| 1. |
- Abdulla, Parosh, et al.
(författare)
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Regular model checking for LTL(MSO)
- 2012
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Ingår i: International Journal on Software Tools for Technology Transfer. - Springer : Springer Science and Business Media LLC. - 1433-2779 .- 1433-2787. ; 14:2, s. 223-241
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Tidskriftsartikel (refereegranskat)abstract
- Regular model checking is a form of symbolic model checking for parameterized and infinite-state systems whose states can be represented as words of arbitrary length over a finite alphabet, in which regular sets of words are used to represent sets of states. We present LTL(MSO), a combination of the logics MSO and LTL as a natural logic for expressing temporal properties to be verified in regular model checking. In other words, LTL(MSO) is a natural specification language for both the system and the property under consideration. LTL(MSO) is a two-dimensional modal logic, where MSO is used for specifying properties of system states and transitions, and LTL is used for specifying temporal properties. In addition, the first-order quantification in MSO can be used to express properties parameterized on a position or process. We give a technique for model checking LTL(MSO), which is adapted from the automata-theoretic approach: a formula is translated to a Buechi regular transition system with a regular set of accepting states, and regular model checking techniques are used to search for models. We have implemented the technique, and show its application to a number of parameterized algorithms from the literature.
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| 2. |
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| 3. |
- Baumann, Jonas, et al.
(författare)
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Organized violence in the Horn of Africa
- 2012
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Ingår i: SIPRI Yearbook 2012. - Oxford : Oxford University Press. - 9780199650583 ; , s. 57-64
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Bokkapitel (refereegranskat)
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| 4. |
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| 5. |
- Carlsson, Annelie, et al.
(författare)
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Low risk HLA-DQ and increased body mass index in newly diagnosed type 1 diabetes children in the Better Diabetes Diagnosis study in Sweden
- 2012
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Ingår i: International Journal of Obesity. - : Nature Publishing Group. - 0307-0565 .- 1476-5497. ; 36:5, s. 718-724
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Tidskriftsartikel (refereegranskat)abstract
- Objective: Type 1 diabetes and obesity has increased in childhood. We therefore tested the hypothesis that type 1 diabetes human leukocyte antigen DQ (HLA-DQ) risk genotypes may be associated with increased body mass index (BMI). less thanbrgreater than less thanbrgreater thanDesign: The type 1 diabetes high-risk HLA-DQ A1*05:01-B1*02:01/A1*03:01-B1*03:02 genotype along with lower risk DQ genotypes were determined at the time of clinical onset by PCR and hybridization with allele-specific probes. BMI was determined after diabetes was stabilized. less thanbrgreater than less thanbrgreater thanSubjects: A total of 2403 incident type 1 diabetes children below 18 years of age were ascertained in the Swedish national Better Diabetes Diagnosis (BDD) study between May 2005 to September 2009. All children classified with type 1 diabetes, including positivity for at least one islet autoantibody, were investigated. less thanbrgreater than less thanbrgreater thanResults: Overall, type 1 diabetes HLA-DQ risk was negatively associated with BMI (Pandlt;0.0008). The proportion of the highest risk A1*05:01-B1*02:01/A1*03:01-B1*03:02 genotype decreased with increasing BMI (Pandlt;0.0004). However, lower risk type 1 diabetes DQ genotypes were associated with an increased proportion of patients who were overweight or obese (Pandlt;0.0001). Indeed, the proportion of patients with the low-risk A1*05:01-B1*02:01/A1*05:01-B1*02:01 genotype increased with increasing BMI (Pandlt;0.003). The magnitude of association on the multiplicative scale between the A1*05:01-B1*02:01/A1*05:01-B1*02:01 genotype and increased BMI was significant (Pandlt;0.006). The odds ratio in patients with this genotype of being obese was 1.80 (95% confidence interval 1.21-2.61; Pandlt;0.006). The increased proportion of overweight type 1 diabetes children with the A1*05:01-B1*02:01 haplotype was most pronounced in children diagnosed between 5 and 9 years of age. less thanbrgreater than less thanbrgreater thanConclusions: Susceptibility for childhood type 1 diabetes was unexpectedly found to be associated with the A1*05:01-B1*02:01/A1*05:01-B1*02:01 genotype and an increased BMI. These results support the hypothesis that overweight may contribute to the risk of type 1 diabetes in children positive for HLA-DQ A1*05:01-B1*02:01.
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| 6. |
- Chapman, Henry N, et al.
(författare)
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Femtosecond X-ray protein nanocrystallography.
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 470:7332, s. 73-7
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Tidskriftsartikel (refereegranskat)abstract
- X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200nm to 2μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.
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| 7. |
- Cieslar-Pobuda, Artur, et al.
(författare)
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Cell Type Related Differences in Staining with Pentameric Thiophene Derivatives
- 2014
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Ingår i: Cytometry Part A. - : John Wiley & Sons. - 1552-4922 .- 1552-4930. ; 85A:7, s. 628-635
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Tidskriftsartikel (refereegranskat)abstract
- Fluorescent compounds capable of staining cells selectively without affecting their viability are gaining importance in biology and medicine. Recently, a new family of optical dyes, denoted luminescent conjugated oligothiophenes (LCOs), has emerged as an interesting class of highly emissive molecules for studying various biological phenomena. Properly functionalized LCOs have been utilized for selective identification of disease-associated protein aggregates and for selective detection of distinct cells. Herein, we present data on differential staining of various cell types, including cancer cells. The differential staining observed with newly developed pentameric LCOs is attributed to distinct side chain functionalities along the thiophene backbone. Employing flow cytometry and fluorescence microscopy we examined a library of LCOs for stainability of a variety of cell lines. Among tested dyes we found promising candidates that showed strong or moderate capability to stain cells to different extent, depending on target cells. Hence, LCOs with diverse imidazole motifs along the thiophene backbone were identified as an interesting class of agents for staining of cancer cells, whereas LCOs with other amino acid side chains along the backbone showed a complete lack of staining for the cells included in the study. Furthermore, for p-HTMI,a LCO functionalized with methylated imidazole moieties, the staining was dependent on the p53 status of the cells, indicating that the molecular target for the dye is a cellular component regulated by p53. We foresee that functionalized LCOs will serve as a new class of optical ligands for fluorescent classification of cells and expand the toolbox of reagents for fluorescent live imaging of different cells.
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| 9. |
- Culverhouse, Robert C, et al.
(författare)
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Protocol for a collaborative meta-analysis of 5-HTTLPR, stress, and depression.
- 2013
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Ingår i: BMC Psychiatry. - 1471-244X. ; 13, s. 304-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Debate is ongoing about what role, if any, variation in the serotonin transporter linked polymorphic region (5-HTTLPR) plays in depression. Some studies report an interaction between 5-HTTLPR variation and stressful life events affecting the risk for depression, others report a main effect of 5-HTTLPR variation on depression, while others find no evidence for either a main or interaction effect. Meta-analyses of multiple studies have also reached differing conclusions.METHODS/DESIGN: To improve understanding of the combined roles of 5-HTTLPR variation and stress in the development of depression, we are conducting a meta-analysis of multiple independent datasets. This coordinated approach utilizes new analyses performed with centrally-developed, standardized scripts. This publication documents the protocol for this collaborative, consortium-based meta-analysis of 5-HTTLPR variation, stress, and depression.STUDY ELIGIBILITY CRITERIA: Our goal is to invite all datasets, published or unpublished, with 5-HTTLPR genotype and assessments of stress and depression for at least 300 subjects. This inclusive approach is to minimize potential impact from publication bias.DATA SOURCES: This project currently includes investigators from 35 independent groups, providing data on at least N = 33,761 participants.The analytic plan was determined prior to starting data analysis. Analyses of individual study datasets will be performed by the investigators who collected the data using centrally-developed standardized analysis scripts to ensure a consistent analytical approach across sites. The consortium as a group will review and interpret the meta-analysis results.DISCUSSION: Variation in 5-HTTLPR is hypothesized to moderate the response to stress on depression. To test specific hypotheses about the role of 5-HTTLPR variation on depression, we will perform coordinated meta-analyses of de novo results obtained from all available data, using variables and analyses determined a priori. Primary analyses, based on the original 2003 report by Caspi and colleagues of a GxE interaction will be supplemented by secondary analyses to help interpret and clarify issues ranging from the mechanism of effect to heterogeneity among the contributing studies. Publication of this protocol serves to protect this project from biased reporting and to improve the ability of readers to interpret the results of this specific meta-analysis upon its completion.
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| 10. |
- Drotz, Marcus K., et al.
(författare)
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Multiple origins of elytral reticulation modifications in the west palearctic Agabus bipustulatus complex (Coleoptera, Dytiscidae)
- 2010
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Ingår i: PLoS ONE. - : Public Library of Science. - 1932-6203. ; 5:2
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Tidskriftsartikel (refereegranskat)abstract
- The Agabus bipustulatus complex includes one of Europe's most widely distributed and common diving beetles. This complex, which is known for its large morphological variation, has a complex demographic and altitudinal variation in elytral reticulation. The various depth of the reticulation imprint, both in smaller and larger meshes, results in both mat and shiny individuals, as well as intermediate forms. The West Palearctic lowland is inhabited by a sexually dimorphic form, with shiny males and mat females. In mountain regions, shiny individuals of both sexes are found intermixed with mat individuals or in pure populations in central and southern areas, whereas pure populations of mat individuals are exclusively found in the northern region at high altitude. Sexual selection is proposed as a driving force in shaping this variation. However, the occurrence of different types of reticulation in both sexes and disjunct geographical distribution patterns suggest an additional function of the reticulation. Here we investigate the phylogeographical history, genetic structure and reticulation variation of several named forms within the Agabus bipustulatus complex including A. nevadensis. The molecular analyses recognised several well-supported clades within the complex. Several of the named forms had two or more independent origins. Few south European populations were uniform in reticulation patterns, and the males were found to display large variation. Reticulation diversity and population genetic variability were clearly correlated to altitude, but no genetic differences were detected among populations with mixed or homogenous forms. Observed reduction in secondary reticulation in female and increased variance in male at high altitude in South Europe may be explained by the occurrence of an additional selective force, beside sexual selection. The combined effect of these selective processes is here demonstrated in an extreme case to generate isolation barriers between populations at high altitudes. Here we discuss this selective force in relation to thermal selection.
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