| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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In: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Research review (peer-reviewed)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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| 3. |
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| 4. |
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| 5. |
- Rocca, J. J., et al.
(author)
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Compact Soft X-ray Lasers for Imaging, Material Processing, and Characterization at the Nanoscale
- 2007
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In: 32nd IEEE/CPMT International Electronic Manufacturing Technology Symposium. - 9781424413355 ; , s. 72-73
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Conference paper (peer-reviewed)abstract
- As manufacturing of devices advances into the nanoscale, critical feature sizes have rapidly shrunk to below the wavelength of visible light. These advances in nanotechnology have created a need to develop better ways of accessing the nanoworld. The extreme ultraviolet (EUV)/ soft x-ray (SXR) region of the spectrum provides an opportunity to use coherent light at wavelengths that are 10- to 100-times shorter than visible light, at 1 to 100 nm. Given the diffraction limit in imaging resolution, these wavelengths allow us to "see" smaller features and "write" smaller patterns than would be possible with visible light. We have developed compact laser-pumped and discharge-pumped lasers operating at wavelengths of λ=13.2 nm [1] and λ=46.9 nm [2] respectively, and have used them in the demonstration of nanoscale full field imaging [3,4], nanopatterning [5], and nanoscale laser ablation [6]. The high brightness and short wavelength output from these lasers when combined with specialized EUV/SXR optics, offer unique opportunities for the implementation of table-top imaging, patterning and metrology tools with superior spatial resolution for applications in nanoscience and nanotechnology. Using these new compact short wavelength lasers we have built two microscopes, using λ=46.9 nm or λ=l 3.2 nm laser illumination. The compact λ=46.9 nm microscope (Fig. 1a and lb) condenses the light using a multilayer coated Schwarzschild mirror, and images the test object using a diffractive zone plate lens. The spatial resolution of this microscopes was assessed by imaging test samples consisting of dense line gratings of half-periods ranging from 200 down to 35 nm. Figure 2(a) and (b) show images of a 100 nm and 70 nm half-period gratings obtained with the λ =46.9 nm microscope. The lineout in the image of the 70 nm lines shows a modulation of ∼30% indicating that the features are fully resolved according to the Rayleigh criterion. By rearranging the optics, the λ=46.9 nm microscope can also image surfaces. An image of fully resolved dense metal lines, with half-period of 170 nm, patterned on the silicon wafer is shown in Figure 2 (c). The shorter wavelength λ= 3.2 nm microscope uses all zone plate optics to render images of transmissive test patterns with increased spatial resolution . An image of fully resolved 50 nm half-period dense lines acquired with a 20 seconds exposure is shown in Figure 2(d). From images like this one, the spatial resolution of the λ=13.2 nm table-top microscope was determined to be better than 38 nm [3]. The high coherence of these short wavelength lasers also allows for the printing of arrays of nanoscale features using interferometric lithography. We have demonstrated combined a λ=46.9 nm capillary discharge laser and a Lloyd's mirror to print arrays of cone-shaped nano-dots with ∼ 58 nm FWHM diameter (Fig 3a) [5]. The same arrangement was used to print arrays of nano-holes 120 nm FWHM and 100 nm in depth over areas in excess of 500 × 500 μm2 in different photoresists using exposure times as short as 80 s. Larger area patterns can be readily printed using precision translation stages and multiple exposures by overlay superposition. The ability to focus SXL laser light into near diffraction-limited spots also opens the possibility to develop new types of nanoprobes. We have demonstrated ablation of sub-100 nm diameter holes by directly focusing the output of a λ=46.9 nm laser onto a sample with a zone plate lens. Figure 3(b) shows an AFM image of a 82 nm diameter crater obtained ablating a 500 nm thick PMMA layer with a single laser shot. The holes were observed to have very clean walls and high reproducibility. We have recently added the capability to spectroscopically analyze the light emitted from the plasma created during the ablation, opening the possibility to develop analytic nanoprobles. All of these results illustrate the capabilities of compact short wavelength lasers for nanotechnology applications.
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| 6. |
- Rocca, J. J., et al.
(author)
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High brightness table-top soft x-ray lasers at high repetition rate : injection-seeding of solid target plasma amplifiers and other developments - art. no. 670202
- 2007
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In: SOFT X-RAY LASERS AND APPLICATIONS VII. - : SPIE. ; , s. 70202-70202
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Conference paper (peer-reviewed)abstract
- We have recently demonstrated high repetition rate tabletop lasers operating at wavelengths as short as 10.9 rim based on collisional transient excitation of ions in plasmas created by laser heating of solid targets. As a further step in the development of these lasers into very high brightness and fully coherent soft x-ray sources, we have demonstrated injection seeding of the amplifiers with high harmonic seed pulses. We report results of an experiment in which a 32.6 rim Ne-like Ti amplifier was used to amplify a seed pulse from the 25(th) harmonic of Ti:Sapphire into the gain saturation regime. Simultaneous amplification of the 27(th) harmonic at 30.1 nm was also observed. The seeded soft x-ray laser beam was measured to approach full spatial coherence. We have demonstrated that this scheme is scalable to shorter wavelengths and that is capable of producing extremely bright soft x-ray laser pulse with essentially full coherence.
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| 7. |
- Davies, Melvyn B, et al.
(author)
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The MODEST questions: Challenges and future directions in stellar cluster research
- 2006
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In: New Astronomy. - : Elsevier BV. - 1384-1092 .- 1384-1076. ; 12:3, s. 201-214
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Research review (peer-reviewed)abstract
- We present a review of some of the current major challenges in stellar cluster research, including young clusters, globular clusters, and galactic nuclei. Topics considered include: primordial mass segregation and runaway mergers, expulsion of gas from clusters, the production of stellar exotica seen in some clusters (e.g., blue stragglers and extreme horizontal-branch stars), binary populations within clusters, the black-hole population within stellar clusters, the final parsec problem, stellar dynamics around a massive black hole, and stellar collisions. The Modest Questions posed here are the outcome of discussions which took place at the Modest-6A workshop held in Lund, Sweden, in December, 2005. Modest-6A was organised as part of the activities of the Modest Collaboration (see www.manybody.org for further details).
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| 8. |
- Hicks, J, et al.
(author)
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Novel patterns of genome rearrangement and their association with survival in breast cancer
- 2006
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In: Genome research. - : Cold Spring Harbor Laboratory. - 1088-9051. ; 16:12, s. 1465-1479
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Journal article (peer-reviewed)abstract
- Representational Oligonucleotide Microarray Analysis (ROMA) detects genomic amplifications and deletions with boundaries defined at a resolution of ∼50 kb. We have used this technique to examine 243 breast tumors from two separate studies for which detailed clinical data were available. The very high resolution of this technology has enabled us to identify three characteristic patterns of genomic copy number variation in diploid tumors and to measure correlations with patient survival. One of these patterns is characterized by multiple closely spaced amplicons, or “firestorms,” limited to single chromosome arms. These multiple amplifications are highly correlated with aggressive disease and poor survival even when the rest of the genome is relatively quiet. Analysis of a selected subset of clinical material suggests that a simple genomic calculation, based on the number and proximity of genomic alterations, correlates with life-table estimates of the probability of overall survival in patients with primary breast cancer. Based on this sample, we generate the working hypothesis that copy number profiling might provide information useful in making clinical decisions, especially regarding the use or not of systemic therapies (hormonal therapy, chemotherapy), in the management of operable primary breast cancer with ostensibly good prognosis, for example, small, node-negative, hormone-receptor-positive diploid cases.
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| 9. |
- Martz, Dale, et al.
(author)
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Large area high efficiency broad bandwidth 800 nm dielectric gratings for high energy laser pulse compression
- 2009
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In: Optics Express. - : Optical Society of America. - 1094-4087. ; 17:26, s. 23809-23816
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Journal article (peer-reviewed)abstract
- We have demonstrated broad bandwidth large area (229 mm x 114 mm) multilayer dielectric diffraction gratings for the efficient compression of high energy 800 nm laser pulses at high average power. The gratings are etched in the top layers of an aperiodic (Nb0.5Ta0.5)2O5-SiO2 multilayer coating deposited by ion beam sputtering. The mean efficiency of the grating across the area is better than 97% at the center wavelength and remains above 96% at wavelengths between 820 nm and 780 nm. The gratings were used to compress 5.5 J pulses from a Ti:sapphire laser with an efficiency above 80 percent.
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| 10. |
- Menoni, C. S., et al.
(author)
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Nanometer-scale imaging and ablation with Extreme Ultraviolet lasers
- 2007
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In: 2007 CONFERENCE ON LASERS & ELECTRO-OPTICS/QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE (CLEO/QELS 2007), VOLS 1-5. - 9781424435906 ; , s. 1401-1402
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Conference paper (peer-reviewed)abstract
- The short wavelength and high brightness of compact extreme ultraviolet lasers is shown to enable the development of microscopes with spatial resolution of tens of nanometers and new types of nanoprobes.
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| 11. |
- Wachulak, P., et al.
(author)
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Interferometric lithography with an amplitude division interferometer and a desktop extreme ultraviolet laser
- 2008
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In: Journal of the Optical Society of America. B, Optical physics. - : Optical Society of America. - 0740-3224 .- 1520-8540. ; 25:7, s. B104-B107
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Journal article (peer-reviewed)abstract
- We demonstrate a compact interferometric lithography nanopatterning tool based on an amplitude division interferometer (ADI) and a 46.9 nm wavelength desktop size capillary discharge laser. The system is designed to print arrays of lines, holes, and dots with sizes below 100 nm on high resolution photoresists for the fabrication of arrays of nanostructures with physical and biological applications. The future combination of this ADI with high repetition rate tabletop lasers operating at shorter wavelengths should allow the printing of arrays of sub-10 nm size features with a tabletop setup.
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| 12. |
- Beheshti, Hoosang M., et al.
(author)
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The strategic and organizational impact of electronic business on large firms
- 2008
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In: Journal of International Business Disciplines. - Frostburg, Maryland, USA : Frostburg State University. - 1934-1822. ; 2:3, s. 48-61
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Journal article (peer-reviewed)abstract
- This research examines the impact of and the benefits derived from e-business integration in large manufacturing and service organizations in Sweden. Business managers are increasingly under pressure to improve the financial performance and the profitability of their companies. The Internet-based electronic business can provide opportunities for business ti improve the efficiency and the effectiveness of their business operations, to form partnership with suppliers, improve customer service, and to manage better their supply chain. The results show that large Swedish firms are benefiting from e-business implementation in many key areas of their business.
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| 13. |
- Brizuela, F., et al.
(author)
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High resolution full-field imaging of nanostructures using compact extreme ultraviolet lasers
- 2009
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In: 9TH INTERNATIONAL CONFERENCE ON X-RAY MICROSCOPY. - : IOP Publishing.
-
Conference paper (peer-reviewed)abstract
- Recent advances in the development of high peak brightness table-top extreme ultraviolet (EUV) and soft x-ray (SRX) lasers have opened new opportunities for the demonstration of compact full-field EUV/SXR microscopes capable of capturing images with short exposures down to a single laser shot. We demonstrate the practical application of table-top zone plate EUV microscopes that can image nanostructures with a spatial resolution of 54 nm and below and exposure times as short as 1.2 ns, the duration of a single laser shot.
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| 14. |
- Brizuela, F., et al.
(author)
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Near-wavelength Resolution Extreme Ultraviolet Imaging With a Desktop-size Laser
- 2008
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In: 2008 CONFERENCE ON LASERS AND ELECTRO-OPTICS & QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE, VOLS 1-9. ; , s. 400-401
-
Conference paper (peer-reviewed)abstract
- We have realized the first demonstration of imaging in the extreme ultraviolet (EUV) with near-wavelength spatial resolution, 54 nm, using a uniquely compact full-field microscope that can produce images with a single one nanosecond exposure.
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| 15. |
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| 16. |
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| 17. |
- Cornett, Dale S, et al.
(author)
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A novel histology-directed strategy for MALDI-MS tissue profiling that improves throughput and cellular specificity in human breast cancer.
- 2006
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In: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 5:10, s. 1975-83
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Journal article (peer-reviewed)abstract
- We describe a novel tissue profiling strategy that improves the cellular specificity and analysis throughput of protein profiles obtained by direct MALDI analysis. The new approach integrates the cellular specificity of histology, the accuracy and reproducibility of robotic liquid dispensing, and the speed and objectivity of automated spectra acquisition. Traditional methodologies for preparing and analyzing tissue samples rely heavily on manual procedures, which for various reasons discussed, restrict cellular specificity and sample throughput. Here, a robotic spotter deposits micron-sized droplets of matrix precisely onto foci of normal mammary epithelium, ductal carcinoma in situ, invasive mammary cancer, and peritumoral stroma selected by a pathologist from high resolution histological images of sectioned human breast cancer samples. The location of each matrix spot was then determined and uploaded into the instrument to facilitate automated profile acquisition by MALDI-TOF. In the example shown, the different lesions were clearly differentiated using mass profiling. Further, the workflow permits a visual projection of any information produced from the profile analyses directly on the histological image for a unique combination of proteomic and histological assessment of sample regions. The higher performance characteristics offered by the new workflow promises to be a significant advancement toward the next generation of tissue profiling studies.
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| 18. |
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| 19. |
- Heinbuch, S, et al.
(author)
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Demonstration of a desk-top size high repetition rate soft x-ray laser
- 2005
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In: Optics express. - : Optical Society of America. - 1094-4087. ; 13:11, s. 4050-4055
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Journal article (peer-reviewed)abstract
- We have demonstrated a new type of high repetition rate 46.9 nm capillary discharge laser that fits on top of a small desk and that it does not require a Marx generator for its excitation. The relatively low voltage required for its operation allows a reduction of nearly one order of magnitude in the size of the pulsed power unit relative to previous capillary discharge lasers. Laser pulses with an energy of ~ 13 microJ are generated at repetition rates up to 12 Hz. About (2-3) x 10 4 laser shots can be generated with a single capillary. This new type of portable laser is an easily accessible source of intense short wavelength laser light for applications.
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| 20. |
- Lelliott, Christopher J., et al.
(author)
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Ablation of PGC-1beta results in defective mitochondrial activity, thermogenesis, hepatic function, and cardiac performance
- 2006
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In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 4:11
-
Journal article (peer-reviewed)abstract
- The transcriptional coactivator peroxisome proliferator-activated receptor-gamma coactivator-1beta (PGC-1beta) has been implicated in important metabolic processes. A mouse lacking PGC-1beta (PGC1betaKO) was generated and phenotyped using physiological, molecular, and bioinformatic approaches. PGC1betaKO mice are generally viable and metabolically healthy. Using systems biology, we identified a general defect in the expression of genes involved in mitochondrial function and, specifically, the electron transport chain. This defect correlated with reduced mitochondrial volume fraction in soleus muscle and heart, but not brown adipose tissue (BAT). Under ambient temperature conditions, PGC-1beta ablation was partially compensated by up-regulation of PGC-1alpha in BAT and white adipose tissue (WAT) that lead to increased thermogenesis, reduced body weight, and reduced fat mass. Despite their decreased fat mass, PGC1betaKO mice had hypertrophic adipocytes in WAT. The thermogenic role of PGC-1beta was identified in thermoneutral and cold-adapted conditions by inadequate responses to norepinephrine injection. Furthermore, PGC1betaKO hearts showed a blunted chronotropic response to dobutamine stimulation, and isolated soleus muscle fibres from PGC1betaKO mice have impaired mitochondrial function. Lack of PGC-1beta also impaired hepatic lipid metabolism in response to acute high fat dietary loads, resulting in hepatic steatosis and reduced lipoprotein-associated triglyceride and cholesterol content. Altogether, our data suggest that PGC-1beta plays a general role in controlling basal mitochondrial function and also participates in tissue-specific adaptive responses during metabolic stress.
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| 21. |
- Menoni, C. S., et al.
(author)
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Advances in Nanoscale Resolution Soft X-Ray Laser Microscopy
- 2009
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In: X-RAY LASERS 2008, PROCEEDINGS. - : Springer Netherlands. - 9781402099236 ; , s. 341-347
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Conference paper (peer-reviewed)abstract
- We review our most recent results on table-top, nanometer-scale resolution, microscopy using compact soft x-ray lasers developed at Colorado State University. We have realized the first demonstration of wavelength-resolution microscopy in the soft x-ray spectral range. Images of carbon nanotubes, 50 nm in diameter, were obtained with a single similar to 1 ns duration laser pulse from a desk-top size capinary discharge 46.9 nm laser. We fully characterized the new microscope by measuring the modulation transfer function of the instrument for zone plate objectives with three different numerical apertures, demonstrating that 54 nm half-period structures can be resolved. The combination of near-wavelength spatial resolution with high temporal resolution imaging opens myriad opportunities for imaging nanoscale structures.
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| 22. |
- Menoni, C. S., et al.
(author)
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Nanoscale resolution microscopy and ablation with extreme ultraviolet lasers
- 2007
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In: 2007 IEEE LEOS ANNUAL MEETING CONFERENCE PROCEEDINGS, VOLS 1 AND 2. - 9781424409242 ; , s. 488-489
-
Conference paper (peer-reviewed)abstract
- We obtain a spatial resolution down to 38 run with full field imaging and laser-ablation systems that exploit the short wavelength and high brightness output from compact extreme ultraviolet lasers in combination with zone plate optics.
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| 23. |
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| 24. |
- Norris, Jeremy L, et al.
(author)
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Processing MALDI Mass Spectra to Improve Mass Spectral Direct Tissue Analysis.
- 2007
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In: International Journal of Mass Spectrometry. - : Elsevier BV. - 1387-3806 .- 1873-2798. ; 260:2-3, s. 212-221
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Journal article (peer-reviewed)abstract
- Profiling and imaging biological specimens using MALDI mass spectrometry has significant potential to contribute to our understanding and diagnosis of disease. The technique is efficient and high-throughput providing a wealth of data about the biological state of the sample from a very simple and direct experiment. However, in order for these techniques to be put to use for clinical purposes, the approaches used to process and analyze the data must improve. This study examines some of the existing tools to baseline subtract, normalize, align, and remove spectral noise for MALDI data, comparing the advantages of each. A preferred workflow is presented that can be easily implemented for data in ASCII format. The advantages of using such an approach are discussed for both molecular profiling and imaging mass spectrometry.
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| 26. |
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| 27. |
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| 28. |
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| 29. |
- Schaaf, Cheri A, et al.
(author)
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Regulation of the Drosophila Enhancer of split and invected-engrailed gene complexes by sister chromatid cohesion proteins
- 2009
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In: PloS one. - : Public Library of Science (PLoS). - 1932-6203. ; 4:7, s. e6202-
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Journal article (peer-reviewed)abstract
- The cohesin protein complex was first recognized for holding sister chromatids together and ensuring proper chromosome segregation. Cohesin also regulates gene expression, but the mechanisms are unknown. Cohesin associates preferentially with active genes, and is generally absent from regions in which histone H3 is methylated by the Enhancer of zeste [E(z)] Polycomb group silencing protein. Here we show that transcription is hypersensitive to cohesin levels in two exceptional cases where cohesin and the E(z)-mediated histone methylation simultaneously coat the entire Enhancer of split and invected-engrailed gene complexes in cells derived from Drosophila central nervous system. These gene complexes are modestly transcribed, and produce seven of the twelve transcripts that increase the most with cohesin knockdown genome-wide. Cohesin mutations alter eye development in the same manner as increased Enhancer of split activity, suggesting that similar regulation occurs in vivo. We propose that cohesin helps restrain transcription of these gene complexes, and that deregulation of similarly cohesin-hypersensitive genes may underlie developmental deficits in Cornelia de Lange syndrome.
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| 30. |
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| 31. |
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Visioning and Engineering the Knowledge Society - A Web Science Perspective : Second World Summit on the Knowledge Society, WSKS 2009, Chania, Crete, Greece, September 2009. Proceedings
- 2009
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Editorial proceedings (peer-reviewed)abstract
- This book, in conjunction with the volume CCIS 49, constitutes the refereed proceedings of the Second World Summit, WSKS 2009, held in Chania, Crete, Greece, in September 2008.The 62 revised full papers presented were carefully reviewed and selected from 256 submissions. The papers are deal with information technologies - knowledge management systems - e-business and business, organizational and inter-organizational information systems for the Knowledge Society, knowledge, learning, education, learning technologies and e-learning for the Knowledge Society, social and humanistic computing for the Knowledge Society – emerging technologies for the society and the humanity, culture and cultural heritage - technology for culture management - management of tourism and entertainment - tourism networks in the Knowledge Society, e-government and e-democracy in the Knowledge Society, innovation, sustainable development and strategic management for the Knowledge Society, service science, management, engineering, and technology, intellectual and human capital development in the Knowledge Society, advanced applications for environmental protection and green economy management, future prospects for the Knowledge Society: from foresight studies to projects and public policies, technologies and business models for the creative industries.
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