| 1. |
- Abenius, Tobias, 1979, et al.
(författare)
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System-scale network modeling of cancer using EPoC
- 2012
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Ingår i: Advances in Experimental Medicine and Biology. - New York, NY : Springer New York. - 0065-2598. - 9781441972095 ; 736:5, s. 617-643
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Tidskriftsartikel (refereegranskat)abstract
- One of the central problems of cancer systems biology is to understand the complex molecular changes of cancerous cells and tissues, and use this understanding to support the development of new targeted therapies. EPoC (Endogenous Perturbation analysis of Cancer) is a network modeling technique for tumor molecular profiles. EPoC models are constructed from combined copy number aberration (CNA) and mRNA data and aim to (1) identify genes whose copy number aberrations significantly affect target mRNA expression and (2) generate markers for long- and short-term survival of cancer patients. Models are constructed by a combination of regression and bootstrapping methods. Prognostic scores are obtained from a singular value decomposition of the networks. We have previously analyzed the performance of EPoC using glioblastoma data from The Cancer Genome Atlas (TCGA) consortium, and have shown that resulting network models contain both known and candidate disease-relevant genes as network hubs, as well as uncover predictors of patient survival. Here, we give a practical guide how to perform EPoC modeling in practice using R, and present a set of alternative modeling frameworks.
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| 2. |
- Adhikari, Deepak
(författare)
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In Vitro Activation of Dormant Follicles for Fertility Preservation
- 2013
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Ingår i: Advances in Experimental Medicine and Biology. - New York : Springer. - 0065-2598. ; 761:Oocyte Biology in Fertility Preservation, s. 29-42
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Tidskriftsartikel (refereegranskat)abstract
- Recent advances in radiotherapy and chemotherapy have led to higher cure rates for female children and adolescents with cancer. However, these treatments adversely affect germ cell survival, and ovarian failure is thus a probable side effect of these anticancer therapies. Moreover, an increasing number of women are choosing to postpone childbearing until later in life, but their primordial follicle reserves degenerate with advancing age. Thus there is a pressing need for the development of fertility preservation methods for these individuals. Ovarian tissue cryopreservation prior to loss of the primordial follicle population either due to cancer treatments or normal aging is a promising option for safeguarding fertility. A complete in vitro maturation (IVM) system could help generate mature eggs for later use without the patient having to undergo the cumbersome process involved in current assisted reproduction methods to generate mature eggs. Cryopreserved ovarian cortical tissues have attracted the attention of reproductive biologists and clinicians because of the large number of safely frozen primordial follicles in them, and it is theoretically possible to use these follicles for in vitro activation (IVA) and subsequent IVM. Ovarian tissue collection is independent of patient age and social or personal conditions. Despite being widely accepted potential techniques for fertility preservation, IVA and IVM of human primordial follicles to obtain fertilizable eggs remains far from reality. This chapter highlights the current achievements and obstacles in obtaining growing follicles through activation of dormant follicles.
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| 3. |
- Ahlgren, Ulf, et al.
(författare)
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Approaches for imaging islets
- 2010
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Ingår i: Advances in Experimental Medicine and Biology. - Dordrecht : Springer Netherlands. - 0065-2598 .- 2214-8019. ; 654, s. 39-57
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Tidskriftsartikel (refereegranskat)abstract
- The establishment of improved technologies for imaging of the pancreas is a key element in addressing several aspects of diabetes pathogenesis. In this respect, the development of a protocol that allows for non-invasive scoring of human islets, or islet beta-cells, is of particular importance. The development of such a technology would have profound impact on both clinical and experimental medicine, ranging from early diagnosis of diabetes to the evaluation of therapeutic regimes. Another important task is the development of modalities for high-resolution imaging of experimental animal models for diabetes. Rodent models for diabetes research have for decades been instrumental to the diabetes research community. The ability to image, and to accurately quantify, key players of diabetogenic processes with molecular specificity will be of great importance for elucidating mechanistic aspects of the disease. This chapter aims to overview current progress within these research areas.
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| 4. |
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| 5. |
- Bjorndahl, L, et al.
(författare)
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Structure of chromatin in spermatozoa
- 2014
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Ingår i: Advances in experimental medicine and biology. - New York, NY : Springer New York. - 0065-2598. ; 791, s. 1-11
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Tidskriftsartikel (refereegranskat)
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| 6. |
- Bruton, JD, et al.
(författare)
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Methods to detect Ca(2+) in living cells
- 2012
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Ingår i: Advances in experimental medicine and biology. - Dordrecht : Springer Netherlands. - 0065-2598. ; 740, s. 27-43
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Tidskriftsartikel (refereegranskat)
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| 7. |
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| 8. |
- Cerenius, Lage, et al.
(författare)
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Crustacean Immunity
- 2010
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Ingår i: Advances in Experimental Medicine and Biology. - Boston, MA : Springer US. - 0065-2598 .- 2214-8019. ; 708, s. 239-259
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Tidskriftsartikel (refereegranskat)abstract
- This chapter provides a review of recent progress in the elucidation of innate immune mechanisms in crustaceans. Mainly due to the importance of crustacean aquaculture interest in this field is large and the subject for extensive research efforts. Here, we provide detailed data on the molecular characterisation of lectins, antiviral reactions, hemocyte formation and differentiation and on the regulation of innate immune pathways.
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| 9. |
- Danielson, Jonas, et al.
(författare)
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Phylogeny of Major Intrinsic Proteins
- 2010
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Ingår i: Advances in Experimental Medicine and Biology. - 0065-2598. ; 679, s. 19-32
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Tidskriftsartikel (refereegranskat)abstract
- Major intrinsic proteins (MIPs) form a large superfamily of proteins that can be divided into different subfamilies and groups according to phylogenetic analyses. Plants encode more MIPs than other organisms and seven subfamilies have been defined, whereof the Nodulin26-like major intrinsic proteins (NIPs) have been shown to permeate metalloids. In this chapter we review the phylogeny of MIPs in general and especially of the plant MIPs. We also identify bacterial NIP-like MIPs and discuss the evolutionary implications of this finding regarding the origin and ancestral transport specificity of the NIPs.
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| 10. |
- Eckerbom, Per, 1974-, et al.
(författare)
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Intravoxel Incoherent Motion MR Imaging of the Kidney : Pilot Study
- 2013
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Ingår i: Advances in Experimental Medicine and Biology. - New York, NY : Springer New York. - 0065-2598 .- 2214-8019. ; 765, s. 55-58
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Tidskriftsartikel (refereegranskat)abstract
- MR examinations (Achieva 3 T, Philips, Best, The Netherlands) were performed at five different occasions in a healthy volunteer (male 60 years) and in one renal cancer patient (male 78 years) with normal renal function (creatinine 88 μmol/L). Intravoxel incoherent motion (IVIM) coefficients D + D* were measured using respiratory-triggered diffusion-weighted spin-echo echo-planar imaging. Perfusion data of the patient were acquired using a saturation-recovery gradient-echo sequence and with the bolus of Gd-BOPTA (Multihance). D + D* were computed by monoexponential fitting of MR signal intensity attenuation versus b for b = 0, 50, 100, 150 s/mm2. Perfusion parameters were evaluated with “NordicICE” software. The map of D + D* was compared qualitatively with the perfusion map computed from the Gd scan. D + D* values of the cortex and medulla were in the range 2.3–2.7 and 1.1–1.6 × 10-3 mm2/s, respectively. In conclusion, in this pilot study a good qualitative relation between IVIM variables D + D* and renal perfusion has been found.
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