Quantification of Stretching in the Ventricular Wall and Corpus Callosum and Corticospinal Tracts in Hydrocephalus before and after Ventriculoperitoneal Shunt Operation

In this study, we establish a quantitative model to define the stretching of brain tissue, especially in ventricular walls, corpus callosum (CC) and corticospinal (CS) fiber tracts, and to investigate the correlation between stretching and regional cerebral blood flow (rCBF) before and after ventriculoperitoneal shunt operations. A nonlinear image registration method was used to calculate the degree of displacement and stretching of axonal fiber tracts based on the medical images of six hydrocephalus patients. Also, the rCBF data from the literature was analyzed and correlated with the strain level quantified in the present study. The results showed substantial increased displacement and strain levels in the ventricular walls as well as in the CC and CS fiber tracts on admission. Following shunt operations the displacement as well as the strain levels reduced substantially. A linear correlation was found to exist between strain level and the rCBF. The reduction in postoperative strain levels correlated with the improvement of rCBF. All patients improved clinically except for one patient due to existing dementia. These new quantitative data provide us with new insight into the mechanical cascade of events due to tissue stretching, thereby provide us with more knowledge into understanding of the role of brain tissue and axonal stretching in some of the hydrocephalus clinical symptoms

Personalization of human body models and beyond via image registration

Finite element human body models (HBMs) are becoming increasingly important numerical tools for traffic safety. Developing a validated and reliable HBM from the start requires integrated efforts and continues to be a challenging task. Mesh morphing is an efficient technique to generate personalized HBMs accounting for individual anatomy once a baseline model has been developed. This study presents a new image registration–based mesh morphing method to generate personalized HBMs. The method is demonstrated by morphing four baseline HBMs (SAFER, THUMS, and VIVA+ in both seated and standing postures) into ten subjects with varying heights, body mass indices (BMIs), and sex. The resulting personalized HBMs show comparable element quality to the baseline models. This method enables the comparison of HBMs by morphing them into the same subject, eliminating geometric differences. The method also shows superior geometry correction capabilities, which facilitates converting a seated HBM to a standing one, combined with additional positioning tools. Furthermore, this method can be extended to personalize other models, and the feasibility of morphing vehicle models has been illustrated. In conclusion, this new image registration–based mesh morphing method allows rapid and robust personalization of HBMs, facilitating personalized simulations

Integrated analysis of miRNAome transcriptome and degradome reveals miRNA-target modules governing floral florescence development and senescence across early- and late-flowering genotypes in tree peony

As a candidate national flower of China, tree peony has extremely high ornamental, medicinal and oil value. However, the short florescence and rarity of early-flowering and late-flowering varieties restrict further improvement of the economic value of tree peony. Specific miRNAs and their target genes engaged in tree peony floral florescence, development and senescence remain unknown. This report presents the integrated analysis of the miRNAome, transcriptome and degradome of tree peony petals collected from blooming, initial flowering, full blooming and decay stages in early-flowering variety Paeonia ostii ‘Fengdan’, an early-flowering mutant line of Paeonia ostii ‘Fengdan’ and late-flowering variety Paeonia suffruticosa ‘Lianhe’. Transcriptome analysis revealed a transcript (‘psu.G.00014095’) which was annotated as a xyloglucan endotransglycosylase/hydrolase precursor XTH-25 and found to be differentially expressed across flower developmental stages in Paeonia ostii ‘Fengdan’ and Paeonia suffruticosa ‘Lianhe’. The miRNA-mRNA modules were presented significant enrichment in various pathways such as plant hormone signal transduction, indole alkaloid biosynthesis, arachidonic acid metabolism, folate biosynthesis, fatty acid elongation, and the MAPK signaling pathway. Multiple miRNA-mRNA-TF modules demonstrated the potential functions of MYB-related, bHLH, Trihelix, NAC, GRAS and HD-ZIP TF families in floral florescence, development, and senescence of tree peony. Comparative spatio-temporal expression investigation of eight floral-favored miRNA-target modules suggested that transcript ‘psu.T.00024044’ and microRNA mtr-miR166g-5p are involved in the floral florescence, development and senescence associated agronomic traits of tree peony. The results might accelerate the understanding of the potential regulation mechanism in regards to floral florescence, development and abscission, and supply guidance for tree peony breeding of varieties with later and longer florescence characteristics

D3.8 Final version of the personalization and positioning software tool with documentation. PIPER EU Project

The aim of this report is to provide an overview of the final version of the PIPER framework and application. The software, along with its documentation, and not the report, constitutes the main part of the deliverable. The software and documentation were already distributed at the Final Workshop and online (under the Open Source license GPLv2 or later for the software, and the GNU FDL 1.3 license for the documentation). The documentation includes detailed descriptions of the framework principles, user interface, metadata, along with the modules and their parameters. It also includes application scenarios (called workflows). Information about the use of the modules is complemented by Tutorials that were developed as part of WP1 (online on the wiki) and explanatory videos were developed as part of WP4 (videos of the final workshop, now available on YouTube). The headers in the source code files (also available online) list the main contributors to the software. The report will therefore not provide details about information that is already available elsewhere but will only provide a very brief summary of the functionalities available. Some of the descriptions are excerpts of the manual

Directorium divini cultus ad Cathedralis Ecclesiae Minoriccensis : eiusque Dioecesis usum

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Finite Element and Neuroimaging Techniques toImprove Decision-Making in Clinical Neuroscience

Our brain, perhaps the most sophisticated and mysterious part of the human body, to some extent, determines who we are. However, it’s a vulnerable organ. When subjected to an impact, such as a traffic accident or sport, it may lead to traumatic brain injury (TBI) which can have devastating effects for those who suffer the injury. Despite lots of efforts have been put into primary injury prevention, the number of TBIs is still on an unacceptable high level in a global perspective. Brain edema is a major neurological complication of moderate and severe TBI, which consists of an abnormal accumulation of fluid within the brain parenchyma. Clinically, local and minor edema may be treated conservatively only by observation, where the treatment of choice usually follows evidence-based practice. In the first study, the gravitational force is suggested to have a significant impact on the pressure of the edema zone in the brain tissue. Thus, the objective of the study was to investigate the significance of head position on edema at the posterior part of the brain using a Finite Element (FE) model. The model revealed that water content (WC) increment at the edema zone remained nearly identical for both supine and prone positions. However, the interstitial fluid pressure (IFP) inside the edema zone decreased around 15% by having the head in a prone position compared with a supine position. The decrease of IFP inside the edema zone by changing patient position from supine to prone has the potential to alleviate the damage to axonal fibers of the central nervous system. These observations suggest that considering the patient’s head position during intensive care and at rehabilitation should be of importance to the treatment of edematous regions in TBI patients. In TBI patients with diffuse brain edema, for most severe cases with refractory intracranial hypertension, decompressive craniotomy (DC) is performed as an ultimate therapy. However, a complete consensus on its effectiveness has not been achieved due to the high levels of severe disability and persistent vegetative state found in the patients treated with DC. DC allows expansion of the swollen brain outside the skull, thereby having the potential in reducing the Intracranial Pressure (ICP). However, the treatment causes stretching of the axons and may contribute to the unfavorable outcome of the patients. The second study aimed at quantifying the stretching and WC in the brain tissue due to the neurosurgical intervention to provide more insight into the effects upon such a treatment. A nonlinear registration method was used to quantify the strain. Our analysis showed a substantial increase of the strain level in the brain tissue close to the treated side of DC compared to before the treatment. Also, the WC was related to specific gravity (SG), which in turn was related to the Hounsfield unit (HU) value in the Computerized Tomography (CT) images by a photoelectric correction according to the chemical composition of the brain tissue. The overall WC of brain tissue presented a significant increase after the treatment compared to the condition seen before the treatment. It is suggested that a quantitative model, which characterizes the stretching and WC of the brain tissue both before as well as after DC, may clarify some of the potential problems with such a treatment. Diffusion Weighted (DW) Imaging technology provides a noninvasive way to extract axonal fiber tracts in the brain. The aim of the third study, as an extension to the second study was to assess and quantify the axonal deformation (i.e. stretching and shearing)at both the pre- and post-craniotomy periods in order to provide more insight into the mechanical effects on the axonal fibers due to DC. Subarachnoid injection of artificial cerebrospinal fluid (CSF) into the CSF system is widely used in neurological practice to gain information on CSF dynamics. Mathematical models are important for a better understanding of the underlying mechanisms. Despite the critical importance of the parameters for accurate modeling, there is a substantial variation in the poroelastic constants used in the literature due to the difficulties in determining material properties of brain tissue. In the fourth study, we developed a Finite Element (FE) model including the whole brain-CSF-skull system to study the CSF dynamics during constant-rate infusion. We investigated the capacity of the current model to predict the steady state of the mean ICP. For transient analysis, rather than accurately fit the infusion curve to the experimental data, we placed more emphasis on studying the influences of each of the poroelastic parameters due to the aforementioned inconsistency in the poroelastic constants for brain tissue. It was found that the value of the specific storage term S_epsilon is the dominant factor that influences the infusion curve, and the drained Young’s modulus E was identified as the dominant parameter second to S_epsilon. Based on the simulated infusion curves from the FE model, Artificial Neural Network (ANN) was used to find an optimized parameter set that best fit the experimental curve. The infusion curves from both the FE simulations and using ANN confirmed the limitation of linear poroelasticity in modeling the transient constant-rate infusion. To summarize, the work done in this thesis is to introduce FE Modeling and imaging technologiesincluding CT, DW imaging, and image registration method as a complementarytechnique for clinical diagnosis and treatment of TBI patients. Hopefully, the result mayto some extent improve the understanding of these clinical problems and improve theirmedical treatments.QC 2012020

Finite Element and Neuroimaging Techniques toImprove Decision-Making in Clinical Neuroscience

Our brain, perhaps the most sophisticated and mysterious part of the human body, to some extent, determines who we are. However, it’s a vulnerable organ. When subjected to an impact, such as a traffic accident or sport, it may lead to traumatic brain injury (TBI) which can have devastating effects for those who suffer the injury. Despite lots of efforts have been put into primary injury prevention, the number of TBIs is still on an unacceptable high level in a global perspective. Brain edema is a major neurological complication of moderate and severe TBI, which consists of an abnormal accumulation of fluid within the brain parenchyma. Clinically, local and minor edema may be treated conservatively only by observation, where the treatment of choice usually follows evidence-based practice. In the first study, the gravitational force is suggested to have a significant impact on the pressure of the edema zone in the brain tissue. Thus, the objective of the study was to investigate the significance of head position on edema at the posterior part of the brain using a Finite Element (FE) model. The model revealed that water content (WC) increment at the edema zone remained nearly identical for both supine and prone positions. However, the interstitial fluid pressure (IFP) inside the edema zone decreased around 15% by having the head in a prone position compared with a supine position. The decrease of IFP inside the edema zone by changing patient position from supine to prone has the potential to alleviate the damage to axonal fibers of the central nervous system. These observations suggest that considering the patient’s head position during intensive care and at rehabilitation should be of importance to the treatment of edematous regions in TBI patients. In TBI patients with diffuse brain edema, for most severe cases with refractory intracranial hypertension, decompressive craniotomy (DC) is performed as an ultimate therapy. However, a complete consensus on its effectiveness has not been achieved due to the high levels of severe disability and persistent vegetative state found in the patients treated with DC. DC allows expansion of the swollen brain outside the skull, thereby having the potential in reducing the Intracranial Pressure (ICP). However, the treatment causes stretching of the axons and may contribute to the unfavorable outcome of the patients. The second study aimed at quantifying the stretching and WC in the brain tissue due to the neurosurgical intervention to provide more insight into the effects upon such a treatment. A nonlinear registration method was used to quantify the strain. Our analysis showed a substantial increase of the strain level in the brain tissue close to the treated side of DC compared to before the treatment. Also, the WC was related to specific gravity (SG), which in turn was related to the Hounsfield unit (HU) value in the Computerized Tomography (CT) images by a photoelectric correction according to the chemical composition of the brain tissue. The overall WC of brain tissue presented a significant increase after the treatment compared to the condition seen before the treatment. It is suggested that a quantitative model, which characterizes the stretching and WC of the brain tissue both before as well as after DC, may clarify some of the potential problems with such a treatment. Diffusion Weighted (DW) Imaging technology provides a noninvasive way to extract axonal fiber tracts in the brain. The aim of the third study, as an extension to the second study was to assess and quantify the axonal deformation (i.e. stretching and shearing)at both the pre- and post-craniotomy periods in order to provide more insight into the mechanical effects on the axonal fibers due to DC. Subarachnoid injection of artificial cerebrospinal fluid (CSF) into the CSF system is widely used in neurological practice to gain information on CSF dynamics. Mathematical models are important for a better understanding of the underlying mechanisms. Despite the critical importance of the parameters for accurate modeling, there is a substantial variation in the poroelastic constants used in the literature due to the difficulties in determining material properties of brain tissue. In the fourth study, we developed a Finite Element (FE) model including the whole brain-CSF-skull system to study the CSF dynamics during constant-rate infusion. We investigated the capacity of the current model to predict the steady state of the mean ICP. For transient analysis, rather than accurately fit the infusion curve to the experimental data, we placed more emphasis on studying the influences of each of the poroelastic parameters due to the aforementioned inconsistency in the poroelastic constants for brain tissue. It was found that the value of the specific storage term S_epsilon is the dominant factor that influences the infusion curve, and the drained Young’s modulus E was identified as the dominant parameter second to S_epsilon. Based on the simulated infusion curves from the FE model, Artificial Neural Network (ANN) was used to find an optimized parameter set that best fit the experimental curve. The infusion curves from both the FE simulations and using ANN confirmed the limitation of linear poroelasticity in modeling the transient constant-rate infusion. To summarize, the work done in this thesis is to introduce FE Modeling and imaging technologiesincluding CT, DW imaging, and image registration method as a complementarytechnique for clinical diagnosis and treatment of TBI patients. Hopefully, the result mayto some extent improve the understanding of these clinical problems and improve theirmedical treatments.QC 2012020

Biomechanical Visualizations as aNew Tool for CRS Awareness : A booklet introducing the theoretical background

QC 20221201</p

Finite element modeling of decompressive craniectomy (DC) and its clinical validation

Decompressive craniectomy (DC) is a reliable neurosurgical approach to reduce a pathologically increased intracranial pressure after neurological diseases such as severe traumatic brain injury (TBI) and stroke. The procedure has substantially reduced the mortality rate but at the expense of increased neurological cognitive impairments. Finite Element (FE) modeling in the past decades has become an important tool to develop innovative treatment strategies in various areas of the clinical neuroscience field. The aim of this study was to develop patient-specific FE models to simulate DC surgery and validate the models against patients' clinical data. The FE models were created based on the Computed Tomography (CT) images of six patients treated with DC. Brain tissue was modeled as poroelastic material. To validate the model prediction, the motion of brain surface at the DC area from the simulation was compared with the measured values from medical images which were derived from image registration. The results from the computational simulations gave a reliable prediction of brain surface motion at DC area for all the six patients evaluated. Both the deformation pattern and the quantitative values of the brain surface displacement from the model simulation were found in good agreement with measured values from medical images. The developed FE model and its validation in this study is a prerequisite for future investigations aiming at finding optimal treatment for a specific patient which hopefully will significantly improve patients' outcome.QC 20190903</p