| 1. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Improving ITS sequence data for identification of plant pathogenic fungi
- 2014
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
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Tidskriftsartikel (refereegranskat)abstract
- Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
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| 2. |
- Adolfsson, Göran, 1981, et al.
(författare)
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Realization of spectrally engineered semiconductor Fabry-Perot lasers with narrow geometrical tolerances
- 2011
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 109:9, s. 093112-
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Tidskriftsartikel (refereegranskat)abstract
- Spectrally engineered semiconductor Fabry-Perot laser resonators are designed to enhance the optical feedback for selected longitudinal modes, which thereby require less gain for lasing. This is achieved by introducing refractive index perturbations along the length of the resonator. However,the physical realization of these resonators is a challenge because of very narrow tolerances; in particular the need for precise positioning of the end facets of the resonator in relation to the perturbations, and the excess propagation loss associated with the perturbations, has been a majorconcern. We report on a method to achieve high-quality end facet mirrors enabling precise positioning relative to the perturbations, the latter which are realized as lateral corrugations of the waveguide. Measurements show that the mirror quality is comparable to that of cleaved mirrorsand that the additional loss introduced by the perturbations adds
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| 3. |
- Baveja, Prashant, 1985, et al.
(författare)
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Impact of device parameters on thermal performance of high speed oxide confined 850 nm VCSELs
- 2012
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Ingår i: IEEE Journal of Quantum Electronics. - 0018-9197 .- 1558-1713. ; 48:1, s. 17-26
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Tidskriftsartikel (refereegranskat)abstract
- We study the impact of device parameters, such asinner-aperture diameter and cavity photon lifetime, on thermal rollover mechanisms in 850-nm, oxide-confined, vertical-cavity surface-emitting lasers (VCSELs) designed for high-speed operation. We perform measurements on four different VCSELs of different designs and use our empirical thermal model for calculating the power dissipated with increasing bias currents through various physical processes such as absorption within the cavity, carrier thermalization, carrier leakage, spontaneous carrier recombination, and Joule heating. When reducing the topmirror reflectivity to reduce internal optical absorption loss we find an increase of power dissipation due to carrier leakage. There is therefore a trade-ff between the powers dissipated owing to optical absorption and carrier leakage in the sense that overcompensating for optical absorption enhances carrier leakage (and vice versa). We further find that carrier leakage places the ultimate limit on the thermal performance for this entire class ofdevices. Our analysis yields useful design optimization strategies for mitigating the impact of carrier leakage and should thereby prove useful for the performance enhancement of 850-nm, highspeed, oxide-confined VCSELs.
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| 4. |
- Baveja, P. P., et al.
(författare)
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Assessment of VCSEL thermal rollover mechanisms from measurements and empirical modeling
- 2011
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Ingår i: Optics Express. - 1094-4087 .- 1094-4087. ; 19:16, s. 15490-15505
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Tidskriftsartikel (refereegranskat)abstract
- We use an empirical model together with experimental measurements for studying mechanisms contributing to thermal rollover in vertical-cavity surface-emitting lasers (VCSELs). The model is based on extraction of the temperature dependence of threshold current, internal quantum efficiency, internal optical loss, series resistance and thermal impedance from measurements of output power, voltage and lasing wavelength as a function of bias current over an ambient temperature range of 15-100 degrees C. We apply the model to an oxide-confined, 850-nm VCSEL, fabricated with a 9-mu m inner-aperture diameter and optimized for highspeed operation, and show for this specific device that power dissipation due to linear power dissipation (sum total of optical absorption, carrier thermalization, carrier leakage and spontaneous carrier recombination) exceeds power dissipation across the series resistance (quadratic power dissipation) at any ambient temperature and bias current. We further show that the dominant contributors to self-heating for this particular VCSEL are quadratic power dissipation, internal optical loss, and carrier leakage. A rapid reduction of the internal quantum efficiency at high bias currents (resulting in high temperatures) is identified as being the major cause of thermal rollover. Our method is applicable to any VCSEL and is useful for identifying the mechanisms limiting the thermal performance of the device and to formulate design strategies to ameliorate them.
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| 5. |
- Baveja, P. P., et al.
(författare)
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Impact of photon lifetime on thermal rollover in 850-nm high-speed VCSELs
- 2012
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Ingår i: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE. - 0277-786X .- 1996-756X. - 9780819489197 ; 8276
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Konferensbidrag (refereegranskat)abstract
- We present an empirical thermal model for VCSELs based on extraction of temperature dependence of macroscopic VCSEL parameters from CW measurements. We apply our model to two, oxide-confined, 850-nm VCSELs, fabricated with a 9-mu m inner-aperture diameter and optimized for high-speed operation. We demonstrate that for both these devices, the power dissipation due to linear heat sources dominates the total self-heating. We further show that reducing photon lifetime down to 2 ps drastically reduces absorption heating and improves device static performance by delaying the onset of thermal rollover. The new thermal model can identify the mechanisms limiting the thermal performance and help in formulating the design strategies to ameliorate them.
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| 6. |
- Castegren, Markus, 1976-, et al.
(författare)
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Endotoxin tolerance variation over 24 h during porcine endotoxemia : association to changes in circulation and organ dysfunction
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:1, s. e53221-
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Tidskriftsartikel (refereegranskat)abstract
- Endotoxin tolerance (ET), defined as reduced inflammatory responsiveness to endotoxin challenge following a first encounter with endotoxin, is an extensively studied phenomenon. Although reduced mortality and morbidity in the presence of ET has been demonstrated in animal studies, little is known about the temporal development of ET. Further, in acute respiratory distress syndrome ET correlates to the severity of the disease, suggesting a complicated relation between ET and organ dysfunction. Eighteen pigs were subjected to intensive care and a continuous endotoxin infusion for 24 h with the aim to study the time course of early ET and to relate ET to outcome in organ dysfunction. Three animals served as non-endotoxemic controls. Blood samples for cytokine analyses were taken and physiological variables registered every third hour. Production of TNF-α, IL-6, and IL-10 before and after endotoxin stimulation ex vivo was measured. The difference between cytokine values after and before ex vivo LPS stimulation (Δ-values) was calculated for all time points. ΔTNF-α was employed as the principal marker of ET and lower ΔTNF-α values were interpreted as higher levels of ET. During endotoxin infusion, there was suppression of ex vivo productions of TNF-α and IL-6 but not of IL-10 in comparison with that at 0 h. The ex vivo TNF-α values followed another time concentration curve than those in vivo. ΔTNF-α was at the lowest already at 6 h, followed by an increase during the ensuing hours. ΔTNF-α at 6 h correlated positively to blood pressure and systemic vascular resistance and negatively to cardiac index at 24 h. In this study a temporal variation of ET was demonstrated that did not follow changes in plasma TNF-α concentrations. Maximal ET occurred early in the course and the higher the ET, the more hyperdynamic the circulation 18 h later.
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| 7. |
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| 8. |
- Chu, Jiangtao, et al.
(författare)
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Impact of static pressure on transmembrane fluid exchange in high molecular weight cut off microdialysis
- 2014
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Ingår i: Biomedical microdevices (Print). - : Springer Science and Business Media LLC. - 1387-2176 .- 1572-8781. ; 16:2, s. 301-310
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Tidskriftsartikel (refereegranskat)abstract
- With the interest of studying larger biomolecules by microdialysis (MD), this sampling technique has reached into the ultrafiltration region of fluid exchange, where fluid recovery (FR) has a strong dependence on pressure. Hence in this study, we focus on the fluid exchange across the high molecular weight cut off MD membrane under the influence of the static pressure in the sampling environment. A theoretical model is presented for MD with such membranes, where FR has a linear dependence upon the static pressure of the sample. Transmembrane (TM) osmotic pressure difference and MD perfusion rate decide how fast FR increases with increased static pressure.A test chamber for in vitro MD under static pressure was constructed and validated. It can hold four MD probes under controlled pressurized conditions. Comparison showed good agreement between experiment and theory. Moreover, test results showed that the fluid recovery of the test chamber MD can be set accurately via the chamber pressure, which is controlled by sample injection into the chamber at precise rate. This in vitro system is designed for modelling in vivo MD in cerebrospinal fluid and studies with biological samples in this system may be good models for in vivo MD.
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| 9. |
- Daka, Bledar, 1976, et al.
(författare)
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Inverse association between serum insulin and sex hormone-binding globulin in a population survey in Sweden
- 2013
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Ingår i: Endocrine Connections. - 2049-3614. ; 2:1, s. 18-22
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: Obesity is associated with low levels of sex hormone-binding globulin (SHBG). While the reason is not fully understood, we aimed to study the association between serum insulin and levels of SHBG in a random population. DESIGN AND METHODS: Between 2001 and 2005, a random sample of 2816 participants aged 30-74 years were enrolled in a cross-sectional survey in the South-west of Sweden. Fasting blood samples were collected and an oral glucose tolerance test (OGTT) was conducted in all subjects without known diabetes. Diabetes mellitus was defined according to criteria from WHO, and clinical characteristics were used to discriminate between type 1 (T1D) and type 2 diabetes (T2D). Analyses of SHBG were successful in 2782 participants (98%), who thus constituted the current study population. RESULTS: WE FOUND SIGNIFICANT INVERSE ASSOCIATION BETWEEN LEVELS OF SHBG AND FASTING SERUM INSULIN IN BOTH GENDERS (MEN: β=-0.090, P=0.001; women: β=-0.197, P<0.001), which was independent of differences in age and BMI. The associations remained when also differences in fasting plasma glucose were accounted for (men: β=-0.062, P=0.022; women: β=-0.176, P≤0.001). Subjects with T1D exhibited higher levels of SHBG than both T2D (men: δ=15.9nmol/l, P<0.001; women: δ=71.1nmol/l, P<0.001) and non-diabetic subjects (men: δ=15.1nmol/l, P<0.001; women: δ=72.9nmol/l, P<0.001) independent of age, BMI and fasting glucose levels. CONCLUSION: These findings are consistent with high levels of SHBG in T1D, and correspondingly low levels in T2D subjects, suggesting an inhibitory effect of insulin on the SHBG production in the liver.
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| 10. |
- Davani, Hooman A., et al.
(författare)
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Polarization investigation of a tunable high-speed short-wavelength bulk-micromachined MEMS-VCSEL
- 2012
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Ingår i: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE. - 0277-786X .- 1996-756X. - 9780819489197 ; 8276, s. Art. no. 82760T-
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Konferensbidrag (refereegranskat)abstract
- We report the investigation of the state of polarization (SOP) of a tunable vertical-cavity surface-emitting laser (VCSEL) operating near 850 nm with a mode-hop free single-mode tuning range of about 12 nm and an amplitude modulation bandwidth of about 5 GHz. In addition, the effect of a sub-wavelength grating on the device and its influence on the polarization stability and polarization switching has been investigated. The VCSEL with an integrated sub-wavelength grating shows a stable SOP with a polarization mode suppression ratio (PMSR) more than 35 dB during the tuning.
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