| 101. |
- Lindström, Tom, et al.
(författare)
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The shape of the spatial kernel and its implications for biological invasions in patchy environments
- 2011
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : Royal Society. - 0962-8452 .- 1471-2954. ; 278:1711, s. 1564-1571
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Tidskriftsartikel (refereegranskat)abstract
- Ecological and epidemiological invasions occur in a spatial context. In the study presented we tested how these processes relate to the distance dependence of spread or dispersal between spatial entities such as habitat patches or infective units. The distance dependence was described by a spatial kernel which can be characterized by its shape, quantified by kurtosis, and width, quantified by the kernel variance. We also introduced a method to analyze or generate non randomly distributed infective units or patches as point pattern landscapes. The method is based on Fourier transform and consists of two measures in the spectral representation; Continuity that relates to autocorrelation and Contrast that refers to difference in density of patches, or infective units, in different areas of the landscape. The method was also used to analyze some relevant empirical data where our results are expected to have implications for ecological or epidemiological studies. We analyzed distributions of large old trees (Quercus and Ulmus) as well as the distributions of farms (both cattle and pig) in Sweden. We tested the invasion speed in generated landscapes with different amount of Continuity and Contrast. The results showed that kurtosis, i.e. the kernel shape, was not important for predicting the invasion speed in randomly distributed patches or infective units. However, depending on the assumptions of dispersal, it may be highly important when the distribution of patches or infective units deviates from randomness, in particular when the Contrast is high. We conclude that speed of invasions and spread of diseases depends on its spatial context through the spatial kernel intertwined to the spatial structure. This implies high demands on the empirical data; it requires knowledge of both shape and width of the spatial kernel as well as spatial structure of patches or infective units.
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| 102. |
- Loman, Stina
(författare)
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Hon skuggar publiken
- 2018
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Ingår i: Biblioteksbladet. - Stockholm : Svensk biblioteksförening. - 1651-5447. ; :3, s. 29-32
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Vilket bibliotek möter dina besökare? Hittar de vad de söker? Ett sätt attfå svar är att testa biblioteket på användarna. Anneli Friberg på Linköpingsuniversitetär en av dem som jobbat längst med UX i biblioteket.
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| 103. |
- Lövfors, William, 1991-, et al.
(författare)
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A comprehensive mechanistic model of adipocyte signaling with layers of confidence
- 2023
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Ingår i: npj Systems Biology and Applications. - : Springer Nature. - 2056-7189. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Adipocyte signaling, normally and in type 2 diabetes, is far from fully understood. We have earlier developed detailed dynamic mathematical models for several well-studied, partially overlapping, signaling pathways in adipocytes. Still, these models only cover a fraction of the total cellular response. For a broader coverage of the response, large-scale phosphoproteomic data and systems level knowledge on protein interactions are key. However, methods to combine detailed dynamic models with large-scale data, using information about the confidence of included interactions, are lacking. We have developed a method to first establish a core model by connecting existing models of adipocyte cellular signaling for: (1) lipolysis and fatty acid release, (2) glucose uptake, and (3) the release of adiponectin. Next, we use publicly available phosphoproteome data for the insulin response in adipocytes together with prior knowledge on protein interactions, to identify phosphosites downstream of the core model. In a parallel pairwise approach with low computation time, we test whether identified phosphosites can be added to the model. We iteratively collect accepted additions into layers and continue the search for phosphosites downstream of these added layers. For the first 30 layers with the highest confidence (311 added phosphosites), the model predicts independent data well (70–90% correct), and the predictive capability gradually decreases when we add layers of decreasing confidence. In total, 57 layers (3059 phosphosites) can be added to the model with predictive ability kept. Finally, our large-scale, layered model enables dynamic simulations of systems-wide alterations in adipocytes in type 2 diabetes.
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| 104. |
- Lööf, Jasmine, 1982-, et al.
(författare)
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Impact of PINCH expression on survival in colorectal cancer patients
- 2011
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Ingår i: BMC CANCER. - : BioMed Central. - 1471-2407. ; 11:103
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Tidskriftsartikel (refereegranskat)abstract
- Background: The adaptor protein PINCH is overexpressed in the stroma of several types of cancer, and is an independent prognostic marker in colorectal cancer. In this study we further investigate the relationship of PINCH and survival regarding the response to chemotherapy in colorectal cancer. Results: Paraffin-embedded tissue sections from 251 primary adenocarcinomas, 149 samples of adjacent normal mucosa, 57 samples of distant normal mucosa and 75 lymph node metastases were used for immunohistochemical staining. Stromal staining for PINCH increased from normal mucosa to primary tumour to metastasis. Strong staining in adjacent normal mucosa was related to worse survival independently of sex, age, tumour location, differentiation and stage (p = 0.044, HR, 1.60, 95% Cl, 1.01-2.52). PINCH staining at the invasive margin tended to be related to survival (p = 0.051). In poorly differentiated tumours PINCH staining at the invasive margin was related to survival independently of sex, age and stage (p = 0.013, HR, 1.90, 95% Cl, 1.14-3.16), while in better differentiated tumours it was not. In patients with weak staining, adjuvant chemotherapy was related to survival (p = 0.010, 0.013 and 0.013 in entire tumour area, invasive margin and inner tumour area, respectively), but not in patients with strong staining. However, in the multivariate analysis no such relationship was seen. Conclusions: PINCH staining in normal adjacent mucosa was related to survival. Further, PINCH staining at the tumour invasive margin was related to survival in poorly differentiated tumours but not in better differentiated tumours, indicating that the impact of PINCH on prognosis was dependent on differentiation status.
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| 105. |
- Magnusson, Rasmus, 1992-, et al.
(författare)
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Deep neural network prediction of genome-wide transcriptome signatures – beyond the Black-box
- 2022
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Ingår i: npj Systems Biology and Applications. - : Springer Nature. - 2056-7189. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Prediction algorithms for protein or gene structures, including transcription factor binding from sequence information, have been transformative in understanding gene regulation. Here we ask whether human transcriptomic profiles can be predicted solely from the expression of transcription factors (TFs). We find that the expression of 1600 TFs can explain >95% of the variance in 25,000 genes. Using the light-up technique to inspect the trained NN, we find an over-representation of known TF-gene regulations. Furthermore, the learned prediction network has a hierarchical organization. A smaller set of around 125 core TFs could explain close to 80% of the variance. Interestingly, reducing the number of TFs below 500 induces a rapid decline in prediction performance. Next, we evaluated the prediction model using transcriptional data from 22 human diseases. The TFs were sufficient to predict the dysregulation of the target genes (rho = 0.61, P < 10−216). By inspecting the model, key causative TFs could be extracted for subsequent validation using disease-associated genetic variants. We demonstrate a methodology for constructing an interpretable neural network predictor, where analyses of the predictors identified key TFs that were inducing transcriptional changes during disease.
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| 106. |
- Mak, Wing Cheung, et al.
(författare)
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Controlled Delivery of Human Cells by Temperature Responsive Microcapsules
- 2015
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Ingår i: Journal of Functional Biomaterials. - : MDPI. - 2079-4983. ; 6:2, s. 439-453
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Tidskriftsartikel (refereegranskat)abstract
- Cell therapy is one of the most promising areas within regenerative medicine. However, its full potential is limited by the rapid loss of introduced therapeutic cells before their full effects can be exploited, due in part to anoikis, and in part to the adverse environments often found within the pathologic tissues that the cells have been grafted into. Encapsulation of individual cells has been proposed as a means of increasing cell viability. In this study, we developed a facile, high throughput method for creating temperature responsive microcapsules comprising agarose, gelatin and fibrinogen for delivery and subsequent controlled release of cells. We verified the hypothesis that composite capsules combining agarose and gelatin, which possess different phase transition temperatures from solid to liquid, facilitated the destabilization of the capsules for cell release. Cell encapsulation and controlled release was demonstrated using human fibroblasts as model cells, as well as a therapeutically relevant cell line—human umbilical vein endothelial cells (HUVECs). While such temperature responsive cell microcapsules promise effective, controlled release of potential therapeutic cells at physiological temperatures, further work will be needed to augment the composition of the microcapsules and optimize the numbers of cells per capsule prior to clinical evaluation.
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| 107. |
- Mathiason, Gunnar, et al.
(författare)
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Exploring a Multi-Tiered Whiteboard Infrastructure for Information Fusion in Wireless Sensor Networks
- 2008
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Ingår i: Proceedings of the second Skövde Workshop on Information Fusion Topics. - Skövde : University of Skövde. - 9789163336874 - 9789163336973 ; , s. 63-66
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Konferensbidrag (refereegranskat)abstract
- It is important for the life time of a wireless sensornetwork (WSN) to reduce the amount of data transferred throughthe network. As a typical approach, sensor data is filtered beforepropagating updates, to a node at the edge of a network, whereit can be fused. Information Fusion inside the network canreduce the amount of data propagated, by fusing data beforeand in propagation, without losing the information value in it. Weexplore infrastructures for distributed fusion, with fusion nodeslocated at strategic nodes inside the network, as an approachof structured distributed fusion for WSNs. We propose aninfrastructure for a white-board approach that uses a distributedreal-time database with virtual full replication. With such anapproach, both raw and fused data are logically available at allnodes and physically available where used, such that only useddata will be propagated and use resources. The actual resourceusage will be relative to the actual demand for data, rather thanto the amount of data published at the white-board. We presentan exploration of such an infrastructure, and points out futurekey research questions for such a white-board approach.
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| 108. |
- Mathiason, Gunnar, et al.
(författare)
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Virtual Full Replication by Adaptive Segmentation
- 2007
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Ingår i: 13th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications (RTCSA 2007). - Los Alamitos, California, USA : IEEE. - 9780769529752 - 0769529755 ; , s. 327-337
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Konferensbidrag (refereegranskat)abstract
- We propose virtual full replication by adaptive segmentation (ViFuR-A), and evaluate its ability to maintain scalability in a replicated real-time database. With full replication and eventual consistency, transaction timeliness becomes independent of network delays for all transactions. However, full replication does not scale well, since all updates must be replicated to all nodes, also when data is needed only at a subset of the nodes. With virtual full replication that adapts to actual data needs, resource usage can be bounded and the database can be made scalable. We propose a scheme for adaptive segmentation that detects new data needs and adapts replication. The scheme includes an architecture, a scalable protocol and a replicated directory service that together maintains scalability. We show that adaptive segmentation bounds the required storage at a significantly lower level compared to static segmentation, for a typical workload where the data needs change repeatedly. Adaptation time can be kept constant for the workload when there are sufficient resources. Also, the storage is constant with an increasing amount of nodes and linear with an increasing rate of change to data needs.
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| 109. |
- Mathiason, Gunnar, et al.
(författare)
-
Virtual Full Replication by Static Segmentation for Multiple Properties of Data Objects
- 2005
-
Ingår i: Proc. of RTIS 2005. - Skövde : University of Skövde. - 9163173492 ; , s. 11-18
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Konferensbidrag (refereegranskat)abstract
- We implement Virtual full replication for a distributed real-time database by segmenting the database on multiple data properties. Virtual full replication provides an image to the application of full replication in a partially replicated database, by replicating data to meet the actual data needs of the users of the data. This is useful since fully replicated real-time databases, that allow updates at all nodes, do not scale well as updates must be replicated to every other node for replica consistency, also to nodes where only a small share of the database will ever be used. We propose an algorithm that segments the database on multiple data properties without causing a combinatorial problem. We show, by analysis and an implementation, that scalability for such a system can be improved due to scalable resource usage, while application semantics of full replication is unchanged.
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| 110. |
- Mathiason, Gunnar, et al.
(författare)
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Virtual Full Replication for Scalable and Adaptive Real-Time Communication in Wireless Sensor Networks
- 2008
-
Ingår i: Proceedings of the Second International Conference on Sensor Technologies and Applications (SENSORCOMM 2008). - Los Alamitos : IEEE. - 9780769533308 ; , s. 55-64
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Konferensbidrag (refereegranskat)abstract
- Sensor networks have limited resources and often support large-scale applications that need scalable propagation of sensor data to users. We propose a white-board style of communication in sensor networks using a distributed real-time database supporting Virtual Full Replication with Adaptive Segmentation. This allows mobile client nodes to access, transparently and efficiently, any sensor data at any node in the network. We present a two-tiered wireless architecture, and an adaptation protocol, for scalable and adaptive white-board communication in large-scale sensor networks. Sensor value readings at nodes of the sensor tier are published at nodes of the database tier as database updates to objects in a distributed real-time database. The search space of client nodes for sensor data is thus limited to the number of database nodes. With this scheme, we can show scalable resource usage and short adaptation times for several hundreds of database nodes and up to 50 moving clients.
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