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  • 1.
    Avenel, Christophe
    et al.
    CADESS Med AB, Uppsala, Sweden.
    Tolf, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    Dragomir, Anca
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology. Department of Pathology, Uppsala University Hospital, Uppsala, Sweden..
    Carlbom, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. CADESS Med AB, Uppsala, Sweden.
    Glandular Segmentation of Prostate Cancer: An Illustration of How the Choice of Histopathological Stain Is One Key to Success for Computational Pathology2019In: Frontiers in Bioengineering and Biotechnology, E-ISSN 2296-4185, Vol. 7, article id 125Article in journal (Refereed)
    Abstract [en]

    Digital pathology offers the potential for computer-aided diagnosis, significantly reducing the pathologists' workload and paving the way for accurate prognostication with reduced inter-and intra-observer variations. But successful computer-based analysis requires careful tissue preparation and image acquisition to keep color and intensity variations to a minimum. While the human eye may recognize prostate glands with significant color and intensity variations, a computer algorithm may fail under such conditions. Since malignancy grading of prostate tissue according to Gleason or to the International Society of Urological Pathology (ISUP) grading system is based on architectural growth patterns of prostatic carcinoma, automatic methods must rely on accurate identification of the prostate glands. But due to poor color differentiation between stroma and epithelium from the common stain hematoxylin-eosin, no method is yet able to segment all types of glands, making automatic prognostication hard to attain. We address the effect of tissue preparation on glandular segmentation with an alternative stain, Picrosirius red-hematoxylin, which clearly delineates the stromal boundaries, and couple this stain with a color decomposition that removes intensity variation. In this paper we propose a segmentation algorithm that uses image analysis techniques based on mathematical morphology and that can successfully determine the glandular boundaries. Accurate determination of the stromal and glandular morphology enables the identification of the architectural pattern that determine the malignancy grade and classify each gland into its appropriate Gleason grade or ISUP Grade Group. Segmentation of prostate tissue with the new stain and decomposition method has been successfully tested on more than 11000 objects including well-formed glands (Gleason grade 3), cribriform and fine caliber glands (grade 4), and single cells (grade 5) glands.

  • 2.
    Bandyopadhyay, Souvik K.
    et al.
    GlaxoSmithKline Asia Pvt. Ltd., Bangalore, India.
    Azharuddin, Mohammad
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Chemistry. Linköping University, Faculty of Medicine and Health Sciences.
    Dasgupta, Anjan K.
    Department of Biochemistry, University of Calcutta, Kolkata, India.
    Ganguli, Bhaswati
    Department of Statistics, University of Calcutta, Kolkata, India.
    SenRoy, Sugata
    Department of Statistics, University of Calcutta, Kolkata, India.
    Patra, Hirak Kumar
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Wolfson College, University of Cambridge, Cambridge, United Kingdom; Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom.
    Deb, Suryyani
    Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Kolkata, India.
    Probing ADP Induced Aggregation Kinetics During Platelet-Nanoparticle Interactions: Functional Dynamics Analysis to Rationalize Safety and Benefits2019In: Frontiers in Bioengineering and Biotechnology, E-ISSN 2296-4185, Vol. 7, p. 163-Article in journal (Refereed)
    Abstract [en]

    Platelets, one of the most sensitive blood cells, can be activated by a range of external and internal stimuli including physical, chemical, physiological, and/or non-physiological agents. Platelets need to respond promptly during injury to maintain blood hemostasis. The time profile of platelet aggregation is very complex, especially in the presence of the agonist adenosine 5′-diphosphate (ADP), and it is difficult to probe such complexity using traditional linear dose response models. In the present study, we explored functional analysis techniques to characterize the pattern of platelet aggregation over time in response to nanoparticle induced perturbations. This has obviated the need to represent the pattern of aggregation by a single summary measure and allowed us to treat the entire aggregation profile over time, as the response. The modeling was performed in a flexible manner, without any imposition of shape restrictions on the curve, allowing smooth platelet aggregation over time. The use of a probabilistic framework not only allowed statistical prediction and inference of the aggregation signatures, but also provided a novel method for the estimation of higher order derivatives of the curve, thereby allowing plausible estimation of the extent and rate of platelet aggregation kinetics over time. In the present study, we focused on the estimated first derivative of the curve, obtained from the platelet optical aggregometric profile over time and used it to discern the underlying kinetics as well as to study the effects of ADP dosage and perturbation with gold nanoparticles. In addition, our method allowed the quantification of the extent of inter-individual signature variations. Our findings indicated several hidden features and showed a mixture of zero and first order kinetics interrupted by a metastable zero order ADP dose dependent process. In addition, we showed that the two first order kinetic constants were ADP dependent. However, we were able to perturb the overall kinetic pattern using gold nanoparticles, which resulted in autocatalytic aggregation with a higher aggregate mass and which facilitated the aggregation rate.

  • 3. Benchaib, Mohamed Amine
    et al.
    Bouchnita, Anass
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Volpert, Vitaly
    Makhoute, Abdelkader
    Mathematical modeling reveals that the administration of EGF can promote the elimination of lymph node metastases by PD-1/PD-L1 blockade2019In: Frontiers in Bioengineering and Biotechnology, E-ISSN 2296-4185, Vol. 7, article id 104Article in journal (Refereed)
  • 4. Chen, Que
    et al.
    Arents, Jos
    Schuurmans, J. Merijn
    Ganapathy, Srividya
    de Grip, Willem J.
    Cheregi, Otilia
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    dos Santos, Filipe Branco
    Hellingwerf, Klaas J.
    Functional Expression of Gloeobacter Rhodopsin in PSI-Less Synechocystis sp. PCC68032019In: Frontiers in Bioengineering and Biotechnology, E-ISSN 2296-4185, Vol. 7, article id 67Article in journal (Refereed)
    Abstract [en]

    The approach of providing an oxygenic photosynthetic organism with a cyclic electron transfer system, i.e., a far-red light-driven proton pump, is widely proposed to maximize photosynthetic efficiency via expanding the absorption spectrum of photosynthetically active radiation. As a first step in this approach, Gloeobacter rhodopsin was expressed in a PSI-deletion strain of Synechocystis sp. PCC6803. Functional expression of Gloeobacter rhodopsin, in contrast to Proteorhodopsin, did not stimulate the rate of photoheterotrophic growth of this Synechocystis strain, analyzed with growth rate measurements and competition experiments. Nevertheless, analysis of oxygen uptake and-production rates of the Gloeobacter rhodopsin-expressing strains, relative to the 1 PSI control strain, confirm that the proton-pumping Gloeobacter rhodopsin provides the cells with additional capacity to generate proton motive force. Significantly, expression of the Gloeobacter rhodopsin did modulate levels of pigment formation in the transgenic strain.

  • 5.
    Kleiven, Svein
    KTH, School of Technology and Health (STH), Medical Engineering, Neuronic Engineering.
    Why most traumatic brain injuries are not caused by linear acceleration but skull fractures are2013In: Frontiers in Bioengineering and Biotechnology, E-ISSN 2296-4185, Vol. 1, no 15, p. 1-5Article in journal (Refereed)
    Abstract [en]

    Injury statistics have found the most common accident situation to be an oblique impact. An oblique impact will give rise to both linear and rotational head kinematics. The human brain is most sensitive to rotational motion. The bulk modulus of brain tissue is roughly five to six orders of magnitude larger than the shear modulus so that for a given impact it tends to deform predominantly in shear. This gives a large sensitivity of the strain in the brain to rotational loading and a small sensitivity to linear kinematics. Therefore, rotational kinematics should be a better indicator of traumatic brain injury risk than linear acceleration. To illustrate the difference between radial and oblique impacts, perpendicular impacts through the center of gravity of the head and 45° oblique impacts were simulated. It is obvious that substantially higher strain levels in the brain are obtained for an oblique impact, compared to a corresponding perpendicular one, when impacted into the same padding using an identical impact velocity. It was also clearly illustrated that the radial impact causes substantially higher stresses in the skull with an associated higher risk of skull fractures, and traumatic brain injuries secondary to those.

  • 6.
    Wang, Ruoli
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, BioMEx. KTH, School of Engineering Sciences (SCI), Mechanics. Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
    Gäverth, J.
    Herman, Pawel
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    Changes in the neural and non-neural related properties of the spastic wrist flexors after treatment with botulinum toxin a in post-stroke subjects: An optimization study2018In: Frontiers in Bioengineering and Biotechnology, E-ISSN 2296-4185, Vol. 9, no June, article id 73Article in journal (Refereed)
    Abstract [en]

    Quantifying neural and non-neural contributions to the joint resistance in spasticity is essential for a better evaluation of different intervention strategies such as botulinum toxin A (BoTN-A). However, direct measurement of muscle mechanical properties and spasticity-related parameters in humans is extremely challenging. The aim of this study was to use a previously developed musculoskeletal model and optimization scheme to evaluate the changes of neural and non-neural related properties of the spastic wrist flexors during passive wrist extension after BoTN-A injection. Data of joint angle and resistant torque were collected from 21 chronic stroke patients before, and 4 and 12 weeks post BoTN-A injection using NeuroFlexor, which is a motorized force measurement device to passively stretch wrist flexors. The model was optimized by tuning the passive and stretch-related parameters to fit the measured torque in each participant. It was found that stroke survivors exhibited decreased neural components at 4 weeks post BoNT-A injection, which returned to baseline levels after 12 weeks. The decreased neural component was mainly due to the increased motoneuron pool threshold, which is interpreted as a net excitatory and inhibitory inputs to the motoneuron pool. Though the linear stiffness and viscosity properties of wrist flexors were similar before and after treatment, increased exponential stiffness was observed over time which may indicate a decreased range of motion of the wrist joint. Using a combination of modeling and experimental measurement, valuable insights into the treatment responses, i.e., transmission of motoneurons, are provided by investigating potential parameter changes along the stretch reflex pathway in persons with chronic stroke.

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