| 1. |
- Gawronska, Barbara
(författare)
-
Information Extraction from Texts : Adapting a System for Summarization of News Reports to the Domain of Bioinformatics
- 2005
-
Ingår i: Transactions on Advanced Research. - : IPSI BgD. - 1820-4511. ; 1:1, s. 20-28
-
Tidskriftsartikel (refereegranskat)abstract
- Natural language serves as important information source in all areas of human activity. The presence of a huge amount of texts on the Internet actualizes the problem of efficient information search; visual scanning of all the textual information is difficult and time-consuming. There is a need for efficient, high-quality systems that extract the relevant information from texts. The paper presents the architecture of an experimental system for automatic text understanding and information extraction, which has originally been developed for the domain of news reports. The possibility of adapting the methodology for the purpose of bioinformatics is discussed, and the similarities and differences between texts in the two different domains are discussed and exemplified.
|
|
| 2. |
- Werngren, J., et al.
(författare)
-
Reevaluation of the Critical Concentration for Drug Susceptibility Testing of Mycobacterium tuberculosis against Pyrazinamide Using Wild-Type MIC Distributions and pncA Gene Sequencing
- 2012
-
Ingår i: Antimicrobial Agents and Chemotherapy. - 1098-6596. ; 56:3, s. 1253-1257
-
Tidskriftsartikel (refereegranskat)abstract
- Pyrazinamide (PZA) is a potent first-line agent for the treatment of tuberculosis (TB) with activity also against a significant part of drug-resistant Mycobacterium tuberculosis strains. Since PZA is active only at acid pH, testing for susceptibility to PZA is difficult and insufficiently reproducible. The recommended critical concentration for PZA susceptibility (MIC, 100 mg/liter) used in the Bactec systems (460 and MGIT 960) has not been critically evaluated against wild-type MIC distributions in clinical isolates of Mycobacterium tuberculosis. Using the Bactec MGIT 960 system, we determined the PZA MICs for 46 clinical M. tuberculosis isolates and compared the results to pncA sequencing and previously obtained Bactec 460 data. For consecutive clinical isolates (n = 15), the epidemiological wild-type cutoff (ECOFF) for PZA was 64 mg/liter (MIC distribution range, <= 8 to 64 mg/liter), and no pncA gene mutations were detected. In strains resistant in both Bactec systems (n = 18), the PZA MICs ranged from 256 to >= 1,024 mg/liter. The discordances between pncA sequencing, susceptibility results in Bactec 460, and MIC determinations in Bactec MGIT 960 were mainly observed in strains with MICs close to or at the ECOFF. We conclude that in general, wild-type and resistant strains were clearly separated and correlated to pncA mutations, although some isolates with MICs close to the ECOFF cause reproducibility problems within and between methods. To solve this issue, we suggest that isolates with MICs of <= 64 mg/liter be classified susceptible, that an intermediary category be introduced at 128 mg/liter, and that strains with MICs of >= 128 mg/liter be classified resistant.
|
|
| 3. |
- Di Baldassarre, Giuliano, et al.
(författare)
-
The interplay between human population dynamics and flooding in Bangladesh : a spatial analysis
- 2014
-
Ingår i: Evolving Water Resources Systems. - : Copernicus GmbH. - 9781907161421 ; , s. 188-191
-
Konferensbidrag (refereegranskat)abstract
- In Bangladesh, socio-economic and hydrological processes are both extremely dynamic and interrelated. Human population patterns are often explained as a response, or adaptation strategy, to physical events, e.g. flooding, salt-water intrusion, and erosion. Meanwhile, these physical processes are exacerbated, or mitigated, by diverse human interventions, e.g. river diversion, levees and polders. In this context, this paper describes an attempt to explore the complex interplay between floods and societies in Bangladeshi floodplains. In particular, we performed a spatially-distributed analysis of the interactions between the dynamics of human settlements and flood inundation patterns. To this end, we used flooding simulation results from inundation modelling, LISFLOOD-FP, as well as global datasets of population distribution data, such as the Gridded Population of the World (20 years, from 1990 to 2010) and HYDE datasets (310 years, from 1700 to 2010). The outcomes of this work highlight the behaviour of Bangladeshi floodplains as complex human water systems and indicate the need to go beyond the traditional narratives based on one-way cause effects, e.g. climate change leading to migrations.
|
|
| 4. |
|
|
| 5. |
- Ananthanarayanan, Durga, et al.
(författare)
-
Phase-field study of IMC growth in Sn-Cu/Cu solder joints including elastoplastic effects
- 2020
-
Ingår i: Acta Materialia. - : Elsevier BV. - 1359-6454 .- 1873-2453. ; 188, s. 241-258
-
Tidskriftsartikel (refereegranskat)abstract
- In this article, we aim to study the problem of the growth of intermetallic phases in solder joints undergoing mechanical deformation, using a phase-field model for multi-phase systems that can treat diffusion, elastic and plastic deformation. A suitable model is formulated and applied to Sn-Cu/Cu lead-free solder joints. The growth of the intermetallic layers during solid-state annealing is simulated for different strain states. We assess the values of stiffness tensors available in literature and perform ab initio calculations to support the selection of reasonable values from literature. We also perform a parametric study with different eigenstrain values and applied strains. We find that there is a significant effect of the considered eigenstrains and applied strains on the growth kinetics of the system and parabolic growth kinetics is followed in cases where the intermetallic layers grow. We thereby establish the importance of strain in the growth of intermetallic layers and the need for more targeted experiments on the role of strain in the reliability of the solder joint.
|
|
| 6. |
- Kravchuk, Oksana, et al.
(författare)
-
Transvection in Drosophila : trans-interaction between yellow enhancers and promoter is strongly suppressed by a cis-promoter only in certain genomic regions
- 2017
-
Ingår i: Chromosoma. - : Springer Science and Business Media LLC. - 0009-5915 .- 1432-0886. ; 126:3, s. 431-441
-
Tidskriftsartikel (refereegranskat)abstract
- Transvection is a phenomenon of interallelic communication whereby enhancers of one allele can activate a promoter located on the homologous chromosome. It has been shown for many independent genes that enhancers preferentially act on the cis-linked promoter, but deletion of this promoter allows the enhancers to act in trans. Here, we tested whether this cis-preference in the enhancer-promoter interaction could be reconstituted outside of the natural position of a gene. The yellow gene was chosen as a model system. Transgenic flies were generated that carried the yellow gene modified by the inclusion of the strategically placed recognition sites for the Cre and Flp recombinases. To facilitate transvection, an endogenous Su(Hw) insulator (1A2) or gypsy insulator was placed behind the yellow gene. Independent action of the recombinases produced a pair of derivative alleles, one containing the promoter-driven yellow gene, and the other, the enhancers and promoter that failed to produce a functional yellow protein. As a result, we observed strong transvection in many genomic regions, suggesting that a complete cis-preference of the enhancer-promoter interactions is mainly restricted to genes in their natural loci.
|
|
| 7. |
|
|
| 8. |
- Zallar, L J, et al.
(författare)
-
Development and initial characterization of a novel ghrelin receptor CRISPR/Cas9 knockout wistar rat model
- 2019
-
Ingår i: International Journal of Obesity. - : Nature Pub. Group. - 0307-0565 .- 1476-5497. ; 43:2, s. 344-354
-
Tidskriftsartikel (refereegranskat)abstract
- Ghrelin, a stomach-derived hormone implicated in numerous behaviors including feeding, reward, stress, and addictive behaviors, acts by binding to the growth hormone secretagogue receptor (GHSR). Here, we present the development, verification, and initial characterization of a novel GHSR knockout (KO) Wistar rat model created with CRISPR genome editing.
|
|
| 9. |
- Von Freiesleben, Pernille, et al.
(författare)
-
Boosting of enzymatic softwood saccharification by fungal GH5 and GH26 endomannanases
- 2018
-
Ingår i: Biotechnology for Biofuels. - : Springer Science and Business Media LLC. - 1754-6834. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Softwood is a promising feedstock for lignocellulosic biorefineries, but as it contains galactoglucomannan efficient mannan-degrading enzymes are required to unlock its full potential. Results: Boosting of the saccharification of pretreated softwood (Canadian lodgepole pine) was investigated for 10 fungal endo-β(1→4)-mannanases (endomannanases) from GH5 and GH26, including 6 novel GH26 enzymes. The endomannanases from Trichoderma reesei (TresMan5A) and Podospora anserina (PansMan26) were investigated with and without their carbohydrate-binding module (CBM). The pH optimum and initial rates of enzyme catalysed hydrolysis were determined on pure β-mannans, including acetylated and deacetylated spruce galactoglucomannan. Melting temperature (Tm) and stability of the endomannanases during prolonged incubations were also assessed. The highest initial rates on the pure mannans were attained by GH26 endomannanases. Acetylation tended to decrease the enzymatic rates to different extents depending on the enzyme. Despite exhibiting low rates on the pure mannan substrates, TresMan5A with CBM1 catalysed highest release among the endomannanases of both mannose and glucose during softwood saccharification. The presence of the CBM1 as well as the catalytic capability of the TresMan5A core module itself seemed to allow fast and more profound degradation of portions of the mannan that led to better cellulose degradation. In contrast, the presence of the CBM35 did not change the performance of PansMan26 in softwood saccharification. Conclusions: This study identified TresMan5A as the best endomannanase for increasing cellulase catalysed glucose release from softwood. Except for the superior performance of TresMan5A, the fungal GH5 and GH26 endomannanases generally performed on par on the lignocellulosic matrix. The work also illustrated the importance of using genuine lignocellulosic substrates rather than simple model substrates when selecting enzymes for industrial biomass applications.
|
|
| 10. |
- Aleksandrova, Krasimira, et al.
(författare)
-
Circulating C-reactive protein concentrations and risks of colon and rectal cancer : a nested case-control study within the European Prospective Investigation into Cancer and Nutrition
- 2010
-
Ingår i: American Journal of Epidemiology. - : Oxford University Press (OUP). - 0002-9262 .- 1476-6256. ; 172:4, s. 407-418
-
Tidskriftsartikel (refereegranskat)abstract
- The authors investigated associations between serum C-reactive protein (CRP) concentrations and colon and rectal cancer risk in a nested case-control study within the European Prospective Investigation into Cancer and Nutrition (1992-2003) among 1,096 incident cases and 1,096 controls selected using risk-set sampling and matched on study center, age, sex, time of blood collection, fasting status, menopausal status, menstrual cycle phase, and hormone replacement therapy. In conditional logistic regression with adjustment for education, smoking, nutritional factors, body mass index, and waist circumference, CRP showed a significant nonlinear association with colon cancer risk but not rectal cancer risk. Multivariable-adjusted relative risks for CRP concentrations of > or = 3.0 mg/L versus <1.0 mg/L were 1.36 (95% confidence interval (CI): 1.00, 1.85; P-trend = 0.01) for colon cancer and 1.02 (95% CI: 0.67, 1.57; P-trend = 0.65) for rectal cancer. Colon cancer risk was significantly increased in men (relative risk = 1.74, 95% CI: 1.11, 2.73; P-trend = 0.01) but not in women (relative risk = 1.06, 95% CI: 0.67, 1.68; P-trend = 0.13). Additional adjustment for C-peptide, glycated hemoglobin, and high density lipoprotein cholesterol did not attenuate these results. These data provide evidence that elevated CRP concentrations are related to a higher risk of colon cancer but not rectal cancer, predominantly among men and independently of obesity, insulin resistance, and dyslipidemia.
|
|
