemistry , Animals , Cell Line , Chondroitin Sulfates/chemistry , Dermatan Sulfate/chemistry , Electrophoresis, Agar Gel , Glucuronic Acid/chemistry , Glycosaminoglycans/isolation & purification , Glycosaminoglycans/standards , Heparitin Sulfate/chemistry , Hexuronic Acids/chemistry , Human Umbilical Vein Endothelial Cells , Humans , Hyaluronic Acid/chemistry , Keratan Sulfate/chemistry , Mice , Retinal Pigment Epithelium/cytology , Retinal Pigment Epithelium/metabolism
13.
Biomed Opt Express ; 7(3): 709-25, 2016 Mar 01.
Article in English | MEDLINE | ID: mdl-27231583

ABSTRACT

We developed an automatic system to identify and differentiate color fundus images containing no lesions, drusen or exudates. Drusen and exudates are lesions with a bright appearance, associated with age-related macular degeneration and diabetic retinopathy, respectively. The system consists of three lesion detectors operating at pixel-level, combining their outputs using spatial pooling and classification with a random forest classifier. System performance was compared with ratings of two independent human observers using human-expert annotations as reference. Kappa agreements of 0.89, 0.97 and 0.92 and accuracies of 0.93, 0.98 and 0.95 were obtained for the system and observers, respectively.

14.
Invest Ophthalmol Vis Sci ; 57(4): 2225-31, 2016 Apr 01.
Article in English | MEDLINE | ID: mdl-27116550

ABSTRACT

PURPOSE: Age-related macular degeneration is a common form of vision loss affecting older adults. The etiology of AMD is multifactorial and is influenced by environmental and genetic risk factors. In this study, we examine how 19 common risk variants contribute to drusen progression, a hallmark of AMD pathogenesis. METHODS: Exome chip data was made available through the International AMD Genomics Consortium (IAMDGC). Drusen quantification was carried out with color fundus photographs using an automated drusen detection and quantification algorithm. A genetic risk score (GRS) was calculated per subject by summing risk allele counts at 19 common genetic risk variants weighted by their respective effect sizes. Pathway analysis of drusen progression was carried out with the software package Pathway Analysis by Randomization Incorporating Structure. RESULTS: We observed significant correlation with drusen baseline area and the GRS in the age-related eye disease study (AREDS) dataset (ρ = 0.175, P = 0.006). Measures of association were not statistically significant between drusen progression and the GRS (P = 0.54). Pathway analysis revealed the cell adhesion molecules pathway as the most highly significant pathway associated with drusen progression (corrected P = 0.02). CONCLUSIONS: In this study, we explored the potential influence of known common AMD genetic risk factors on drusen progression. Our results from the GRS analysis showed association of increasing genetic burden (from 19 AMD associated loci) to baseline drusen load but not drusen progression in the AREDS dataset while pathway analysis suggests additional genetic contributors to AMD risk.


Subject(s)
Genetic Predisposition to Disease , Retinal Drusen/genetics , Aged , Disease Progression , Female , Fundus Oculi , Genetic Association Studies , Genotyping Techniques , Humans , Macular Degeneration/diagnosis , Macular Degeneration/genetics , Male , Oligonucleotide Array Sequence Analysis , Polymorphism, Single Nucleotide/genetics , Retinal Drusen/diagnosis , Risk Factors
15.
IEEE Trans Med Imaging ; 35(5): 1273-1284, 2016 05.
Article in English | MEDLINE | ID: mdl-26886969

ABSTRACT

Convolutional neural networks (CNNs) are deep learning network architectures that have pushed forward the state-of-the-art in a range of computer vision applications and are increasingly popular in medical image analysis. However, training of CNNs is time-consuming and challenging. In medical image analysis tasks, the majority of training examples are easy to classify and therefore contribute little to the CNN learning process. In this paper, we propose a method to improve and speed-up the CNN training for medical image analysis tasks by dynamically selecting misclassified negative samples during training. Training samples are heuristically sampled based on classification by the current status of the CNN. Weights are assigned to the training samples and informative samples are more likely to be included in the next CNN training iteration. We evaluated and compared our proposed method by training a CNN with (SeS) and without (NSeS) the selective sampling method. We focus on the detection of hemorrhages in color fundus images. A decreased training time from 170 epochs to 60 epochs with an increased performance-on par with two human experts-was achieved with areas under the receiver operating characteristics curve of 0.894 and 0.972 on two data sets. The SeS CNN statistically outperformed the NSeS CNN on an independent test set.


Subject(s)
Fundus Oculi , Image Interpretation, Computer-Assisted/methods , Neural Networks, Computer , Retinal Hemorrhage/diagnostic imaging , Databases, Factual , Humans , Machine Learning
16.
Invest Ophthalmol Vis Sci ; 56(9): 5229-37, 2015 Aug.
Article in English | MEDLINE | ID: mdl-26244299

ABSTRACT

PURPOSE: Abnormal choroidal blood flow is considered important in the pathogenesis of chronic central serous chorioretinopathy (CSC). Optical coherence tomography (OCT) angiography can image ocular blood cell flow and could thus provide novel insights in disease mechanisms of CSC. We evaluated depth-resolved flow in chronic CSC by OCT angiography compared to fluorescein angiography (FA) and indocyanine green angiography (ICGA). METHODS: Eighteen eyes with chronic CSC, and six healthy controls, were included. Two human observers annotated areas of staining, hypofluorescence, and hotspots on FA and ICGA, and areas of abnormal flow on OCT angiography. Interobserver agreement in annotating OCT angiography and FA/ICGA was measured by Jaccard indices (JIs). We assessed colocation of flow abnormalities and subretinal fluid visible on OCT, and the distance between hotspots on ICGA from flow abnormalities. RESULTS: Abnormal areas were most frequently annotated in late-phase ICGA and choriocapillary OCT angiography, with moderately high (median JI, 0.74) and moderate (median JI, 0.52) interobserver agreement, respectively. Abnormalities on late-phase ICGA and FA colocated with those on OCT angiography. Aberrant choriocapillary OCT angiography presented as foci of reduced flow surrounded by hyperperfused areas. Hotspots on ICGA were located near hypoperfused spots on OCT angiography (mean distance, 168 µm). Areas with current or former subretinal fluid were colocated with flow abnormalities. CONCLUSIONS: On OCT angiography, chronic CSC showed irregular choriocapillary flow patterns, corresponding to ICGA abnormalities. These results suggest focal choriocapillary ischemia with surrounding hyperperfusion that may lead to subretinal fluid leakage.


Subject(s)
Central Serous Chorioretinopathy/diagnosis , Choroid/pathology , Fluorescein Angiography/methods , Fluorescein , Indocyanine Green , Tomography, Optical Coherence/methods , Adult , Aged , Chronic Disease , Coloring Agents , Contrast Media , Female , Follow-Up Studies , Fundus Oculi , Humans , Male , Middle Aged , Reproducibility of Results , Retrospective Studies , Visual Acuity
17.
Biomed Opt Express ; 6(5): 1632-47, 2015 May 01.
Article in English | MEDLINE | ID: mdl-26137369

ABSTRACT

A growing body of evidence suggests that phototransduction can be studied in the human eye in vivo by imaging of fast intrinsic optical signals (IOS). There is consensus concerning the limiting influence of motion-associated imaging noise on the reproducibility of IOS-measurements, especially in those employing spectral-domain optical coherence tomography (SD-OCT). However, no study to date has conducted a comprehensive analysis of this noise in the context of IOS-imaging. In this study, we discuss biophysical correlates of IOS, and we address motion-associated imaging noise by providing correctional post-processing methods. In order to avoid cross-talk of adjacent IOS of opposite signal polarity, cellular resolution and stability of imaging to the level of individual cones is likely needed. The optical Stiles-Crawford effect can be a source of significant IOS-imaging noise if alignment with the peak of the Stiles-Crawford function cannot be maintained. Therefore, complete head stabilization by implementation of a bite-bar may be critical to maintain a constant pupil entry position of the OCT beam. Due to depth-dependent sensitivity fall-off, heartbeat and breathing associated axial movements can cause tissue reflectivity to vary by 29% over time, although known methods can be implemented to null these effects. Substantial variations in reflectivity can be caused by variable illumination due to changes in the beam pupil entry position and angle, which can be reduced by an adaptive algorithm based on slope-fitting of optical attenuation in the choriocapillary lamina.

18.
Appl Microbiol Biotechnol ; 99(14): 5907-15, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25851715

ABSTRACT

Creating novel biosynthetic pathways and modulating the synthesis of important compounds are one of the hallmarks of synthetic biology. Understanding the key parameters controlling the flux of chemicals throughout a metabolic pathway is one of the challenges ahead. Isoprenoids are the most functionally and structurally diverse group of natural products from which numerous medicines and relevant fine chemicals are derived. The well-characterized and broadly used production organism Bacillus subtilis forms an ideal background for creating and studying novel synthetic routes. In comparison to other bacteria, B. subtilis emits the volatile compound isoprene, the smallest representative of isoprenoids, in high concentrations and thus represents an interesting starting point for an isoprenoid cell factory. In this study, the effect of systematic overexpression of the genes involved in the methylerythritol phosphate (MEP) pathway on isoprenoid production in B. subtilis was investigated. B. subtilis strains harboring a plasmid containing C30 carotenoid synthetic genes, crtM and crtN, were combined with pHCMC04G plasmids carrying various synthetic operons of the MEP pathway genes. The levels of produced carotenoids, diaponeurosporene and diapolycopene, were used as indication of the role of the various enzymes on the flux of the MEP pathway. It was shown that the production of carotenoids can be increased significantly by overexpressing the MEP pathway enzymes. More broadly, the strains developed in this study can be used as a starting point for various isoprenoid cell factories.


Subject(s)
Bacillus subtilis/genetics , Bacillus subtilis/metabolism , Biosynthetic Pathways/genetics , Carotenoids/biosynthesis , Gene Expression , Metabolic Engineering/methods , Genetic Vectors , Plasmids
19.
Invest Ophthalmol Vis Sci ; 56(1): 633-9, 2015 Jan 08.
Article in English | MEDLINE | ID: mdl-25574052

ABSTRACT

PURPOSE: To examine human performance and agreement on reticular pseudodrusen (RPD) detection and quantification by using single- and multimodality grading protocols and to describe and evaluate a machine learning system for the automatic detection and quantification of reticular pseudodrusen by using single- and multimodality information. METHODS: Color fundus, fundus autofluoresence, and near-infrared images of 278 eyes from 230 patients with or without presence of RPD were used in this study. All eyes were scored for presence of RPD during single- and multimodality setups by two experienced observers and a developed machine learning system. Furthermore, automatic quantification of RPD area was performed by the proposed system and compared with human delineations. RESULTS: Observers obtained a higher performance and better interobserver agreement for RPD detection with multimodality grading, achieving areas under the receiver operating characteristic (ROC) curve of 0.940 and 0.958, and a κ agreement of 0.911. The proposed automatic system achieved an area under the ROC of 0.941 with a multimodality setup. Automatic RPD quantification resulted in an intraclass correlation (ICC) value of 0.704, which was comparable with ICC values obtained between single-modality manual delineations. CONCLUSIONS: Observer performance and agreement for RPD identification improved significantly by using a multimodality grading approach. The developed automatic system showed similar performance as observers, and automatic RPD area quantification was in concordance with manual delineations. The proposed automatic system allows for a fast and accurate identification and quantification of RPD, opening the way for efficient quantitative imaging biomarkers in large data set analysis.


Subject(s)
Diagnosis, Computer-Assisted , Image Processing, Computer-Assisted , Multimodal Imaging , Retinal Drusen/diagnosis , Algorithms , Artificial Intelligence , Cohort Studies , Fluorescein Angiography , Humans , Observer Variation , Photography , Prospective Studies , ROC Curve , Spectroscopy, Near-Infrared
20.
Invest Ophthalmol Vis Sci ; 55(11): 7085-92, 2014 Oct 09.
Article in English | MEDLINE | ID: mdl-25301878

ABSTRACT

PURPOSE: We describe the differences and similarities in clinical characteristics and phenotype of familial and sporadic patients with age-related macular degeneration (AMD). METHODS: We evaluated data of 1828 AMD patients and 1715 controls enrolled in the European Genetic Database. All subjects underwent ophthalmologic examination, including visual acuity testing and fundus photography. Images were graded and fundus photographs were used for automatic drusen quantification by a machine learning algorithm. Data on disease characteristics, family history, medical history, and lifestyle habits were obtained by a questionnaire. RESULTS: The age at first symptoms was significantly lower in AMD patients with a positive family history (68.5 years) than in those with no family history (71.6 years, P = 1.9 × 10(-5)). Risk factors identified in sporadic and familial subjects were increasing age (odds ratio [OR], 1.08 per year; P = 3.0 × 10(-51), and OR, 1.15; P = 5.3 × 10(-36), respectively) and smoking (OR, 1.01 per pack year; P = 1.1 × 10(-6) and OR, 1.02; P = 0.005). Physical activity and daily red meat consumption were significantly associated with AMD in sporadic subjects only (OR, 0.49; P = 3.7 × 10(-10) and OR, 1.81; P = 0.001). With regard to the phenotype, geographic atrophy and cuticular drusen were significantly more prevalent in familial AMD (17.5% and 21.7%, respectively) compared to sporadic AMD (9.8% and 12.1%). CONCLUSIONS: Familial AMD patients become symptomatic at a younger age. The higher prevalence of geographic atrophy and cuticular drusen in the familial AMD cases may be explained by the contribution of additional genetic factors segregating within families.


Subject(s)
Macula Lutea/pathology , Macular Degeneration/diagnosis , Risk Assessment/methods , Age Distribution , Aged , Disease Progression , Female , Humans , Macular Degeneration/epidemiology , Male , Middle Aged , Netherlands/epidemiology , Odds Ratio , Prevalence , Risk Factors , Surveys and Questionnaires
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