| 1. |
- Karlsson, Anna K, et al.
(författare)
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Mutational and gene fusion analyses of primary large cell and large cell neuroendocrine lung cancer.
- 2015
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Ingår i: Oncotarget. - 1949-2553. ; 6:26, s. 22028-22037
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Tidskriftsartikel (refereegranskat)abstract
- Large cell carcinoma with or without neuroendocrine features (LCNEC and LC, respectively) constitutes 3-9% of non-small cell lung cancer but is poorly characterized at the molecular level. Herein we analyzed 41 LC and 32 LCNEC (including 15 previously reported cases) tumors using massive parallel sequencing for mutations in 26 cancer-related genes and gene fusions in ALK, RET, and ROS1. LC patients were additionally subdivided into three immunohistochemistry groups based on positive expression of TTF-1/Napsin A (adenocarcinoma-like, n = 24; 59%), CK5/P40 (squamous-like, n = 5; 12%), or no marker expression (marker-negative, n = 12; 29%). Most common alterations were TP53 (83%), KRAS (22%), MET (12%) mutations in LCs, and TP53 (88%), STK11 (16%), and PTEN (13%) mutations in LCNECs. In general, LCs showed more oncogene mutations compared to LCNECs. Immunomarker stratification of LC revealed oncogene mutations in 63% of adenocarcinoma-like cases, but only in 17% of marker-negative cases. Moreover, marker-negative LCs were associated with inferior overall survival compared with adenocarcinoma-like tumors (p = 0.007). No ALK, RET or ROS1 fusions were detected in LCs or LCNECs. Together, our molecular analyses support that LC and LCNEC tumors follow different tumorigenic paths and that LC may be stratified into molecular subgroups with potential implications for diagnosis, prognostics, and therapy decisions.
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| 2. |
- Alström, Per, et al.
(författare)
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Dramatic niche shifts and morphological change in two insular bird species
- 2015
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Ingår i: Royal Society Open Science. - : The Royal Society. - 2054-5703. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis, from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has diverged mainly in plumage, which may be the result of selection for improved camouflage in its new arboreal niche, while selection pressures for other morphological changes have probably been weak owing to preadaptations for the novel niche. By contrast, we suggest that Amaurocichla's niche change has led to divergence in both structure and plumage.
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| 3. |
- Isaksson, Sofi, et al.
(författare)
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CA 19-9 and CA 125 as potential predictors of disease recurrence in resectable lung adenocarcinoma
- 2017
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Ingår i: PLOS ONE. - : PUBLIC LIBRARY SCIENCE. - 1932-6203. ; 12:10
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Tidskriftsartikel (refereegranskat)abstract
- Objectives Among patients who underwent primary surgery for non-small cell lung cancer (NSCLC), recurrent disease is frequent and cannot be accurately predicted solely from TNM stage and histopathological features. The aim of this study was to examine the association of tumor markers in pre-operative serum with recurrent disease. Material and methods Blood samples were collected prior to lung cancer surgery from 107 patients with stage I-III lung adenocarcinoma surgically treated at Lund University hospital, Lund, Sweden, between 2005 and 2011. The serum tumor markers Carcinoembryonic antigen (CEA), Neuron-specific enolase (NSE), Cancer antigen 125 (CA 125), Human epididymis protein 4 (HE4) and Carbohydrate antigen (CA 19-9) were analyzed retrospectively and clinical follow-up data were collected from patient charts. Forty (37%) patients were diagnosed with recurrent disease. Results Sixty-eight (64%) patients had at least one elevated tumor marker prior to surgery. In analysis of disease-free survival (DFS), CA 125 and/or CA 19-9 were significantly associated with recurrent disease adjusted to stage and adjuvant treatment (hazard ratio 2.8, 95% confidence interval 1.4-5.7, p = 0.006). Conclusion High pre-operative serum CA 19-9 and/or CA 125 might indicate an increased incidence of recurrent disease in resectable lung adenocarcinomas.
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| 4. |
- Jönsson, Henrik, et al.
(författare)
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Abundances of disk and bulge giants from high-resolution optical spectra I. O, Mg, Ca, and Ti in the solar neighborhood and Kepler field samples
- 2017
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Ingår i: Astronomy and Astrophysics. - : EDP SCIENCES S A. - 0004-6361 .- 1432-0746. ; 598
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Tidskriftsartikel (refereegranskat)abstract
- Context. The Galactic bulge is an intriguing and significant part of our Galaxy, but it is hard to observe because it is both distant and covered by dust in the disk. Therefore, there are not many high-resolution optical spectra of bulge stars with large wavelength coverage, whose determined abundances can be compared with nearby, similarly analyzed stellar samples. Aims. We aim to determine the diagnostically important alpha elements of a sample of bulge giants using high-resolution optical spectra with large wavelength coverage. The abundances found are compared to similarly derived abundances from similar spectra of similar stars in the local thin and thick disks. In this first paper we focus on the solar neighborhood reference sample. Methods. We used spectral synthesis to derive the stellar parameters as well as the elemental abundances of both the local and bulge samples of giants. We took special care to benchmark our method of determining stellar parameters against independent measurements of effective temperatures from angular diameter measurements and surface gravities from asteroseismology. Results. In this first paper we present the method used to determine the stellar parameters and elemental abundances, evaluate them, and present the results for our local disk sample of 291 giants. Conclusions. When comparing our determined spectroscopic temperatures to those derived from angular diameter measurements, we reproduce these with a systematic difference of + 10 K and a standard deviation of 53 K. The spectroscopic gravities reproduce those determined from asteroseismology with a systematic off set of + 0.10 dex and a standard deviation of 0.12 dex. When it comes to the abundance trends, our sample of local disk giants closely follows trends found in other works analyzing solar neighborhood dwarfs, showing that the much brighter giant stars are as good abundance probes as the often used dwarfs.
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| 5. |
- Lindquist, Kajsa Ericson, et al.
(författare)
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Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer
- 2017
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Ingår i: Oncotarget. - : Impact Journals, LLC. - 1949-2553. ; 8:21, s. 34796-34810
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Tidskriftsartikel (refereegranskat)abstract
- Precision medicine requires accurate multi-gene clinical diagnostics. We describe the implementation of an Illumina TruSight Tumor (TST) clinical NGS diagnostic framework and parallel validation of a NanoString RNA-based ALK, RET, and ROS1 gene fusion assay for combined analysis of treatment predictive alterations in non-small cell lung cancer (NSCLC) in a regional healthcare region of Sweden (Scandinavia). The TST panel was clinically validated in 81 tumors (99% hotspot mutation concordance), after which 533 consecutive NSCLCs were collected during one-year of routine clinical analysis in the healthcare region (~90% advanced stage patients). The NanoString assay was evaluated in 169 of 533 cases. In the 533-sample cohort 79% had 1-2 variants, 12% >2 variants and 9% no detected variants. Ten gene fusions (five ALK, three RET, two ROS1) were detected in 135 successfully analyzed cases (80% analysis success rate). No ALK or ROS1 FISH fusion positive case was missed by the NanoString assay. Stratification of the 533-sample cohort based on actionable alterations in 11 oncogenes revealed that 66% of adenocarcinomas, 13% of squamous carcinoma (SqCC) and 56% of NSCLC not otherwise specified harbored ≥1 alteration. In adenocarcinoma, 10.6% of patients (50.3% if including KRAS) could potentially be eligible for emerging therapeutics, in addition to the 15.3% of patients eligible for standard EGFR or ALK inhibitors. For squamous carcinoma corresponding proportions were 4.4% (11.1% with KRAS) vs 2.2%. In conclusion, multiplexed NGS and gene fusion analyses are feasible in NSCLC for clinical diagnostics, identifying notable proportions of patients potentially eligible for emerging molecular therapeutics.
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| 6. |
- Afrasiabi, Roodabeh, et al.
(författare)
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Integration of a droplet-based microfluidic system and silicon nanoribbon FET sensor
- 2016
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Ingår i: Micromachines. - : MDPI AG. - 2072-666X. ; 7:8
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Tidskriftsartikel (refereegranskat)abstract
- We present a novel microfluidic system that integrates droplet microfluidics with a silicon nanoribbon field-effect transistor (SiNR FET), and utilize this integrated system to sense differences in pH. The device allows for selective droplet transfer to a continuous water phase, actuated by dielectrophoresis, and subsequent detection of the pH level in the retrieved droplets by SiNR FETs on an electrical sensor chip. The integrated microfluidic system demonstrates a label-free detection method for droplet microfluidics, presenting an alternative to optical fluorescence detection. In this work, we were able to differentiate between droplet trains of one pH-unit difference. The pH-based detection method in our integrated system has the potential to be utilized in the detection of biochemical reactions that induce a pH-shift in the droplets.
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| 7. |
- Andersson, Martin, et al.
(författare)
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HYPERFINE-DEPENDENT gf -VALUES OF Mn i LINES IN THE 1.49–1.80 μm H BAND
- 2015
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Ingår i: The Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 216:1
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Tidskriftsartikel (refereegranskat)abstract
- The three Mn I lines at 17325, 17339, and 17349 angstrom are among the 25 strongest lines (log(gf) > 0.5) in the H band. They are all heavily broadened due to hyperfine structure, and the profiles of these lines have so far not been understood. Earlier studies of these lines even suggested that they were blended. In this work, the profiles of these three infrared (IR) lines have been studied theoretically and compared to experimental spectra to assist in the complete understanding of the solar spectrum in the IR. It is shown that the structure of these lines cannot be described in the conventional way using the diagonal A and B hyperfine interaction constants. The off-diagonal hyperfine interaction not only has a large impact on the energies of the hyperfine levels, but also introduces a large intensity redistribution among the hyperfine lines, changing the line profiles dramatically. By performing large-scale calculations of the diagonal and off-diagonal hyperfine interaction and the gf-values between the upper and lower hyperfine levels and using a semi-empirical fitting procedure, we achieved agreement between our synthetic and experimental spectra. Furthermore, we compare our results with observations of stellar spectra. The spectra of the Sun and the K1.5 III red giant star Arcturus were modeled in the relevant region, 1.73-1.74 mu m, using our theoretically predicted gf-values and energies for each individual hyperfine line. Satisfactory fits were obtained and clear improvements were found using our new data compared with the old available Mn I data. A complete list of energies and gf-values for all the 3d(5)4s(S-7)4d e(6)D - 3d(5)4s(S-7)4f w(6)F hyperfine lines are available as supporting material, whereas only the stronger lines are presented and discussed in detail in this paper.
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| 8. |
- Beery, Thomas, et al.
(författare)
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Perceptions of the ecosystem services concept: Opportunities and challenges in the Swedish municipal context
- 2016
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Ingår i: Ecosystem Services. - : Elsevier BV. - 2212-0416. ; 17, s. 123-130
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Tidskriftsartikel (refereegranskat)abstract
- A current focus of ecosystem services (ES) implementation is on the municipal level of government where international and national legislation and policies have to be translated into practice. Given this focus, an understanding of perceptions within municipalities of the ES concept is crucial to support the implementation process. Against this background, this paper examines the perceptions of Swedish municipal stakeholders for the ES concept. A 2013 Swedish federal mandate that states that the values of ecosystem services should be considered in relevant decision-making processes, provides a timely context. Current perceptions, preconditions and awareness are explored via interviews and analyses. The results show that the views on the ecosystem services concept and its usefulness are generally very positive. Conceptual knowledge use is perceived as important as is the recognition of monetary valuation of ES. However, clarification of the distinction between implicit and explicit use of the concept by stakeholders is needed. Finally, results indicate that a deeper understanding of monetary valuation of ecosystem services by municipal staff members is connected with a more critical view on monetary valuation. It is concluded that detailed and clear definitions and guidelines are needed in order to support the process of implementing ES in municipalities.
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| 9. |
- Bieron, Jacek, et al.
(författare)
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Ab initio MCDHF calculations of electron-nucleus interactions
- 2015
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Ingår i: Physica Scripta. - : Institute of Physics Publishing (IOPP). - 0031-8949 .- 1402-4896. ; 90:5
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Tidskriftsartikel (refereegranskat)abstract
- We present recent advances in the development of atomic ab initio multiconfiguration Dirac– Hartree–Fock theory, implemented in the GRASP relativistic atomic structure code. For neutral atoms, the deviations of properties calculated within the Dirac–Hartree–Fock (DHF) method (based on independent particle model of an atomic cloud) are usually dominated by electron correlation effects, i.e. the non-central interactions of individual electrons. We present the recent advances in accurate calculations of electron correlation effects in small, medium, and heavy neutral atoms. We describe methods of systematic development of multiconfiguration expansions leading to systematic, controlled improvement of the accuracy of the ab initio calculations. These methods originate from the concept of the complete active space (CAS) model within the DHF theory, which, at least in principle, permits fully relativistic calculations with full account of electron correlation effects. The calculations within the CAS model on currently available computer systems are feasible only for very light systems. For heavier atoms or ions with more than a few electrons, restrictions have to be imposed on the multiconfiguration expansions. We present methods and tools, which are designed to extend the numerical calculations in a controlled manner, where multiconfiguration expansions account for all leading electron correlation effects. We show examples of applications of the GRASP code to calculations of hyperfine structure constants, but the code may be used for calculations of arbitrary bound-state atomic properties. In recent years it has been applied to calculations of atomic and ionic spectra (transition energies and rates), to determinations of nuclear electromagnetic moments, as well as to calculations related to interactions of bound electrons with nuclear electromagnetic moments leading to violations of discrete symmetries.
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| 10. |
- Björemark, Per Martin, 1975, et al.
(författare)
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Absolute Asymmetric Synthesis: Viedma Ripening of Co(bpy)(3) (2+) and Solvent-Free Oxidation to Co(bpy)(3) (3+)
- 2015
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Ingår i: Chemistry-a European Journal. - : Wiley. - 0947-6539. ; 21:30, s. 10630-33
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Tidskriftsartikel (refereegranskat)abstract
- Syntheses of [Co(bpy)(3)](2+) yield racemic solutions because the - and -enantiomers are stereochemically labile. However, crystallization and attrition-enhanced deracemization can give homochiral crystal batches of either handedness in quantitative yield. Subsequently, solvent-free oxidation with bromine vapour fixes the chirality because [Co(bipy)(3)](3+) does not enantiomerize in solution at ambient temperature. This combination of Viedma ripening and the labile/inert Co-II/Co-III couple constitutes a convenient method of absolute asymmetric synthesis.
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