| 1. |
- Moretti, Rocco, et al.
(författare)
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Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
- 2013
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Ingår i: Proteins. - : Wiley. - 0887-3585 .- 1097-0134. ; 81:11, s. 1980-1987
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Tidskriftsartikel (refereegranskat)abstract
- Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side-chain sampling and backbone relaxation, evaluated packing, electrostatic, and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies. Proteins 2013; 81:1980-1987.
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| 2. |
- Wang, Yang, et al.
(författare)
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Prognostic value of the extent of lymphadenectomy for esophageal cancer-specific survival among T1 patients
- 2021
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Ingår i: BMC Cancer. - : Springer Science and Business Media LLC. - 1471-2407. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Clinically, there are no clear guidelines on the extent of lymphadenectomy in patients with T1 esophageal cancer. Studying the minimum number of lymph nodes for resection may increase cancer-specific survival.Methods: Patients who underwent esophagectomy and lymphadenectomy at T1 stage were selected from the Surveillance, Epidemiology and End Results Program (United States, 1998–2014). Maximally selected rank and Cox proportional hazard models were used to examine three variables: the number of lymph nodes examined, the number of negative lymph nodes and the lymph node ratio.Results: Approximately 18% had lymph node metastases, where the median values were 10, 10 and 0 for the number of lymph nodes examined, the number of negative lymph nodes and the lymph node ratio, respectively. All three examined variables were statistically associated with cancer-specific survival probability. Dividing patients into two groups shows a clear difference in cancer-specific survival compared to four or five groups for all three variables: there was a 29% decrease in the risk of death with the number of lymph nodes examined ≥14 vs < 14 (hazard ratio 0.71, 95% confidence interval: 0.57–0.89), a 35% decrease in the risk of death with the number of negative lymph nodes ≥13 vs < 13 (hazard ratio 0.65, 95% confidence interval: 0.52–0.81), and an increase of 1.21 times in the risk of death (hazard ratio 2.21, 95% confidence interval: 1.76–2.77) for the lymph node ratio > 0.05 vs ≤ 0.05.Conclusions: The extent of lymph node dissection is associated with cancer-specific survival, and the minimum number of lymph nodes that need to be removed is 14. The number of negative lymph nodes and the lymph node ratio also have prognostic value after lymphadenectomy among T1 stage patients.
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| 3. |
- Wen, Qianyun, 1993-
(författare)
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Decision Support for Energy Transition : Application of Multi-criteria Decision Making on Danish Residential Heating
- 2023
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- With the increasing awareness of the impact of climate change, there has been more intention to reduce greenhouse gas emissions and achieve carbon neutrality targets. However, as one essential element for human well-being, residential heating remains a major contributor to global greenhouse gas emissions. The complex, interdependent, and sometimes contradictory nature of factors influencing residential heating choices makes it a difficult problem to address. Multiple actors with different goals and priorities further complicate the decision-making process. Moreover, given the current energy crisis, selecting an appropriate heating system for residential areas has become even more crucial. Therefore, there is a need for decision support tools that can consider multi-dimensional factors and heating alternatives, which usually have a long-term impact involved in residential heating choices. Thus, this thesis aims to improve the understanding of what influences decisions to choose a heating technology alternative and how decision support tools can sup-port these decisions. Among the decision-making techniques, multi-criteria decision-making (MCDM) methods have been chosen because they are capable of considering a wide range of factors and are simple to understand and use, taking into account data availability and capability. A systematic literature review is conducted to understand the criteria and MCDM methods commonly used in the field. Two appended papers applied different approaches of MCDM methods to support the Danish residential heating transition. These applications also act as case studies to address the research questions. This thesis highlights financial, technical, and environmental factors for decision-making on heating technologies and addresses common problems that might occur during the decision-support process. Specifically, it suggests considering financial costs, environmental emissions, technical efficiency and lifetime when choosing a heating technology and using distance-to-ideal MCDM combining other methods. Furthermore, the thesis reflects on the complexity of MCDM applications in decision support and presents a publicly available online decision support tool based on the research (https://api.flexsus.org/MCDM). This thesis contributes to knowledge for academics and fills gaps in residential heating decision-making. For practitioners, a useful tool is provided for improving the quality of decision-making in residential heating, offering a practical and scientific perspective for making informed decisions without consuming extra resources. By increasing the under-standing of influencing factors and decision-support methods for heating technologies, this thesis helps facilitate the heating transition.
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| 4. |
- Yu, Chen, et al.
(författare)
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Chinese Rural Road Traffic Safety Characteristics Analysis and Traffic Safety Countermeasures
- 2013
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Ingår i: Proceedings of the 16th International Conference Road Safety on Four Continents. - Linköping : Statens väg- och transportforskningsinstitut.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Depending on the alignment data of the western rural road by the “GIPSI-TRAC” highway alignment gathering vehicle, the observation data about the vehicle composition, running speed on the typical rural road section, the traffic accidents and archives of the major traffic accidents for the consecutive five years, the major traffic accident statistics of the death number than or equal to 10 in an accident for the consecutive three years, and the investigation of the accident-prone sections in rural road, the article analysis the traffic accident characteristics and traffic features of the rural road, particular focus on the analysis of major accidents; The paper presents the rural roads feature such as composition of complex traffic, the lack of typical models, low-speed, low technical indicators highways , and summarizes the accident form, accident vehicle type, and accident location and other characteristics in the rural road; To reduce the probability of accident occurrence and improve traffic safety of the rural road, the author brings up some suggestions on the safety countermeasures of the rural road.
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